October 14, 2015
Bioconductors:
We are pleased to announce Bioconductor 3.2, consisting of 1104 software packages, 257 experiment data packages, and 917 up-to-date annotation packages.
There are 80 new software packages, and many updates and improvements to existing packages; Bioconductor 3.2 is compatible with R 3.2, and is supported on Linux, 32- and 64-bit Windows, and Mac OS X. This release includes an updated Bioconductor Amazon Machine Image and Docker containers.
Visit http://bioconductor.org for details and downloads.
To update to or install Bioconductor 3.2:
Install R 3.2. Bioconductor 3.2 has been designed expressly for this version of R.
Follow the instructions at http://bioconductor.org/install/ .
There are 80 new packages in this release of Bioconductor.
ABAEnrichment - The package ABAEnrichment is designed to test for enrichment of user defined candidate genes in the set of expressed genes in different human brain regions. The core function ‘aba_enrich’ integrates the expression of the candidate gene set (averaged across donors) and the structural information of the brain using an ontology, both provided by the Allen Brain Atlas project. ‘aba_enrich’ interfaces the ontology enrichment software FUNC to perform the statistical analyses. Additional functions provided in this package like ‘get_expression’ and ‘plot_expression’ facilitate exploring the expression data.
acde - This package provides a multivariate inferential analysis method for detecting differentially expressed genes in gene expression data. It uses artificial components, close to the data’s principal components but with an exact interpretation in terms of differential genetic expression, to identify differentially expressed genes while controlling the false discovery rate (FDR). The methods on this package are described in the vignette or in the article ‘Multivariate Method for Inferential Identification of Differentially Expressed Genes in Gene Expression Experiments’ by J. P. Acosta, L. Lopez-Kleine and S. Restrepo (2015, pending publication).
AnnotationHubData - These recipes convert a wide variety and a growing number of public bioinformatic data sets into easily-used standard Bioconductor data structures.
BBCAnalyzer - BBCAnalyzer is a package for visualizing the relative or absolute number of bases, deletions and insertions at defined positions in sequence alignment data available as bam files in comparison to the reference bases. Markers for the relative base frequencies, the mean quality of the detected bases, known mutations or polymorphisms and variants called in the data may additionally be included in the plots.
biobroom - This package contains methods for converting standard objects constructed by bioinformatics packages, especially those in Bioconductor, and converting them to tidy data. It thus serves as a complement to the broom package, and follows the same the tidy, augment, glance division of tidying methods. Tidying data makes it easy to recombine, reshape and visualize bioinformatics analyses.
caOmicsV - caOmicsV package provides methods to visualize multi-dimentional cancer genomics data including of patient information, gene expressions, DNA methylations, DNA copy number variations, and SNP/mutations in matrix layout or network layout.
CausalR - Causal Reasoning algorithms for biological networks, including predictions, scoring, p-value calculation and ranking
ChIPComp - ChIPComp detects differentially bound sharp binding sites across multiple conditions considering matching control.
CNPBayes - Bayesian hierarchical mixture models for batch effects and copy number.
CNVPanelizer - A method that allows for the use of a collection of non-matched normal tissue samples. Our approach uses a non-parametric bootstrap subsampling of the available reference samples to estimate the distribution of read counts from targeted sequencing. As inspired by random forest, this is combined with a procedure that subsamples the amplicons associated with each of the targeted genes. The obtained information allows us to reliably classify the copy number aberrations on the gene level.
DAPAR - This package contains a collection of functions for the visualisation and the statistical analysis of proteomic data.
DChIPRep - The DChIPRep package implements a methodology to assess differences between chromatin modification profiles in replicated ChIP-Seq studies as described in Chabbert et. al - http://www.dx.doi.org/10.15252/msb.20145776.
DeMAND - DEMAND predicts Drug MoA by interrogating a cell context specific regulatory network with a small number (N >= 6) of compound-induced gene expression signatures, to elucidate specific proteins whose interactions in the network is dysregulated by the compound.
destiny - Create and plot diffusion maps
DiffLogo - DiffLogo is an easy-to-use tool to visualize motif differences.
DNABarcodes - The package offers a function to create DNA barcode sets capable of correcting insertion, deletion, and substitution errors. Existing barcodes can be analysed regarding their minimal, maximal and average distances between barcodes. Finally, reads that start with a (possibly mutated) barcode can be demultiplexed, i.e., assigned to their original reference barcode.
dupRadar - Duplication rate quality control for RNA-Seq datasets.
ELMER - ELMER is designed to use DNA methylation and gene expression from a large number of samples to infere regulatory element landscape and transcription factor network in primary tissue.
EnrichedHeatmap - Enriched heatmap is a special type of heatmap which visualizes the enrichment of genomic signals on specific target regions. Here we implement Enriched heatmap by ComplexHeatmap package. Since this type of heatmap is just a normal heatmap but with some special settings, with the functionality of ComplexHeatmap, it would be much easier to customize the heatmap as well as concatenating to a list of heatmaps to show correspondance between different data sources.
erma - Software and data to support epigenomic road map adventures.
eudysbiome - eudysbiome a package that permits to annotate the differential genera as harmful/harmless based on their ability to contribute to host diseases (as indicated in literature) or as unknown based on their ambiguous genus classification. Further, the package statistically measures the eubiotic (harmless genera increase or harmful genera decrease) or dysbiotic(harmless genera decrease or harmful genera increase) impact of a given treatment or environmental change on the (gut-intestinal, GI) microbiome in comparison to the microbiome of the reference condition.
fCI - (f-divergence Cutoff Index), is to find DEGs in the transcriptomic & proteomic data, and identify DEGs by computing the difference between the distribution of fold-changes for the control-control and remaining (non-differential) case-control gene expression ratio data. fCI provides several advantages compared to existing methods.
FindMyFriends - A framework for doing microbial comparative genomics in R. The main purpose of the package is assisting in the creation of pangenome matrices where genes from related organisms are grouped by similarity, as well as the analysis of these data. FindMyFriends provides many novel approaches to doing pangenome analysis and supports a gene grouping algorithm that scales linearly, thus making the creation of huge pangenomes feasible.
gcatest - GCAT is an association test for genome wide association studies that controls for population structure under a general class of trait. models.
GeneBreak - Recurrent breakpoint gene detection on copy number aberration profiles.
genotypeeval - Takes in a gVCF or VCF and reports metrics to assess quality of calls.
GEOsearch - GEOsearch is an extendable search engine for NCBI GEO (Gene Expression Omnibus). Instead of directly searching the term, GEOsearch can find all the gene names contained in the search term and search all the alias of the gene names simultaneously in GEO database. GEOsearch also provides other functions such as summarizing common biology keywords in the search results.
GUIDEseq - The package implements GUIDE-seq analysis workflow including functions for obtaining unique cleavage events, estimating the locations of the cleavage sites, aka, peaks, merging estimated cleavage sites from plus and minus strand, and performing off target search of the extended regions around cleavage sites.
Guitar - The package is designed for visualization of RNA-related genomic features with respect to the landmarks of RNA transcripts, i.e., transcription starting site, start codon, stop codon and transcription ending site.
hierGWAS - Testing individual SNPs, as well as arbitrarily large groups of SNPs in GWA studies, using a joint model of all SNPs. The method controls the FWER, and provides an automatic, data-driven refinement of the SNP clusters to smaller groups or single markers.
HilbertCurve - Hilbert curve is a type of space-filling curves that fold one dimensional axis into a two dimensional space, but with still keep the locality. This package aims to provide a easy and flexible way to visualize data through Hilbert curve.
iCheck - QC pipeline and data analysis tools for high-dimensional Illumina mRNA expression data.
iGC - This package is intended to identify differentially expressed genes driven by Copy Number Alterations from samples with both gene expression and CNA data.
Imetagene - This package provide a graphical user interface to the metagene package. This will allow people with minimal R experience to easily complete metagene analysis.
INSPEcT - INSPEcT (INference of Synthesis, Processing and dEgradation rates in Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in order to evaluate synthesis, processing and degradation rates and asses via modeling the rates that determines changes in mature mRNA levels.
IONiseR - IONiseR provides tools for the quality assessment of Oxford Nanopore MinION data. It extracts summary statistics from a set of fast5 files and can be used either before or after base calling. In addition to standard summaries of the read-types produced, it provides a number of plots for visualising metrics relative to experiment run time or spatially over the surface of a flowcell.
ldblock - Define data structures for linkage disequilibrium measures in populations.
LedPred - This package aims at creating a predictive model of regulatory sequences used to score unknown sequences based on the content of DNA motifs, next-generation sequencing (NGS) peaks and signals and other numerical scores of the sequences using supervised classification. The package contains a workflow based on the support vector machine (SVM) algorithm that maps features to sequences, optimize SVM parameters and feature number and creates a model that can be stored and used to score the regulatory potential of unknown sequences.
lfa - LFA is a method for a PCA analogue on Binomial data via estimation of latent structure in the natural parameter.
LOLA - Provides functions for testing overlap of sets of genomic regions with public and custom region set (genomic ranges) databases. This make is possible to do automated enrichment analysis for genomic region sets, thus facilitating interpretation of functional genomics and epigenomics data.
MEAL - Package to integrate methylation and expression data. It can also perform methylation or expression analysis alone. Several plotting functionalities are included as well as a new region analysis based on redundancy analysis. Effect of SNPs on a region can also be estimated.
metagenomeFeatures - metagenomeFeatures was developed for use in exploring the taxonomic annotations for a marker-gene metagenomic sequence dataset. The package can be used to explore the taxonomic composition of a marker-gene database or annotated sequences from a marker-gene metagenome experiment.
metaX - The package provides a integrated pipeline for mass spectrometry-based metabolomic data analysis. It includes the stages peak detection, data preprocessing, normalization, missing value imputation, univariate statistical analysis, multivariate statistical analysis such as PCA and PLS-DA, metabolite identification, pathway analysis, power analysis, feature selection and modeling, data quality assessment.
miRcomp - Based on a large miRNA dilution study, this package provides tools to read in the raw amplification data and use these data to assess the performance of methods that estimate expression from the amplification curves.
mirIntegrator - Tools for augmenting signaling pathways to perform pathway analysis of microRNA and mRNA expression levels.
miRLAB - Provide tools exploring miRNA-mRNA relationships, including popular miRNA target prediction methods, ensemble methods that integrate individual methods, functions to get data from online resources, functions to validate the results, and functions to conduct enrichment analyses.
motifbreakR - We introduce motifbreakR, which allows the biologist to judge in the first place whether the sequence surrounding the polymorphism is a good match, and in the second place how much information is gained or lost in one allele of the polymorphism relative to another. MotifbreakR is both flexible and extensible over previous offerings; giving a choice of algorithms for interrogation of genomes with motifs from public sources that users can choose from; these are 1) a weighted-sum probability matrix, 2) log-probabilities, and 3) weighted by relative entropy. MotifbreakR can predict effects for novel or previously described variants in public databases, making it suitable for tasks beyond the scope of its original design. Lastly, it can be used to interrogate any genome curated within Bioconductor (currently there are 22).
myvariant - MyVariant.info is a comprehensive aggregation of variant annotation resources. myvariant is a wrapper for querying MyVariant.info services
NanoStringDiff - This Package utilizes a generalized linear model(GLM) of the negative binomial family to characterize count data and allows for multi-factor design. NanoStrongDiff incorporate size factors, calculated from positive controls and housekeeping controls, and background level, obtained from negative controls, in the model framework so that all the normalization information provided by NanoString nCounter Analyzer is fully utilized.
OGSA - OGSA provides a global estimate of pathway deregulation in cancer subtypes by integrating the estimates of significance for individual pathway members that have been identified by outlier analysis.
OperaMate - OperaMate is a flexible R package dealing with the data generated by PerkinElmer’s Opera High Content Screening System. The functions include the data importing, normalization and quality control, hit detection and function analysis.
Oscope - Oscope is a statistical pipeline developed to identifying and recovering the base cycle profiles of oscillating genes in an unsynchronized single cell RNA-seq experiment. The Oscope pipeline includes three modules: a sine model module to search for candidate oscillator pairs; a K-medoids clustering module to cluster candidate oscillators into groups; and an extended nearest insertion module to recover the base cycle order for each oscillator group.
Path2PPI - Package to predict pathway specific protein-protein interaction (PPI) networks in target organisms for which only a view information about PPIs is available. Path2PPI uses PPIs of the pathway of interest from other well established model organisms to predict a certain pathway in the target organism. Path2PPI only depends on the sequence similarity of the involved proteins.
pathVar - This package contains the functions to find the pathways that have significantly different variability than a reference gene set. It also finds the categories from this pathway that are significant where each category is a cluster of genes. The genes are separated into clusters by their level of variability.
PGA - This package provides functions for construction of customized protein databases based on RNA-Seq data, database searching, post-processing and report generation. This kind of customized protein database includes both the reference database (such as Refseq or ENSEMBL) and the novel peptide sequences form RNA-Seq data.
Prize - The high throughput studies often produce large amounts of numerous genes and proteins of interest. While it is difficult to study and validate all of them. Analytic Hierarchy Process (AHP) offers a novel approach to narrowing down long lists of candidates by prioritizing them based on how well they meet the research goal. AHP is a mathematical technique for organizing and analyzing complex decisions where multiple criteria are involved. The technique structures problems into a hierarchy of elements, and helps to specify numerical weights representing the relative importance of each element. Numerical weight or priority derived from each element allows users to find alternatives that best suit their goal and their understanding of the problem.
Prostar - This package provides a GUI interface for DAPAR.
ProteomicsAnnotationHubData - These recipes convert a variety and a growing number of public proteomics data sets into easily-used standard Bioconductor data structures.
RareVariantVis - Genomic variants can be analyzed and visualized using many tools. Unfortunately, number of tools for global interrogation of variants is limited. Package RareVariantVis aims to present genomic variants (especially rare ones) in a global, per chromosome way. Visualization is performed in two ways - standard that outputs png figures and interactive that uses JavaScript d3 package. Interactive visualization allows to analyze trio/family data, for example in search for causative variants in rare Mendelian diseases.
rCGH - A comprehensive pipeline for analyzing and interactively visualizing genomic profiles generated through Agilent and Affymetrix microarrays. As inputs, rCGH supports Agilent dual-color Feature Extraction files (.txt), from 44 to 400K, and Affymetrix SNP6.0 and cytoScan probeset.txt, cychp.txt, and cnchp.txt files, exported from ChAS or Affymetrix Power Tools. This package takes over all the steps required for a genomic profile analysis, from reading the files to the segmentation and genes annotations, and provides several visualization functions (static or interactive) which facilitate profiles interpretation. Input files can be in compressed format, e.g. .bz2 or .gz.
RCy3 - Vizualize, analyze and explore graphs, connecting R to Cytoscape >= 3.2.1.
RiboProfiling - Starting with a BAM file, this package provides the necessary functions for quality assessment, read start position recalibration, the counting of reads on CDS, 3’UTR, and 5’UTR, plotting of count data: pairs, log fold-change, codon frequency and coverage assessment, principal component analysis on codon coverage.
rnaseqcomp - Several quantitative and visualized benchmarks for RNA-seq quantification pipelines. Two-replicate quantifications for genes, transcripts, junctions or exons by each pipeline with nessasery meta information should be organizd into numeric matrix in order to proceed the evaluation.
ropls - Latent variable modeling with Principal Component Analysis (PCA) and Partial Least Squares (PLS) are powerful methods for visualization, regression, classification, and feature selection of omics data where the number of variables exceeds the number of samples and with multicollinearity among variables. Orthogonal Partial Least Squares (OPLS) enables to separately model the variation correlated (predictive) to the factor of interest and the uncorrelated (orthogonal) variation. While performing similarly to PLS, OPLS facilitates interpretation. Successful applications of these chemometrics techniques include spectroscopic data such as Raman spectroscopy, nuclear magnetic resonance (NMR), mass spectrometry (MS) in metabolomics and proteomics, but also transcriptomics data. In addition to scores, loadings and weights plots, the package provides metrics and graphics to determine the optimal number of components (e.g. with the R2 and Q2 coefficients), check the validity of the model by permutation testing, detect outliers, and perform feature selection (e.g. with Variable Importance in Projection or regression coefficients). The package can be accessed via a user interface on the Workflow4Metabolomics.org online resource for computational metabolomics (built upon the Galaxy environment).
RTCGA - The Cancer Genome Atlas (TCGA) Data Portal provides a platform for researchers to search, download, and analyze data sets generated by TCGA. It contains clinical information, genomic characterization data, and high level sequence analysis of the tumor genomes. The key is to understand genomics to improve cancer care. RTCGA package offers download and integration of the variety and volume of TCGA data using patient barcode key, what enables easier data possession. This may have an benefcial infuence on impact on development of science and improvement of patients’ treatment. Furthermore, RTCGA package transforms TCGA data to tidy form which is convenient to use.
RTCGAToolbox - Managing data from large scale projects such as The Cancer Genome Atlas (TCGA) for further analysis is an important and time consuming step for research projects. Several efforts, such as Firehose project, make TCGA pre-processed data publicly available via web services and data portals but it requires managing, downloading and preparing the data for following steps. We developed an open source and extensible R based data client for Firehose pre-processed data and demonstrated its use with sample case studies. Results showed that RTCGAToolbox could improve data management for researchers who are interested with TCGA data. In addition, it can be integrated with other analysis pipelines for following data analysis.
sbgr - R client for Seven Bridges Genomics API.
SEPA - Given single-cell RNA-seq data and true experiment time of cells or pseudo-time cell ordering, SEPA provides convenient functions for users to assign genes into different gene expression patterns such as constant, monotone increasing and increasing then decreasing. SEPA then performs GO enrichment analysis to analysis the functional roles of genes with same or similar patterns.
SICtools - This package is to find SNV/Indel differences between two bam files with near relationship in a way of pairwise comparison thourgh each base position across the genome region of interest. The difference is inferred by fisher test and euclidean distance, the input of which is the base count (A,T,G,C) in a given position and read counts for indels that span no less than 2bp on both sides of indel region.
SISPA - Sample Integrated Gene Set Analysis (SISPA) is a method designed to define sample groups with similar gene set enrichment profiles.
SNPhood - To date, thousands of single nucleotide polymorphisms (SNPs) have been found to be associated with complex traits and diseases. However, the vast majority of these disease-associated SNPs lie in the non-coding part of the genome, and are likely to affect regulatory elements, such as enhancers and promoters, rather than function of a protein. Thus, to understand the molecular mechanisms underlying genetic traits and diseases, it becomes increasingly important to study the effect of a SNP on nearby molecular traits such as chromatin environment or transcription factor (TF) binding. Towards this aim, we developed SNPhood, a user-friendly Bioconductor R package to investigate and visualize the local neighborhood of a set of SNPs of interest for NGS data such as chromatin marks or transcription factor binding sites from ChIP-Seq or RNA-Seq experiments. SNPhood comprises a set of easy-to-use functions to extract, normalize and summarize reads for a genomic region, perform various data quality checks, normalize read counts using additional input files, and to cluster and visualize the regions according to the binding pattern. The regions around each SNP can be binned in a user-defined fashion to allow for analysis of very broad patterns as well as a detailed investigation of specific binding shapes. Furthermore, SNPhood supports the integration with genotype information to investigate and visualize genotype-specific binding patterns. Finally, SNPhood can be employed for determining, investigating, and visualizing allele-specific binding patterns around the SNPs of interest.
subSeq - Subsampling of high throughput sequencing count data for use in experiment design and analysis.
SummarizedExperiment - The SummarizedExperiment container contains one or more assays, each represented by a matrix-like object of numeric or other mode. The rows typically represent genomic ranges of interest and the columns represent samples.
SWATH2stats - This package is intended to transform SWATH data from the OpenSWATH software into a format readable by other statistics packages while performing filtering, annotation and FDR estimation.
synlet - Select hits from synthetic lethal RNAi screen data. For example, there are two identical celllines except one gene is knocked-down in one cellline. The interest is to find genes that lead to stronger lethal effect when they are knocked-down further by siRNA. Quality control and various visualisation tools are implemented. Four different algorithms could be used to pick up the interesting hits. This package is designed based on 384 wells plates, but may apply to other platforms with proper configuration.
TarSeqQC - The package allows the representation of targeted experiment in R. This is based on current packages and incorporates functions to do a quality control over this kind of experiments and a fast exploration of the sequenced regions. An xlsx file is generated as output.
TCGAbiolinks - The aim of TCGAbiolinks is : i) facilitate the TCGA open-access data retrieval, ii) prepare the data using the appropriate pre-processing strategies, iii) provide the means to carry out different standard analyses and iv) allow the user to download a specific version of the data and thus to easily reproduce earlier research results. In more detail, the package provides multiple methods for analysis (e.g., differential expression analysis, identifying differentially methylated regions) and methods for visualization (e.g., survival plots, volcano plots, starburst plots) in order to easily develop complete analysis pipelines.
traseR - traseR performs GWAS trait-associated SNP enrichment analyses in genomic intervals using different hypothesis testing approaches, also provides various functionalities to explore and visualize the results.
variancePartition - Quantify and interpret multiple sources and biological and technical variation in gene expression experiments. Uses linear mixed model to quantify variation in gene expression attributable to individual, tissue, time point, or technical variables.
XBSeq - We developed a novel algorithm, XBSeq, where a statistical model was established based on the assumption that observed signals are the convolution of true expression signals and sequencing noises. The mapped reads in non-exonic regions are considered as sequencing noises, which follows a Poisson distribution. Given measureable observed and noise signals from RNA-seq data, true expression signals, assuming governed by the negative binomial distribution, can be delineated and thus the accurate detection of differential expressed genes.
Package maintainers can add NEWS files describing changes to their packages since the last release. The following package NEWS is available:
Changes in version 0.99.0:
NEW FEATURES
Changes in version 2.9.3 (2015-05-30):
Fixed Note about require(Cairo).
Fixed failure with changes in ffbase and not exporting min.ff and max.ff
Changes in version 2.9.2 (2015-05-07):
Changes in version 2.9.1 (2015-04-30):
Added the CITATION file (which was never uploaded to the svn repos)
Added in one reference in pSegement.Rd
Changes in version 1.41.7 (2015-09-14):
Changes in version 1.41.6 (2015-07-29):
Changes in version 1.41.5 (2015-06-17):
Changes in version 1.41.4 (2015-05-26):
Changes in version 1.41.3 (2015-05-13):
Changes in version 1.41.2 (2015-05-05):
BUG FIX/ROBUSTNESS: readCelHeader() and readCel() would core dump R/affxparser if trying to read multi-channel CEL files (Issue #16). Now an error is generated instead. Multi-channel CEL files (e.g. Axiom) are not supported by affxparser. Thanks to Kevin McLoughlin (Lawrence Livermore National Laboratory, USA) for reporting on this.
BUG FIX/ROBUSTNESS: readCelHeader() and readCel() on corrupt CEL files could core dump R/affparser (Issues #13 & #15). Now an error is generated instead. Thanks to Benilton Carvalho (Universidade Estadual de Campinas, Sao Paulo, Brazil) and Malte Bismarck (Martin Luther University of Halle-Wittenberg) for reports.
Changes in version 1.41.1 (2015-04-25):
Changes in version 1.41.0 (2015-04-16):
Changes in version 1.8.0:
NEW FEATURES
genotype accessor requires reference and alternative allele information
genotype setter requires reference allele information
reference fraction is now accessed through fraction(ASEset, top.allele.criteria=”ref”)
for a more robust performance unit tests are now covering the most crucial calculations, such as e.g. fraction, frequency, summary, mapbias and phase specific calculations.
Changes in version 1.47:
DEFUNCT
probesByLL is now defunct; use AnnotationDbi::select() instead.
blastSequences supports multiple sequence queries; use as=”data.frame” for output.
Improve blastSequences strategy for result retrieval, querying the appropriate API for status every 10 seconds after initial estimated processing time.
Changes in version 1.31:
NEW FEATURES and API changes
columns() and keytypes() sort their return values.
ls() on a Bimap option returns keys in sort()ed order, by default * *
Changes in version 2.1.26:
SIGNIFICANT USER-VISIBLE CHANGES
Changes in version 1.0.0:
BUG FIXES
Changes in version 0.0.214:
NEW FEATURES
Have added vcf files from the following genome builds for humans “human_9606/VCF/clinical_vcf_set/”, “human_9606_b141_GRCh37p13/VCF/”, “human_9606_b142_GRCh37p13/VCF/”, “human_9606_b142_GRCh37p13/VCF/clinical_vcf_set/”
For each genome build, where available, the following VCF file formats are available a) all.vcf.gz b) all_papu.vcf.gz c) common_all.vcf.gz d) clinvar.vcf.gz e) clinvar_papu f) common_and_clinical g) common_no_known_medical_impact
The user can refer to http://www.ncbi.nlm.nih.gov/variation/docs/human_variation_vcf/ for VCF file type formats
Changes in version 1.9.1:
Add NEWS file
Add code to compute expression variability measure from Alemu, et al. NAR 2014.
Changes in version 2.99.0 (2015-10-06):
Changes in version 2.1.1:
bug fix in texpr, eexpr, iexpr, and gexpr methods; they no longer crash with single-replicate objects
Small documentation clarifications
Changes in version 1.0.0:
Changes in version 1.20.0:
BUG FIXES
Changes in version 1.8.0:
R Markdown templates for Bioconductor HTML and PDF documents
Suggest ‘rmarkdown’ as the default engine for .Rmd documents
Simplified use with ‘rmarkdown’ - no need to include a separate code chunk calling ‘BiocStyle::markdown’ anymore
Functions facilitating the inclusion of document compilation date and package version in the .Rmd document header
Changes in version 1.37.2:
NEW FEATURES
Changes in version 1.9.8:
BUG FIXES
Changes in version 1.5:
new function strandCollapse for collapsing forward and reverse strand data to be unstranded.
Updated read.bismark() to support the cytosine report files; both formats are supported. Other minor updates (mostly internal) to read.bismark(). Greatly improved documentation of this function, paying particular attention to differences in file formats between versions of Bismark.
Changes in version 1.25.3:
BUG FIXES
Changes in version 1.25.2:
USER VISIBLE CHANGES
Changes in version 1.25.1:
BUG FIXES
Changes in version 1.1.0:
BUG FIXES
Fixed bug in formatting m/z labels affecting R 3.2.2
Removed dependency on ‘fields’ because ‘maps’ is broken on Windows
Changes in version 3.3.8:
Changes in version 3.3.7:
FIX BUGS
Changes in version 3.3.6:
NEW FEATURE
add new function featureAlignedSignal, featureAlignedDistribution, featureAlignedHeatmap, pie1
add new dataset HOT.spots, wgEncodeTfbsV3
update annoGR class
update vignettes
Changes in version 3.3.5:
NEW FEATURE
remove all the RangedData
add annoGR class
update vignettes
Changes in version 3.3.4:
NEW FEATURE
toGRanges from MACS2, narrowPeak.
calculate the p value of overlapping peaks by reagioneR
update documentation
Changes in version 3.3.3:
NEW FEATURE
Changes in version 3.3.2:
NEW FEATURE
Changes in version 3.3.1:
NEW FEATURE
Changes in version 1.5.11:
remove ellipsis parameter in enrichPeakOverlap function and extend it to support GRanges objects <2015-10-08, Thu> + see https://support.bioconductor.org/p/73069/
fixed the issue, https://github.com/GuangchuangYu/ChIPseeker/issues/13 <2015-10-05, Mon>
update GEO info, now contains >18,000 bed file information <2015-09-24, Thu>
Changes in version 1.5.10:
dropAnno function, eg. drop nearest gene annotation that far from TSS (>10k). <2015-09-17, Thu> + see https://github.com/GuangchuangYu/ChIPseeker/issues/9 + add parameter distanceToTSS_cutoff to enrichAnnoOverlap
use base::subset in plotDistToTSS instead of subsetting data within geom_bar <2015-09-17, Thu> + see https://github.com/hadley/ggplot2/issues/1295 + subset parameter in layer will be removed in next release of ggplot2.
Changes in version 1.5.9:
bug fixed of enrichAnnoOverlap <2015-08-26, Wed>
change parameter order.matrix to order.by in upsetplot to meet the change of UpSetR pkg <2015-08-26, Wed>
Changes in version 1.5.8:
Changes in version 1.5.7:
add vennpie parameter in upsetplot <2015-07-20, Mon>
upsetplot function for csAnno object <2015-07-20, Mon>
Changes in version 1.5.6:
update citation info <2015-07-09, Thu>
BED file +1 shift for BED coordinate system start at 0 <2015-07-07, Tue>
Changes in version 1.5.5:
Changes in version 1.5.4:
Changes in version 1.5.3:
Changes in version 1.5.1:
Changes in version 1.4.0:
Weighted voting mode that uses the distance from an observation to the nearest crossover point of the class densities added.
Bartlett Test selection function included.
New class SelectResult. rankPlot and selectionPlot can additionally work with lists of SelectResult objects. All feature selection functions now return a SelectResult object or a list of them.
priorSelection is a new selection function for using features selected in a prior cross validation for a new dataset classification.
New weighted voting mode, where the weight is the distance of the x value from the nearest crossover point of the two densities. Useful for predictions with skewed features.
Changes in version 1.7.2:
Changes in version 1.7.1:
BUG FIXES
Changes in version 1.8.0:
NEW FEATURES
Changes in version 2.3.8:
dropGO function <2015-09-24, Thu> + see https://github.com/GuangchuangYu/clusterProfiler/issues/26
use_internal_data = TRUE in enrichKEGG example to speedup compilation of vignette and prevent error when online is not available <2015-09-23, Wed>
Changes in version 2.3.7:
bug fixed in sorting pvalue of compareClusterResult. <2015-09-16, Wed> For compareCluster(fun=groupGO), there is no pvalue, use Count for sorting
use_internal_data= TRUE in enrichKEGG and gseKEGG demonstrated in vignette due to the issue https://github.com/GuangchuangYu/clusterProfiler/issues/20 <2015-08-26, Wed>
Changes in version 2.3.6:
merge_result function <2015-07-15, Wed>
add citation of ChIPseeker <2015-07-09, Thu>
add ‘Functional analysis of NGS data’ section in vignette <2015-06-29, Mon>
update vignette <2015-06-24, Wed>
Changes in version 2.3.5:
Changes in version 2.3.4:
Changes in version 2.3.3:
Changes in version 2.3.2:
bug fixed of build_Anno <2015-05-07, Thu>
add plotGOgraph function <2015-05-05, Tue>
Changes in version 2.3.1:
remove import RDAVIDWebService <2015-04-29, Wed>
update buildGOmap <2015-04-29, Wed>
remove import KEGG.db <2015-04-29, Wed>
Changes in version 0.99.12:
Changes in version 0.99.11:
Changes in version 0.99.10:
Changes in version 0.99.9:
Add fix for inconsistencies
Remove CheckSignificance documentation for function not available
Fix for vignette plot inconsistency bootstrap count
Increment version number
Changes in version 0.99.8:
Changes in version 0.99.7:
Specificity improvements BUG FIXES
Improve code Styling
Add documentation
Changes in version 0.99.6:
Initial Bioconductor release BUG FIXES
Add required imports at NAMESPACE
Improve code Styling
Add documentation
Remove unnecessary files
Changes in version 1.38.0:
Fixed error reading Codelink files with option type=”Raw” or type=”Norm”.
Now readCodelinkSet() accepts “path=” as argument to enable reading files from a target directory.
Changes in version 1.2.0 (2015-09-01):
update exmaple dataset.
add drug repositioning gene sets and anlaysis.
Changes in version 1.3.4:
Changes in version 1.3.3:
Changes in version 1.3.2:
Changes in version 1.5.1:
oncoPrint
: there are default graphics if type of alterations is
less than two.
anno_*
: get rid of lazy loading
Changes in version 2.0.6 (2015-06-15):
Changes in version 2.0.5 (2015-06-10):
Changes in version 2.0.4 (2015-06-05):
Changes in version 2.0.3 (2015-05-06):
Changes in version 2.0.2 (2015-04-24):
Changes in version 2.0.1 (2015-04-18):
Implemented resetting the original work directory upon exit of CopywriteR functions
Corrected R dependency to version 3.2
Updated DESCRIPTION file
Fixed bug resulting in failure to calculate loesses RELEASE (version 2.0)
Changes in version 1.3.2:
Modified the fields title and description of the file DESCRIPTION to cerrect the title in the citation of the package.
Modified the field title of the file COSNet-package.Rd USER VISIBLE CHANGES BUG FIXES PLANS
Changes in version 1.3.14:
Added clusterFDR() function to compute the FDR for clusters of DB windows.
Added checkBimodality() function to compute bimodality scores for regions.
Modified normalize(), asDGEList() to allow manual specification of library sizes.
Switched from normalizeCounts(), normalize() to S4 method normOffsets().
Modified default parameter specification in strandedCounts(), to avoid errors.
Switched to warning from error when a restricted chromosome is specified in extractReads().
Modified extractReads() interface with improved support for extended read and paired read extraction.
Added normalization options to filterWindows() when using control samples.
Fixed bug for proportional filtering in filterWindows().
Allowed correlateReads() to accept paired-end specification when extracting data.
Added maximizeCcf() function to estimate the average fragment length.
Added support for strand-specific overlapping in detailRanges().
Increased the fidelity of retained information in dumped BAM file from dumpPE().
Modified strand specification arguments for profileSites(), allowed reporting of individual profiles.
Removed param= specification from wwhm().
Switched to RangedSummarizedExperiment conventions for all relevant functions.
Switched to mapqFilter for scanBam() when filtering on mapping quality.
Added tests for previously untested functions.
Slight updates to documentation, user’s guide.
Changes in version 1.8.2:
UPDATED FUNCTIONS
Changes in version 1.7.2:
NEW FEATURES
add html documentation
customize the x axis as the amino acid physical position
update the documentation
BUG FIXES
Changes in version 1.7.1:
NEW FEATURES
BUG FIXES
Changes in version 1.17.1:
Changes in version 0.99.5:
Changes in version 0.99.4:
Changes in version 0.99.3:
updated the python script to be executable
python script help in the vignette is now “live”
added negative tests for empty and flawed input in test_dataInput.R
small fixes in the tests and the source code
Changes in version 0.99.2:
updated general package help
small fixes in the vignette
updated newsfile
Changes in version 0.99.1:
fixed typos in the documentation
clarified dimensions of the count tables in the vignette
added additional checks to the data import functions
Changes in version 0.99.0:
Changes in version 1.24.0:
QuantStudio (LifeTechnologies) output files are now supported
All packages that were ‘depended on’ are not explicitly ‘imported from’. This has the effect that scripts depending on ddCt may explicitly load libraries (such as RColorBrewer and Biobase) to use functions therein.
ColMap is now simplied to contain only three slots: Sample, Detector, and Ct.
Class ‘CSVReader’ is now renamed into ‘TSVReader’ since it supports rather tab-delimited file, instead of comma-separated file
A direct way to convert a data.frame to a InputFrame object is documented. See ‘example(InputFrame)’.
Changes in version 1.99.3 (2013-07-25):
Updates
A few changes to shearwater vignette
Renamed arguments pi.gene and pi.backgr in makePrior()
Bugfixes
Changes in version 1.99.2 (2013-07-11):
Updates
Updated CITATION
Added verbose option to bam2R to suppress output
Changed mode() to “integer” for value of loadAllData()
Bugfixes
Changes in version 1.99.1 (2013-06-25):
Updates
Using knitr for prettier vignettes
Including shearwater vignette
Bugfixes
fixed issues with deletions in bf2Vcf()
makePrior() adds background on all sites
Changes in version 1.99.0 (2013-04-30):
Updates
New shearwater algorithm
Including VCF output through summary(deepSNV, value=”VCF”)
1.4.0: 07-03-2015 Lorena Pantano lorena.pantano@gmail.com FIX SOME TEXT IN VIGNETTE, AND CLEAN DEPENDS FLAG
Changes in version 1.9.0:
Changes in version 1.3.3:
SIGNIFICANT USER-VISIBLE CHANGES
Changes in version 1.3.2:
SIGNIFICANT USER-VISIBLE CHANGES
Changes in version 1.3.1:
SIGNIFICANT USER-VISIBLE CHANGES
Changes in version 1.3.1:
NEW FEATURES
Changes in version 1.3.4:
SIGNIFICANT USER-VISIBLE CHANGES
Changes in version 1.3.3:
NEW FEATURES
Changes in version 1.3.2:
NEW FEATURES
Changes in version 1.3.1:
SIGNIFICANT USER-VISIBLE CHANGES
Changes in version 1.10.0:
Added MLE argument to plotMA().
Added normTransform() for simple log2(K/s + 1) transformation, where K is a count and s is a size factor.
When the design contains an interaction, DESeq() will use betaPrior=FALSE. This makes coefficients easier to interpret.
Independent filtering will be less greedy, using as a threshold the lowest quantile of the filter such that the number of rejections is within 1 SD from the maximum. See ?results.
summary() and plotMA() will use ‘alpha’ from results().
Changes in version 1.16.0:
Roll up bugfixes
dba.plotHeatmap returns binding sites in row order
Changes in version 1.1.17:
Renamed normalize() to normOffsets().
Added library size specification to DIList methods normOffsets(), asDGEList().
Fixed bugs under pathological settings in plotPlaid(), plotDI(), rotPlaid(), rotDI().
Optimized C++ code for connectCounts(), squareCounts().
Streamlined various R utilities used throughout all functions.
Added iter_map.py to inst/python, for iterative mapping of DNase Hi-C data.
Added the neighborCounts() function, for simultaneous read counting and enrichment calculation.
Added exclude for enrichedPairs(), to provide an exclusion zone in the local neighborhood.
Switched default colour in rotPlaid(), plotPlaid() to black.
Added compartmentalize() function to identify genomic compartments.
Added domainDirections() function to help identify domains.
Modified correctedContact() to allow distance correction and report factorized probabilities directly.
Modified marginCounts() function for proper single-end-like treatment of Hi-C data.
Extended clusterPairs() to merge bin pairs from multiple DILists.
Switched to reporting ranges directly from boxPairs(), added support for minimum bounding box output.
Modified consolidatePairs() to accept index vectors for greater modularity.
Added reference argument for large bin pairs, in filterDirect() and filterTrended().
Added filterDiag() convenience function for filtering of (near-)diagonal bin pairs.
Slight change to preparePairs() diagnostic reports when dedup=FALSE, and for unpaired reads.
Added option for a distance-based threshold to define invalid chimeras in preparePairs().
Updated documentation, tests and user’s guide.
Added diffHic paper entry to CITATION.
Changes in version 2.7.12:
Changes in version 2.7.11:
check whether input geneList is sorted <2015-09-22, Tue>
order first followed by showCategory subsetting in barplot <2015-09-08, Tue> + https://support.bioconductor.org/p/71917/#71939
bug fixed in EXTID2NAME, keytype is TAIR for arabidopsis and ORF for malaria <2015-08-26, Wed>
Changes in version 2.7.10:
add Giovanni Dall’Olio as contributor in author list. <2015-07-21, Tue>
update NCG data to version cancergenes_4.9.0_20150720 contributed by Giovanni Dall’Olio. https://github.com/GuangchuangYu/DOSE/pull/8 <2015-07-21, Tue>
geneInCategory may simplify to vector by R in very rare case, which violate the assumption of list in S4 validation checking. This issue was fixed. <2015-07-19, Sun>
Changes in version 2.7.9:
add citation of ChIPseeker <2015-07-09, Thu>
add ‘Disease analysis of NGS data’ section in vignette <2015-06-29, Mon>
convert vignette from Rnw to Rmd <2015-06-24, Wed>
Changes in version 2.7.8:
Changes in version 2.7.7:
speed up by using sample.int instead of sample <2015-06-04, Thu>
add seed = FALSE to control reproduciblility of gsea function. to make result reproducible, explicitly set seed=TRUE <2015-06-04, Thu>
Changes in version 2.7.6:
Changes in version 2.7.5:
Changes in version 2.7.4:
Changes in version 2.7.3:
add setType slot in gseaResult <2015-05-15, Tue>
add universe and geneSets slots in enrichResult <2015-05-05, Tue>
Changes in version 2.7.2:
Changes in version 2.7.1:
Changes in version 2.8.0:
Changes in version 0.99.3:
DOCUMENTATION
First release to Bioconductor
NEWS
file was added.
Changes in version 2.5.6:
Ported changes from version 2.4.5 - 2.4.7
Added a function to create the synthetic transcripts
Deprecated functions fetchAnnotation and knowOrganisms are now defunct
Export ‘basename’, ‘seqlevels’, ‘seqlevels<-‘ and ‘seqnames<-‘
Changes in version 2.5.5:
Changes in version 2.5.4:
Changes in version 2.5.3:
Ported changed from release version 2.4.1
Adapted to the genomeIntervals API changes (change from seq_name to seqnames and addition of the coercion methods to GRanges and consort).
Changes in version 2.5.2:
Changes in version 2.5.1:
Changes in version 2.5.0:
Changes in version 4.12.0:
NEW FEATURES
SIGNIFICANT USER-VISIBLE CHANGES
deprecated ‘…GreyScale’ morphological functions; use common functions ‘dilate’, ‘erode’, ‘opening’, ‘closing’, ‘whiteTopHat’, ‘blackTopHat’ and ‘selfComplementaryTopHat’ for filtering both binary and grayscale images
‘resize’ doesn’t perform bilinear filtering at image borders anymore in order to prevent the blending of image edges with the background when the image is upscaled; to switch on bilinear sampling at image borders use the function argument ‘antialias = TRUE’
‘floodFill’ and ‘fillHull’ preserve storage mode
PERFORMANCE IMPROVEMENTS
all morphological operations use the efficient Urbach-Wilkinson algorithm (up to 3x faster compared to the previous implementation)
‘rotate’: perform lossless 90/180/270 degree rotations by disabling bilinear filtering
BUG FIXES
reimplemented the Urbach-Wilkinson algorithm used to perform grayscale morphological transformations
improved pixel-level accuracy of spatial linear transformations: ‘affine’, ‘resize’, ‘rotate’ and ‘translate’
‘display(…, method = “raster”)’: displaying of single-channel color images
‘drawCircle’: corrected x-y offset
‘equalize’: in case of a single-valued histogram issue a warning and return its argument
‘hist’: accept images with ‘colorMode = Color’ containing less than three color channels
‘image’: corrected handling of image frames
‘medianFilter’: filter size check
‘normalize’: normalization of a flat image when the argument ‘separate’ is set to ‘FALSE’
‘reenumerate’: corrected handling of images without background
‘stackObjects’: corrected handling of blank images without any objects
‘tile’: reset dimnames
Changes in version 1.9.3:
Correct typos in GetDEResults help file.
Include an additional method for normalization.
Changes in version 1.9.2:
Changes in version 1.9.1:
Changes in version 2.3:
Added function getGeneLengthAndGCContent to compute gene length and GC-content.
Updated vignette.
Changes in version 2.1.1:
Moderated F-test has been added for likelihood ratio test
Weights can be inputted into odp/lrt which allows it to work for RNA-Seq experiments with low samples
added function apply_jackstraw
fixed bug in build_study
Changes in version 3.12.0:
New argument tagwise for estimateDisp(), allowing users not to estimate tagwise dispersions.
estimateTrendedDisp() has more stable performance and does not return negative trended dispersion estimates.
New plotMD methods for DGEList, DGEGLM, DGEExact and DGELRT objects to make a mean-difference plot (aka MA plot).
readDGE() now recognizes HTSeq style meta genes.
Remove the F-test in glmLRT().
New argument contrast for diffSpliceDGE(), allowing users to specify the testing contrast.
glmTreat() returns both logFC and unshrunk.logFC in the output table.
New method implemented in glmTreat() to increase the power of the test.
New kegga methods for DGEExact and DGELRT objects to perform KEGG pathway analysis of differentially expressed genes using Entrez Gene IDs.
New dimnames<- methods for DGEExact and DGELRT objects.
Bug fix to dimnames<- method for DGEGLM objects.
User’s Guide updated. Three old case studies are replaced by two new comprehensive case studies.
Changes in version 1.2.0:
Removed function QCfilter
Heavily modified function QCinfo
Add an argument exSample to preprocessENmix
Changes in version 0.99.3:
anno_enrich
: get rid of lazy loading
smoothing by locfit
Changes in version 0.99.2:
Changes in version 0.99.1:
system.file()
nowChanges in version 0.99.0:
Changes in version 1.1.9:
BUG FIXES
Changes in version 1.1.6:
BUG FIXES
Changes in version 1.1.5:
NEW FEATURES
Changes in version 1.1.4:
NEW FEATURES
Changes in version 1.1.3:
SIGNIFICANT USER-VISIBLE CHANGES
Added method ensemblVersion that returns the Ensembl version the package bases on.
Added method getGenomeFaFile that queries AnnotationHub to retrieve the Genome FaFile matching the Ensembl version of the EnsDb object.
Changes in version 1.1.2:
SIGNIFICANT USER-VISIBLE CHANGES
Added examples to the vignette for building an EnsDb using AnnotationHub along with the matching genomic sequence.
Added an example for fetching the sequences of genes, transcripts and exons to the vignette.
BUG FIXES
Changes in version 1.1.1:
SIGNIFICANT USER-VISIBLE CHANGES
Changes in version 1.10.0:
NEW FEATURES
Changes in version 1.6.1:
Changes in version 1.3.5:
SIGNIFICANT USER-VISIBLE CHANGES
BUG FIXES AND MINOR IMPROVEMENTS
Changes in version 1.3.4:
SIGNIFICANT USER-VISIBLE CHANGES
BUG FIXES AND MINOR IMPROVEMENTS
Fixed allReps and labelReps value assignment
Fixed bug for duplicate row names in array data
Fixed warning for incorrect sample names
Changes in version 1.3.3:
SIGNIFICANT USER-VISIBLE CHANGES
BUG FIXES AND MINOR IMPROVEMENTS
Added warnings to initDat function for incorrect sample names and missing 1:1 controls from userMixFileß
Set minimum version requirements for ggplot2 and gridExtra
Changes in version 1.3.2:
SIGNIFICANT USER-VISIBLE CHANGES
Vignette is updated to include use of grid.arrange for viewing figures
multiplot function is deprecated and removed from the package, function is replaced with grid.arrange
BUG FIXES AND MINOR IMPROVEMENTS
Changes in version 1.3.1:
SIGNIFICANT USER-VISIBLE CHANGES
BUG FIXES AND MINOR IMPROVEMENTS
Changes in version 1.9.2:
Changes in version 1.9.1:
integrated the RMT tool for extracting the combinatorial RNA methylome from multiple MeRIP-Seq datasets, see ?RMT
3 authors: Jia Meng, Lin Zhang and Lian Liu
added another citation (Liu 2015)
Changes in version 3.4:
Added argument ‘downloadFile’ to fea_david() to choose whether to save the analysis results to the current directory
DAVID now requires https. This causes errors in some systems. A (hopefully) temporary solution is to install some certificates locally. See RDAVIDWebService help: https://support.bioconductor.org/p/70090/#72226
Changes in version 0.99.0:
Changes in version 1.7.3:
add the header ie the sample names to the output tables (created when using output.type=’table’)
correct little bug concerning the SAM file when header is present (see samio.cpp first test over linecount replace by totalnumread)
Changes in version 1.4.0:
NEW FEATURES
BUG FIXES
OTHER NOTES
added LazyData: true in the DESCRIPTION
updated travis.yml to use native R integration
vignette: improved structure, to enhance readability and usability; removed rgl hook which was not used anyway
documentation: slight updates and enhancements
Changes in version 1.1.1:
NEW FEATURES
Changes in version 2.7.0:
Changes in version 1.6.0:
Changes in version 1.11.1:
Changes in version 2.0.0:
Added functions for PC-Relate. PC-Relate provides model-free estimation of recent genetic relatedness in general samples. It can be used to estimate kinship coefficients, IBD sharing probabilities, and inbreeding coefficients using genome-wide SNP data. PC-Relate accounts for population structure (ancestry) among sample individuals through the use of ancestry representative principal components (PCs) to provide accurate relatedness estimates due only to recent family (pedigree) structure.
GENESIS now imports the package gdsfmt.
Changes in version 1.9.3:
Changes in version 1.9:
Added CITATION
GenesRanking help: How to create a GenesRanking object based on scores provided by another algorithm
Several message and warning improvements
Bugfix: 0 IQR filter now returns the original matrix
Changes in version 1.1.27:
IMPROVEMENTS AND BUG FIXES
Changes in version 1.1.26:
NEW FUNCTIONS AND FEATURES
Changes in version 1.1.25:
IMPROVEMENTS AND BUG FIXES
Changes in version 1.1.24:
IMPROVEMENTS AND BUG FIXES
Changes in version 1.1.23:
IMPROVEMENTS AND BUG FIXES
Changes in version 1.1.22:
NEW FUNCTIONS AND FEATURES
Changes in version 1.1.21:
IMPROVEMENTS AND BUG FIXES
Changes in version 1.1.20:
IMPROVEMENTS AND BUG FIXES
Changes in version 1.1.19:
NEW FUNCTIONS AND FEATURES
Arithmetic, indicator and logic operations as well as subsetting work on ScoreMatrix, ScoreMatrixBin and ScoreMatrixList objects. New functionality at “ScoreMatrix-class” and “ScoreMatrixList-class” are documented in help pages.
Commented examples of functions are uncommented or \donttest{} is used.
Changes in version 1.1.18:
NEW FUNCTIONS AND FEATURES
Changes in version 1.1.17:
IMPROVEMENTS AND BUG FIXES
Changes in version 1.1.16:
IMPROVEMENTS AND BUG FIXES
Changes in version 1.1.15:
IMPROVEMENTS AND BUG FIXES
Changes in version 1.1.14:
IMPROVEMENTS AND BUG FIXES
Changes in version 1.1.13:
IMPROVEMENTS AND BUG FIXES
add new argument cex.legend to plotTargetAnnotation() to specify the size of the legend.
changed ScoreMatrixBin() to run faster when noCovNA=TRUE
check not only for .bw but also .bigWig and .bigwig extensions of BigWig file in ScoreMatrix() and ScoreMatrixBin()
Changes in version 1.1.12:
IMPROVEMENTS AND BUG FIXES
Changes in version 1.1.11:
IMPROVEMENTS AND BUG FIXES
Changes in version 1.1.10:
IMPROVEMENTS AND BUG FIXES
Changes in version 1.1.9:
IMPROVEMENTS AND BUG FIXES
Changes in version 1.1.8:
IMPROVEMENTS AND BUG FIXES
Changes in version 1.1.7:
IMPROVEMENTS AND BUG FIXES
Changes in version 1.1.6:
IMPROVEMENTS AND BUG FIXES
Changes in version 1.1.5:
IMPROVEMENTS AND BUG FIXES
Changes in version 1.1.4:
IMPROVEMENTS AND BUG FIXES
Changes in version 1.1.3:
IMPROVEMENTS AND BUG FIXES
Functions that read data from text files re-written from data.table::fread() to readr::read_delim() and now they can read compressed files from a URL
Changes in readBed(), readNarrowPeak(), readBroadPeak() and gffToGRanges() arguments; All of them have now track.line argument that can be FALSE, “auto” or an integer indicating number of first lines to skip. The zero.based argument was added to readBed() that tells whether ranges in the bed file are in 0 or 1-based coordinate system. Implemented by Katarzyna Wręczycka.
Changes in version 1.1.2:
IMPROVEMENTS AND BUG FIXES
Changes in version 1.1.1:
NEW FUNCTIONS AND FEATURES
IMPROVEMENTS AND BUG FIXES
Changes in version 1.25.3:
Changes in version 1.25.2:
Changes in version 1.25.1:
Changed readGff3 to use closed intervals by default. Implemented two sub-functions that implement reading a gff3 as base-pair features only (no zero length intervals, i.e. right-closed intervals) or which allows for zero length intervals, i.e. right-open intervals, when start equals end)
Deprecated the seq_name accessors in favour of the BiocGenerics seqnames
Added a width accessor - similar to the IRanges functionality
Added coercion to GRangesList and RangedData
Edited some of the documentation (man page) and NAMESPACE generation to use roxygen2
Changes in version 1.25.0:
Changes in version 1.6.0:
NEW FEATURES
Add strandMode() getter and setter for GAlignmentPairs objects in response to the following post: https://support.bioconductor.org/p/65844/ See ?strandMode for more information.
The readGAlignment*() functions now allow repeated seqnames in the BAM header.
Add “coverage” method for GAlignmentsList objects.
The strand setter now works on a GAlignmentsList object in a restricted way (only strand(x) <- “+” or “-“ or “*” is supported).
SIGNIFICANT USER-LEVEL CHANGES
summarizeOverlaps() now returns a RangedSummarizedExperiment object (defined in the new SummarizedExperiment package) instead of an “old” SummarizedExperiment object (defined in the GenomicRanges package).
Slightly modify the behavior of junctions() on a GAlignmentPairs object so that the returned ranges now have the “real strand” set on them. See ?junctions and the documentation of the ‘real.strand’ argument in the man page of GAlignmentPairs objects for more information.
Add ‘real.strand’ argument to first() and last() getters for GAlignmentPairs objects.
DEPRECATED AND DEFUNCT
Deprecate left() and right() getters and strand() setter for GAlignmentPairs objects.
Deprecate ‘invert.strand’ argument of first() and last() getters for GAlignmentPairs objects.
Deprecate ‘order.as.in.query’ argument of “grglist” method for GAlignmentPairs objects.
Deprecate ‘order.as.in.query’ argument in “rglist” method for GAlignmentsList objects (this concept is not defined for these objects in general and the argument was ignored anyway).
After being deprecated in BioC 3.1, the “mapCoords” and “pmapCoords” methods are now defunct. mapToAlignments() should be used instead.
After being deprecated in BioC 3.1, the readGAlignmentFromBam() functions are now defunct. Everybody says “Let’s all use the readGAlignment() functions instead! (no FromBam suffix). Yeah!”
BUG FIXES
Changes in version 1.22:
NEW FEATURES
Add coverageByTranscript() and pcoverageByTranscript(). See ?coverageByTranscript for more information.
Various improvements to makeTxDbFromGFF(): - Now supports ‘format=”auto”’ for auto-detection of the file format. - Now supports naming features by dbxref tag (like GeneID). This has proven useful when importing GFFs from NCBI.
Improvements to the coordinate mapping methods: - Support recycling when length(transcripts) == 1 for parallel mapping functions. - Add pmapToTranscripts,Ranges,GRangesList and pmapFromTranscripts,Ranges,GRangesList methods.
Adds ‘taxonomyId’ argument to the makeTxDbFrom*() functions.
Improvements to makeTxDbPackage(): - Add ‘pkgname’ argument to makeTxDbPackage() to let the user override the automatic naming of the package to be generated. - Support person objects for ‘maintainer’ and ‘author’ arguments to makeTxDbPackage().
The ‘chrominfo’ vector passed to makeTxDb() can now mix NAs and non-NAs.
SIGNIFICANT USER-VISIBLE CHANGES
Improve handling of ‘circ_seqs’ argument by makeTxDbFromUCSC(), makeTxDbFromGFF(), and makeTxDbFromBiomart(): no more annoying warning when none of the strings in DEFAULT_CIRC_SEQS matches the seqlevels of the TxDb object to be made.
2 minor changes to makeTxDbFromBiomart(): - Now drops unneeded chromosome info when importing an incomplete transcript dataset. - Now returns a TxDb object with ‘Full dataset’ field set to ‘no’ when makeTxDbFromBiomart() is called with user-supplied ‘filters’.
makeTxDbPackage() now includes data source in the package name by default (for non UCSC and BioMart databases).
The following changes were made to the coordinate mapping methods: - mapToTranscripts() now reports mapped position with respect to the transcription start site regardless of strand. - Change ‘ignore.strand’ default from TRUE to FALSE in all coordinate mapping methods for consistency with other functions that already have the ‘ignore.strand’ argument. - Name matching in mapFromTranscripts() is now done with seqnames(x) and names(transcripts). - The pmapFromTranscripts,*,GRangesList methods now return a GRangesList object. Also they no longer use ‘UNMAPPED’ seqname for unmapped ranges. - Remove uneeded ellipisis from the argument list of various coordinate mapping methods.
Change behavior of seqlevels0() getter so it does what it was always intended to do.
The order of the transcripts returned by transcripts() has changed: now they are guaranteed to be in the same order as in the GRangesList object returned by exonsBy().
Code improvements and speedup to the transcripts(), exons(), cds(), exonsBy(), and cdsBy() extractors.
DEPRECATED AND DEFUNCT
After being deprecated in BioC 3.1, the makeTranscriptDb*() functions are now defunct.
After being deprecated in BioC 3.1, the ‘exonRankAttributeName’, ‘gffGeneIdAttributeName’, ‘useGenesAsTranscripts’, ‘gffTxName’, and ‘species’ arguments of makeTxDbFromGFF() are now defunct.
Remove sortExonsByRank() (was defunct in BioC 3.1).
BUG FIXES
Fix bug in fiveUTRsByTranscript() and threeUTRsByTranscript() extractors when the TxDb object had “user defined” seqlevels and/or a set of “active/inactive” seqlevels defined on it.
Fix bug in isActiveSeq() setter when the TxDb object had “user defined” seqlevels on it.
Fix many issues with seqlevels() setter for TxDb objects. In particular make the ‘seqlevels(x) <- seqlevels0(x)’ idiom work on TxDb objects.
Fix bug in makeTxDbFromBiomart() when using it to retrieve a dataset that doesn’t provide the cds_length attribute (e.g. sitalica_eg_gene dataset in plants_mart_26).
Changes in version 1.6.0:
BUG FIXES
Changes in version 1.3.9:
NEW FEATURES
InteractionTrack class for plotting interactions with Gviz
plotAvgViewpoint for plotting summarised interactions around a set of features
summariseByFeaturePairs: to summarise interactions between all pairs of two feature sets
SIGNIFICANT USER-LEVEL CHANGES
annotateInteractions is significantly faster
Data import has been made stricter and more consistent across different file formats. Homer interaction files now have data imported that was previously discarded.
BUG FIXES
single viewpoint plotting (plotViewpoint)
is.dt, is.pt
calculateDistances
some import/export issues
Changes in version 1.22.0:
NEW FEATURES
Support coercions back and forth between a GRanges object and a character vector (or factor) with elements in the format ‘chr1:2501-2800’ or ‘chr1:2501-2800:+’.
Add facilities for manipulating “genomic variables”: bindAsGRanges(), mcolAsRleList(), and binnedAverage(). See ?genomicvars for more information.
Add “narrow” method for GRangesList objects.
Enhancement to the GRanges() constructor. If the ‘ranges’ argument is not supplied then the constructor proceeds in 2 steps: 1. An initial GRanges object is created with ‘as(seqnames, “GRanges”)’. 2. Then this GRanges object is updated according to whatever other arguments were supplied to the call to GRanges(). Because of this enhancement, GRanges(x) is now equivalent to ‘as(x, “GRanges”)’ e.g. GRanges() can be called directly on a character vector representing ranges, or on a data.frame, or on any object for which coercion to GRanges is supported.
Add ‘ignore.strand’ argument to “range” and “reduce” methods for GRangesList objects.
Add coercion from SummarizedExperiment to RangedSummarizedExperiment (also available via updateObject()). See 1st item in DEPRECATED AND DEFUNCT section below for more information about this.
GNCList objects are now subsettable.
“coverage” methods now accept ‘shift’ and ‘weight’ supplied as an Rle.
SIGNIFICANT USER-LEVEL CHANGES
Modify behavior of “*” strand in precede() / follow() to mimic ‘ignore.strand=TRUE’.
Revisit “pintersect” methods for GRanges#GRanges, GRangesList#GRanges, and GRanges#GRangesList: - Sanitize their semantic. - Add ‘drop.nohit.ranges’ argument (FALSE by default). - If ‘drop.nohit.ranges’ is FALSE, the returned object now has a “hit” metadata column added to it to indicate the elements in ‘x’ that intersect with the corresponding element in ‘y’.
binnedAverage() now treats ‘numvar’ as if it was set to zero on genomic positions where it’s not set (typically happens when ‘numvar’ doesn’t span the entire chromosomes because it’s missing the trailing zeros).
GRanges() constructor no more mangles the names of the supplied metadata columns (e.g. if the column is “_tx_id”).
makeGRangesFromDataFrame() now accepts “.” in strand column (treated as
GNCList() constructor now propagates the metadata columns.
Remove “seqnames” method for RangesList objects.
DEPRECATED AND DEFUNCT
The SummarizedExperiment class defined in GenomicRanges is deprecated and replaced by 2 new classes defined in the new SummarizedExperiment package: SummarizedExperiment0 and RangedSummarizedExperiment. In BioC 2.3, the SummarizedExperiment class will be removed from the GenomicRanges package and the SummarizedExperiment0 class will be renamed SummarizedExperiment. To facilitate this transition, a coercion method was added to coerce from old SummarizedExperiment to new RangedSummarizedExperiment (this coercion is performed when calling updateObject() on an old SummarizedExperiment object).
makeSummarizedExperimentFromExpressionSet() and related stuff was moved to the new SummarizedExperiment package.
After being deprecated in BioC 3.1, the rowData accessor is now defunct (replaced with the rowRanges accessor).
After being deprecated in BioC 3.1, GIntervalTree objects and the “intervaltree” algorithm in findOverlaps() are now defunct.
After being deprecated in BioC 3.1, mapCoords() and pmapCoords() are now defunct.
BUG FIXES
Changes in version 0.99.0:
genotypeeval in use at Genentech and HLI.
genotypeeval submitted to Bioconductor.
2.36: New Features * New, faster SOFT format parsing (Leonardo Gama) * Turned on unit tests in Travis CI * Test coverage metrics added Bug fixes * default download method no longer assumes that curl is installed on linux * GSEMatrix parsing from file now finds cached GPLs
Changes in version 1.1.20:
fixed bug in geom_tiplab when x contains NA (eg, removing by collapse function) <2015-10-01, Thu>
bug fixed in %add2%, if node available use node, otherwise use label <2015-09-04, Fri>
bug fixed of subview for considering aes mapping of x and y <2015-09-03, Thu>
update vignette by adding r8s example <2015-09-02, Wed>
bug fixed in fortify.multiPhylo, convert df$.id to factor of levels=names(multiPhylo_object) <2015-09-02, Wed>
update scale_x_ggtree to support Date as x-axis <2015-09-01, Tue>
add mrsd parameter for user to specify ‘most recent sampling date’ for time tree <2015-09-01, Tue> - remove ‘time_scale’ parameter.
defined ‘raxml’ class for RAxML bootstrapping analysis result <2015-09-01, Tue> + see http://sco.h-its.org/exelixis/web/software/raxml/hands_on.html + read.raxml, parser function + plot, get.tree, get.fields, groupOTU, groupClade, scale_color, gzoom and show methods + fortify.raxml method
Changes in version 1.1.19:
use fortify instead of fortify.phylo in fortify.multiPhylo, so that multiPhylo can be a list of beast/codeml or other supported objects. <2015-08-31, Mon>
support multiPhylo object, should use + facet_wrap or + facet_grid <2015-08-31, Mon>
remove dependency of EBImage and phytools to speedup the installation process of ggtree <2015-08-31, Mon> + these two packages is not commonly used, and will be loaded automatically when needed.
Changes in version 1.1.18:
layout name change to ‘rectangular’, ‘slanted’, ‘circular’/’fan’ for phylogram and cladogram (if branch.length = ‘none’) ‘unroot’ is not changed. <2015-08-28. Fri>
implement geom_point2, geom_text2, geom_segment2 to support subsetting <2015-08-28, Fri> see https://github.com/hadley/ggplot2/issues/1295
update geom_tiplab according to geom_text2 and geom_segment2 <2015-08-28, Fri>
add geom_tippoint, geom_nodepoint and geom_rootpoint <2015-08-28, Fri>
Changes in version 1.1.17:
bug fixed in rm.singleton.newick by adding support of scientific notation in branch length <2015-08-27, Thu>
bug fixed in gheatmap, remove inherit aes from ggtree <2015-08-27, Thu>
add ‘width’ parameter to add_legend, now user can specify the width of legend bar <2015-08-27, Thu>
add ‘colnames_position’ parameter to gheatmap, now colnames can be display on the top of heatmap <2015-08-27, Thu>
theme_transparent to make background transparent <2015-08-27, Thu>
subview for adding ggplot object (subview) to another ggplot object (mainview) <2015-08-27, Thu>
Changes in version 1.1.16:
Changes in version 1.1.15:
open text angle parameter for annotation_clade/annotation_clade2 <2015-08-13, Thu>
support changing size of add_legend <2015-08-13, Thu>
reroot methods for phylo and beast <2015-08-07, Fri>
Changes in version 1.1.14:
Changes in version 1.1.13:
implement annotation_image <2015-08-01, Sat>
better implementation of geom_tiplab for accepting aes mapping and auto add align dotted line <2015-08-01, Sat>
open group_name parameter of groupOTU/groupClade to user <2015-08-01, Sat>
Changes in version 1.1.12:
update vignette according to the changes <2015-07-31, Fri>
add mapping parameter in ggtree function <2015-07-31, Fri>
extend groupClade to support operating on tree view <2015-07-31, Fri>
extend groupOTU to support operating on tree view <2015-07-31, Fri>
new implementation of groupClade & groupOTU <2015-07-31, Fri>
Changes in version 1.1.11:
annotation_clade and annotation_clade2 functions. <2015-07-30, Thu>
better add_legend implementation. <2015-07-30, Thu>
add … in theme_tree & theme_tree2 for accepting additional parameter. <2015-07-30, Thu>
better geom_tree implementation. Now we can scale the tree with aes(color=numVar). <2015-07-30, Thu>
Changes in version 1.1.10:
Changes in version 1.1.9:
update add_legend to align legend text <2015-07-06, Mon>
bug fixed in internal function, getChild.df, which should not include root node if selected node is root <2015-07-01, Wed>
rotate function for ratating a clade by 180 degree and update vignette <2015-07-01, Wed>
get_taxa_name function will return taxa name vector of a selected clade <2015-06-30, Tue>
add example of flip function in vignette <2015-06-30, Tue>
flip function for exchanging positions of two selected branches <2015-06-30, Tue>
Changes in version 1.1.8:
update get.placement <2015-06-05, Fri>
edgeNum2nodeNum for converting edge number to node number for EPA/pplacer output <2015-06-04, Thu>
mv scale_x_gheatmap to scale_x_ggtree, which also support msaplot <2015-06-02, Tue>
add mask function <2015-06-02, Tue>
Changes in version 1.1.7:
add example of msaplot in vignette <2015-05-22, Fri>
msaplot for adding multiple sequence alignment <2015-05-22, Fri>
Changes in version 1.1.6:
add vertical_only parameter to scaleClade and set to TRUE by default. only vertical will be scaled by default. <2015-05-22, Fri>
update add_colorbar & add_legend <2015-05-21, Thu>
add example of add_legend and gheatmap in vignette <2015-05-18, Mon>
gheatmap implementation of gplot <2015-05-18, Mon>
add_legend for adding evolution distance legend <2015-05-18, Mon>
Changes in version 1.1.5:
Changes in version 1.1.4:
better performance of parsing beast tree <2015-05-11, Mon> + support beast tree begin with ‘tree tree_1 = ‘ and other forms. + support file that only contains one evidence for some of the nodes/tips
update add_colorbar to auto determine the position <2015-05-04, Mon>
add_colorbar function <2015-04-30, Thu>
Changes in version 1.1.3:
add space between residue substitution (e.g. K123R / E155D) <2015-04-30, Thu>
remove slash line in heatmap legend <2015-04-30, Thu>
update vignette to add example of merge_tree <2015-04-29, Wed>
Changes in version 1.1.2:
in addition to parsing beast time scale tree in XXX_year[\.\d], now supports XXX/year[\.\d] <2015-04-29, Wed>
add examples folder in inst that contains sample data <2015-04-29, Wed>
update gplot, now rowname of heatmap will not be displayed <2015-04-28, Tue>
add line break if substitution longer than 50 character <2015-04-28, Tue>
support calculating branch for time scale tree <2015-04-28, Tue>
remove parsing tip sequence from mlb and mlc file <2015-04-28, Tue>
remove tip.fasfile in read.paml_rst for rstfile already contains tip sequence <2015-04-28, Tue>
scale_color accepts user specific interval and output contains ‘scale’ attribute that can be used for adding legend <2015-04-28, Tue>
extend fortify methods to support additional fields <2015-04-28, Tue>
extend get.fields methods to support additional fields <2015-04-28, Tue>
extend tree class to support additional info by merging two tree <2015-04-28, Tue>
implement merge_tree function to merge two tree objects into one <2015-04-28, Tue>
Changes in version 1.1.1:
minor bug fixed in extracting node ID of rst file <2015-04-27, Mon>
update parsing beast time scale tree to support _year (originally supports _year.\d+) <2015-04-27, Mon>
add Tommy in author <2015-04-27, Mon>
Changes in version 1.21.1:
Changes in version 1.3.2:
BUG FIX
Changes in version 1.3.1:
BUG FIX
Changes in version 1.27.4:
Changes in version 1.27.3:
Changes in version 1.27.2:
Changes in version 1.27.1:
Changes in version 1.15.3 (2015-10-07):
Updated all pathway data.
More descriptive edge types.
Use the package “rappdirs” to select a directory for cached files.
Changes in version 1.1.1:
Changes in version 1.4.0:
Changes in version 1.31:
SIGNIFICANT USER-VISIBLE CHANGES
BUG FIXES
Changes in version 1.1.1:
print message if input chromosome names are without ‘chr’
call start()
and end()
explictely with GenomicRanges::
unit of x-axis is correct now
Changes in version 0.99.9:
Changes in version 2.1.0:
USER VISIBLE CHANGES
GWAS catalog data curated at EMBL/EBI will now be used with makeCurrentGwascat: Updated 3 August 2015, as comma-space delim. for genes and EFO tags has been introduced
Interfaces to the Experimental Factor Ontology (www.ebi.ac.uk/efo/) are provided: efo.obo.g is an annotated graphNEL with the ontology
Vignette gwascatOnt.Rmd introduced
Changes in version 1.15.16:
Changes in version 1.15.15:
Changes in version 1.15.13:
Changes in version 1.15.12:
Changes in version 1.15.11:
Changes in version 1.15.10:
Changes in version 1.15.8:
Changes in version 1.15.7:
Changes in version 1.15.5:
Changes in version 1.15.3:
Changes in version 1.15.2:
Changes in version 1.15.1:
Changes in version 1.3.4 (2015-09-08):
Changes in version 1.3.3 (2015-07-20):
Updated output format of core functions.
Fixed minor bugs.
Changes in version 1.3.2 (2015-05-26):
Updated DESCRIPTION FILE.
Updated the CITATION file.
Changes in version 1.3.1 (2015-05-12):
Updated DESCRIPTION FILE.
Updated the CITATION file.
Updated documentation.
Changes in version 2.15.2:
Changes in version 1.3.2:
Changes in version 1.3.1:
Changes in version 1.6.0:
Changes in version 0.99.3:
Removed hlr dependency and added the MEL function
Fixed computation of r2 when the SNP_index = NULL
Changes in version 0.99.3:
Changes in version 0.99.2:
Changes in version 0.99.1:
Changes in version 0.99.0:
Changes in version 1.4.0:
Changes in version 1.13.2:
SIGNIFICANT USER-VISIBLE CHANGES
Change in the way the interaction matrix is loaded. During the import, the lazyload option will force the data to be stored as triangular matrix. Note that a symmetric matrix is not triangular by construction. Then, to avoid any error in the data processing, the triangular matrix is always converted into symmetrical matrix before being returned by the intdata method.
Update of track display in mapC function. Off-set plot of adjacent features
BUG FIXES
Bug fixed in quality control function when empty maps are used
Bug fixed when plotting empty matrix
Changes in version 1.13.1:
NEW FEATURES
SIGNIFICANT USER-VISIBLE CHANGES
getCombinedContact is now able to merge HTCexp objects for non complete HiTClist objects. Missing maps are replaced by NA matrices
Update of isComplete, isPairwise, getCombinedIntervals methods for Hi-C data with no intrachromosomal maps
When the maxrange argument is set in the mapC function, all maps are displayed on the same scale so that they can be compared to each other
BUG FIXES
Bug fixed in mapC with the contact map is empty
Bug fixed in seqlevels(HTClist) method
Changes in version 1.11.1:
Changes in version 1.11.0:
Changes in version 1.0.0:
Changes in version 0.11.2 (2015-09-11):
BUG FIX: readIDAT() can now read non-encrypted IDAT files with strings longer than 127 characters.
BUG FIX: readIDAT() incorrectly assumed that there were exactly two blocks in RunInfo fields of non-encrypted (v3) IDAT files. Thanks to Gordon Bean (GitHub @brazilbean) for reporting on and contributing with code for the above two bugs.
Changes in version 0.11.1 (2015-07-29):
Changes in version 0.11.0 (2015-04-16):
1.1.1: NEW FEATRUES: * A normalization step which the sample cell-clusters to the common meta-cluster model is included an optionally activated during the major meta-clustering process. CHANGES: * The meta.ME C-binding and return value was modified in a way that the A-Posterior probability matrix Z for a cell-cluster belonging to a meta-cluster is also calculated and returned. BUFIXES: * Ellipse position were not correct when ploting a parameter subset
Changes in version 1.1.9:
Changes in version 1.1.8:
BUG FIXES
Changes in version 1.1.7:
BUG FIXES
Changes in version 1.1.6:
BUG FIXES
Changes in version 1.1.5:
BUG FIXES
Changes in version 1.1.4:
BUG FIXES
Changes in version 1.1.3:
BUG FIXES
Changes in version 1.1.2:
BUG FIXES
Changes in version 1.1.1:
BUG FIXES
Changes in version 1.7:
NEW FEATURES
BUG FIXES
Changes in version 2.4.0:
NEW FEATURES
Add “cbind” methods for binding Rle or RleList objects together.
Add coercion from Ranges to RangesList.
Add “paste” method for CompressedAtomicList objects.
Add “expand” method for Vector objects for expanding a Vector object ‘x’ based on a column in mcols(x).
Add overlapsAny,integer,Ranges method.
coverage” methods now accept ‘shift’ and ‘weight’ supplied as an Rle.
SIGNIFICANT USER-VISIBLE CHANGES
The following was moved to S4Vectors: - The FilterRules stuff. - The “aggregate” methods. - The “split” methods.
The “sum”, “min”, “max”, “mean”, “any”, and “all” methods on CompressedAtomicList objects are 100X faster on lists with 500k elements, 80X faster for 50k elements.
Tweak “c” method for CompressedList objects to make sure it always returns an object of the same class as its 1st argument.
NCList() constructor now propagates the metadata columns.
DEPRECATED AND DEFUNCT
RangedData/RangedDataList are not formally deprecated yet but the documentation now officially declares them as superseded by GRanges/GRangesList and discourage their use.
After being deprecated in BioC 3.1, IntervalTree and IntervalForest objects and the “intervaltree” algorithm in findOverlaps() are now defunct.
After being deprecated in BioC 3.1, mapCoords() and pmapCoords() are now defunct.
Remove seqapply(), mseqapply(), tseqapply(), seqsplit(), and seqby() (were defunct in BioC 3.1).
BUG FIXES
Fix FactorList() constructor when ‘compress=TRUE’ (note that the levels are combined during compression).
Fix c() on CompressedFactorList objects (was returning a CompressedIntegerList object).
Changes in version 1.3.4:
correction of Ubuntu problem with realloc for 0 elements in linearKernel generating a sparse empty kernel matrix
correction of problem with feature weights and prediction profiles for position specific gappy pair kernel
correction of problem with feature weights and prediction profiles for position specific motif kernel
corrections for feature weights, prediction via feature weights and prediction profile for distance weighted kernels
update of KeBABS citation
Changes in version 1.3.3:
new export kebabsCollectInfo for collection of package info
update of version dependency to Biostrings, XVector, S4Vector
correction for leading + or - in factor label
change of bibtex style sheet in vignette to plainnat.bst
Changes in version 1.3.2:
correction of error in kernel lists
user defined sequence kernel example SpectrumKernlabKernel moved to separate directory
Changes in version 1.3.1:
correction of error in model selection for processing via dense LIBSVM
remove problem in check for loading of SparseM
Changes in version 1.3.0:
Changes in version 1.27.2 (2015-05-25):
Changes in version 1.27.1 (2015-05-04):
Changes in version 1.1.1:
A new function, the “probes2pathways” has been added.
I have added to more network reconstruction approaches. The “aracne.a” and the “aracne.m” as included in the “parmigene” r-package.
I have replaced in the “preprocess” function the type of the produced image from jpeg to tiff format, with resolution=300dpi.
Changes in version 1.3.6:
Changes in version 1.3.1:
Changes in version 2.2.0:
Added checks to avoid producing identical matrices or data frame when the parameters are still the same after first function call.
Splitted the analysis in multiple (optionnal) intermediate steps (add_design, produce_matrices and produce_data_frame).
narrowPeak and broadPeak format is now supported.
Added multiple getter to access metagene members that are all now private (get_params, get_design, get_regions, get_matrices, get_data_frame, get_plot, get_raw_coverages and get_normalized_coverages.
Added the NCIS algorithm for noise removal.
Replaced the old datasets with promoters_hg19, promoters_hg18, promoters_mm10 and promoters_mm9 that can be accessed with data(promoters_????).
Added flip_regions and unflip_regions to switch regions orientation based on the strand.
Changes in version 0.0.0.9 (2015-09-14):
Changes in version 1.11:
Adding fitFeatureModel - a feature based zero-inflated log-normal model.
Added MRcoefs,MRtable,MRfulltable support for fitFeatureModel output.
Added mention in vignette.
Added support for normalizing matrices instead of just MRexperiment objects.
Fixed cumNormStat’s non-default qFlag option
Changes in version 1.9.21 (2015-10-08):
NEW FEATURES
BUG FIXES
Fixed broken dependency with removed CRAN package MADAM which was used for the Fisher p-value combination. The fix was done by copying the two required functions from the last MADAM archived version (1.2).
Fixed a bug in make.sample.list which rendered the function unusable (credits to Marina Adamou-Tzani).
Fixed a very special-case small bug in the report generation only a single gene passes the multiple testing correction cutoff (thans to Martic Reszcko, BSRC ‘Alexander Fleming’).
Fixed problem with Fisher p-value combination method (returning all NA due to the inexistence of names in the p-value vecror).
Fixed bug with flags of biotype filtered genes.
Changes in version 1.9.0 (2015-05-27):
NEW FEATURES
BUG FIXES
Changes in version 0.1.0:
Changes in version 1.3.3:
Changes in version 1.3.2:
Changes in version 1.15:
Adding testing for preprocessNoob, preprocessFunnorm.
Fxing some verbose output of preprocessNoob.
Adding non-exported function .digestVector for testing.
Changes in version 1.49.8:
Changes in version 1.49.7:
Changes in version 1.49.1:
Changes in version 1.1.1:
NEW FEATURES
Changes in version 1.13.8:
NEW FEATURES
Changes in version 1.13.7:
Changes in version 1.13.6:
BUG FIXES
Changes in version 1.13.5:
NEW FEATURES
Changes in version 1.13.4:
NEW FEATURES
BUG FIXES
Changes in version 1.13.3:
NEW FEATURES
BUG FIXES
Changes in version 1.13.2:
NEW FEATURES
BUG FIXES
Changes in version 1.13.1:
NEW FEATURES
BUG FIXES
Changes in version 1.2.0:
Changes in version 1.17.16:
Changes in version 1.17.15:
Changes in version 1.17.14:
Changes in version 1.17.13:
partly rewrite writeMgfData <2015-05-16 Thu>
initial hmap function <2015-07-16 Thu>
fix bug in plotting MS1 spectra (closes issue #59) <2015-07-16 Thu>
new image implementation, based on @vladpetyuk’s vp.misc::image_msnset <2015-07-25 Sat>
Changed the deprecated warning to a message when reading MzTab data version 0.9, as using the old reader can not only be achived by accident and will be kept for backwards file format compatibility <2015-07-30 Thu>
Changes in version 1.17.12:
Changes in version 1.17.11:
adding unit tests <2015-07-01 Wed>
fix abundance column selection when creating MSnSet form MzTab <2015-07-01 Wed>
new mzTabMode and mzTabType shortcut accessors for mode and type of an mzTab data <2015-07-01 Wed>
Changes in version 1.17.10:
Changes in version 1.17.9:
calculateFragments’ “neutralLoss” argument is now a list (was a logical before), see #47. <2015-06-24 Wed>
add defaultNeutralLoss() function to fill calculateFragments’ modified “neutralLoss” argument, see #47. <2015-06-24 Wed>
Changes in version 1.17.8:
coercion from IBSpectra to MSnSet, as per user request <2015-06-23 Tue>
new iPQF combineFeature method <2015-06-24 Wed>
Changes in version 1.17.7:
Changes in version 1.17.6:
Export metadata,MzTab-method <2015-06-19 Fri>
Replace spectra,MzTab-method by psms,MzTab-method <2015-06-20 Sat>
Change the meaning of calculateFragments’ “modifications” argument. Now the modification is added to the mass of the amino acid/peptide. Before it was replaced. <2015-06-21 Sun>
calculateFragments gains the feature to handle N-/C-terminal modifications, see #47. <2015-06-21 Sun>
update readMzTabData example <2015-06-22 Mon>
Changes in version 1.17.5:
Changes in version 1.17.4:
New lengths method for FoICollection instances <2015-06-06 Sat>
New image2 function for matrix object, that behaves like the method for MSnSets <2015-06-10 Wed>
image,MSnSet labels x and y axis as Samples and Features <2015-06-10 Wed>
fixed bug in purityCorrect, reported by Dario Strbenac <2015-06-11 Thu>
Changes in version 1.17.3:
Changes in version 1.17.2:
Changes in version 1.17.1:
new MSnSetList class <2015-04-19 Sun>
new commonFeatureNames function <2015-04-14 Tue>
new compareMSnSets function <2015-04-19 Sun>
splitting and unsplitting MSnSets/MSnSetLists <2015-04-19 Sun>
Changes in version 1.17.0:
Changes in version 1.3.1:
Changes in version 3.0.12:
Changes in version 3.0.9:
dataProcess
add options for ‘cutoffCensored=“minFeatureNRun”’.
summaryMethods=“TMP” : output will have ‘more50missing’column.
remove50missing=FALSE option : remove runs which has more than 50% of missing measurement. It will be affected for TMP, with censored option.
MBimpute : impute censored by survival model (AFT) with cutoff censored value
featureSubset option : “all”,”top3”, “highQuality”
change the default. -groupComparisonPlots
heatmap, for logBase=10, fix the bug for setting breaks.
Changes in version 3.0.8:
dataProcess : when censoredInt=“0”, intensity=0 works even though skylineReport=FALSE.
dataProcess, with censored=“0” or “NA” : fix the bug for certain run has completely missing.
cutoffCensored=“minRun” or “minFeature” : cutoff for each Run or each feature is little less (99%) than minimum abundance. -summaryMethod=“TMP”, censored works. censoredInt=NA or 0, and cutoffCensored=0, minFeature, minRun
Changes in version 3.0.3:
dataProcess : new option, skylineReport. for skyline MSstats report, there is ‘Truncated’ column. If Truncated==True, remove them. and keep zero value for summaryMethod=“skyline”.
groupComparison : for skyline option, t.test, val.equal=TRUE, which is no adjustment for degree of freedom, just pooled variance.
Changes in version 1.7.1:
Imports generics from ProtGenerics
Export base classes
Changes in version 2.3.3:
Changes in version 2.3.2:
Changes in version 2.3.1:
Changes in version 0.99.0:
NEW FEATURES
1.1.1: package. Added covariance matrix as output of screen_cvglasso.
Changes in version 1.99.0:
Added option for the output of model parameters.
Added option for multiple imputation.
Added option for the model function.
Changes in version 1.5.1:
Changes in version 1.9.1:
NEW FEATURES
Changes in version 1.1.0:
Changes:
the modelList has been added to provide the user a list of currently implemented methods.
The ‘verbose’ argument in fs.stability, fs.ensembl.stability, & fit.only.model has been changed to a character option indicating the extent of verbose output.
Canberra stability has been added as the previous implementation was not compatible with RPT. See ?canberra.stability for more details.
Many more tests have been implemented to make the package more stable.
Changes in version 1.99.9 (2015-10-08):
Fixed NEWS file.
Removed empty file.
Changes in version 1.99.8 (2015-10-01):
Changes in version 1.99.7 (2015-09-27):
Changes in version 1.99.6 (2015-09-26):
Improved test coverage and removed stringsAsfactors from tests.
Consistent handling of corner cases in Bozic.
Miscell minor documentation improvements.
Changes in version 1.99.5 (2015-06-25):
Changes in version 1.99.4 (2015-06-22):
Plotting true phylogenies.
Tried randutils, from O’Neill. Won’t work with gcc-4.6.
bool issue in Windows/gcc-4.6.
Most all to all.equal in tests.
Changes in version 1.99.3 (2015-06-19):
More examples to vignette
Using Makevars
More functionality to plot.fitnessEffects
Will Windoze work now?
Changes in version 1.99.2 (2015-06-19):
Changes in version 1.99.01 (2015-06-17):
Many MAJOR changes: we are done moving to v.2
New way of specifying restrictions (v.2) that allows arbitrary epistatic interactions and order effects, and very large (larger than 50000 genes) genomes.
When onlyCancer = TRUE, all iterations now in C++.
Many tests added.
Random DAG generation.
Some defaults for v.1 changed.
Changes in version 1.99.1 (2015-06-18):
Try to compile in Windoze with the SSTR again.
Reduce size of RData objects with resaveRdaFiles.
Try to compile in Mac: mt RNG must include random in all files.
Changes in version 1.99.00 (2015-04-23):
Accumulated changes of former 99.1.2 to 99.1.14:
changes in intermediate version 1.99.1.14 (2015-04-23):
Now are things OK (I messed up the repos)
changes in intermediate version 99.1.13 (2015-04-23)
Added a couple of drop = FALSE. Their absence lead to crashes in some strange, borderline cases.
Increased version to make unambiguous version used for anal. CBN.
changes in intermediate version 99.1.12 (2015-04-22)
Removed lots of unused conversion helpers and added more strict checks and tests of those checks.
changes in intermediate version 99.1.11 (2015-04-18)
Tests of conversion helpers now really working.
changes in intermediate version 99.1.10 (2015-04-16)
Added conversion helpers as separate file.
Added tests of conversion helpers.
Added generate-random-trees code (separate file).
More strict now on the poset format and conversions.
changes in intermediate version 99.1.9 (2015-04-09)
added null mutation for when we run out of mutable positions, and since not clear how to use BNB then.
changes in intermediate version 99.1.8 (2015-04-03)
added extraTime.
changes in intermediate version 99.1.7 (2015-04-03)
endTimeEvery removed. Now using minDDrPopSize if needed.
changes in intermediate version 99.1.6 (2015-03-20)
untilcancer and oncoSimulSample working together
changes in intermediate version 99.1.5 (2015-03-20)
Using the untilcancer branch
changes in intermediate version 99.1.4 (2014-12-24)
Added computation of min. of ratio birth/mutation and death/mutation.
changes in intermediate version 99.1.3 (2014-12-23)
Fixed segfault when hitting wall time and sampling only once.
changes in intermediate version 99.1.2 (2014-12-16)
Sampling only once
Changes in version 1.7.1:
Enhancements
Changes in version 1.3.3 (2015-07-14):
GENERAL
NEW FEATURES
IMPROVEMENTS
MODIFICATIONS
BUG FIXES
Changes in version 1.3.2 (2015-06-22):
GENERAL
Update to the latest R version which has been released a few days ago (2015-06-18).
Built with R-3.2.1
NEW FEATURES
IMPROVEMENTS
MODIFICATIONS
BUG FIXES
Changes in version 1.3.1 (2015-06-17):
GENERAL
The optional rlm normalization (for ProtoArrays) used by the functions normalizeArrays(), plotNormMethods() and plotMAPlots() has been completely reimplemented in order to fix some bugs and simplify the usage of these functions (details: see below).
Built with R-3.2.0
NEW FEATURES
IMPROVEMENTS
MODIFICATIONS
BUG FIXES
Changes in version 3.2.0:
Initial version of pandaR implements the PANDA algorithm for gene regulatory network inference from gene expression, sequence motif and protein-protein interaction data.
Includes functions for subsetting bipartite network and discretizing TF-gene edgeweights.
Utilizes igraph library for displaying a subsetted gene regulatory network of interest.
Changes in version 1.9.3:
pathview can accept a vector of multiple pathway ids, and map/render the user data onto all these pathways in one call.
one extra column “all.mapped” was added to pathview output data.frames as to show all the gene/compound IDs mapped to each node.
add geneannot.map as a generic function for gene ID or annotation mapping.
sim.mol.data now generate data with all major gene ID types for all 19 species in bods, not just human.
download.kegg now let the user to choose from xml, png or both file types to download for each input pathway. In the meantime, it uses the KEGG REST API instead of the classical KEGG download links. All potential pathways including the general pathways can be downloaded this way.
solve the redundant import from graph package.
import specific instead of all functions from XML package.
Changes in version 1.9.1:
Changes in version 0.9.1:
Changes in version 0.9.0:
Changes in version 1.5.2 (2015-08-07):
ADDED FUNCTIONS
Changes in version 0.1.0:
Changes in version 2.3.1:
NEW FUNCTIONALITY
COMPATIBILITY ISSUES
Changes in version 1.13.6:
BUG FIXES
droplevels suggestion for sample-data https://github.com/joey711/phyloseq/pull/476
DESeq2 migrated to suggests https://github.com/joey711/phyloseq/pull/533
extend_metagenomeSeq
functionality
https://github.com/joey711/phyloseq/pull/533
bugs related to previous version distance uptick, mostly in tests and vignette
Changes in version 1.13.5:
USER-VISIBLE CHANGES
Help avoid cryptic errors due to name collision of distance
with
external loaded packages by making distance
a formal S4 method in
phyloseq.
Improve documentation of distance
function and the downstream
procedures on which it depends
Migrate the list of supported methods to a documented, exported list
object, called distanceMethodList
.
Improved distance unit tests with detailed checks that dispatch works and gives exactly expected distance matrices for all methods defined in distanceMethodList.
Improved JSD doc, performance, code, deprecated unnecessary
parallel
argument in JSD
Changes in version 1.13.4:
BUG FIXES
psmelt
bug if user has also loaded the original “reshape” package,
due to name collision on the function called melt
. psmelt
now
explicitly calls reshape2::melt
to avoid confusion.
https://github.com/joey711/phyloseq/pull/489
Fix following note… There are ::: calls to the package’s namespace in its code. A package almost never needs to use ::: for its own objects: ‘JSD.pair’
Changes in version 1.10:
Changes in version 1.1.3:
Changes in version 1.1.2:
Changes in version 1.1.1:
Changes in version 1.1.0:
1.99.3: NB function now exported
1.99.3: note that version 1.99.3 on GitHub was version 1.1.0 on Bioconductor.
1.99.2: bug fix in fragment generation (last 2 bases of transcript were never sequenced)
Changes in version 1.9.7:
New SpatProtVis visualisation class <2015-08-13 Thu>
add link to explanation of supportive/uncertain reliability scores in tl vignette <2015-09-02 Wed>
Changes in version 1.9.6:
Update REAMDE with TL ref
Update refs in lopims documentation <2015-07-30 Thu>
Changes in version 1.9.5:
Changes in version 1.9.4:
Add reference to TL paper and link to lpSVM code <2015-07-06 Mon>
highlightOnPlot throws a warning and invisibly returns NULL instead of an error when no features are in the object <2015-07-08 Wed>
highlightOnPlot has a new labels argument <2015-07-10 Fri>
Changes in version 1.9.3:
Clarify error when no annotation params are provided <2015-05-11 Mon>
support for matrix-encoded markers <2015-05-19 Tue>
New default in addLegend: bty = “n” <2015-05-20 Wed>
getMarkers now supports matrix markers <2015-05-20 Wed>
getMarkerClasses now supports matrix markers <2015-05-20 Wed>
markerMSnSet and unknownMSnSet now support matrix markers <2015-05-20 Wed>
sampleMSnSet now supports matrix markers <2015-05-23 Sat>
updated yeast markers and added uniprot ids <2015-05-27 Wed>
plot2D support a pre-calculated dim-reduced data matrix as method parameter to avoid recalculation <2015-05-27 Wed>
Changes in version 1.9.2:
Changes in version 1.9.1:
new plot2Ds function to overlay two data sets on the same PCA plot [2015-04-17 Fri]
regenerate biomart data used by setAnnotationParams [2015-04-24 Fri]
new setStockcolGui function to set the default colours manually via a simple interface [2015-04-29 Wed]
new move2Ds function to produce an transition movie between two MSnSets [2015-04-29 Wed]
functions to convert GO ids to/from terms. See ?goTermToId for details <2015-05-08 Fri>
Changes in version 1.9.0:
Changes in version 1.3.2:
Changes in version 1.3.1:
new plotMat2D function <2015-05-20 Wed>
Fix query search in pRolocVis, contributed by pierremj <2015-05-27 Wed>
pRolocVis has new method arg <2015-05-29 Fri>
Changes in version 1.3.0:
Changes in version 0.99.0:
Changes in version 0.99.3:
Changes in version 0.99.2:
Changes in version 0.99.1:
Changes in version 0.99.0:
Changes in version 1.1.1:
Changes in version 1.1.0:
Changes in version 4.5.1:
Convert log(P-values) back to P-values for human using a chi-sq distribution Version 4:
New algorithm for human backgrounds
New function: toPWM() that takes both PFMs and PPMs
Changes in version 1.1.10:
include threshold parameter into ‘readTFdata’ function
change STRINGdb to version 10
Changes in version 1.1.1:
rename consensus-based dynamic analysis
adjust vignette workflow figure
Changes in version 1.6.0:
RELEASE
IMPROVEMENTS
BUG FIXES
Changes in version 1.4.2 (2015-08-20):
BUG FIXES
Changes in version 1.4.1 (2015-06-30):
IMPROVEMENTS
Changes in version 2.40:
BUG FIXES
Changes in version 1.10.0:
NEW FEATURES
qExportWig gained createBigWig argument and can now create bigWig files directly
qQCReport now also produces base quality plots for bam-file projects by sampling reads from the bam files
qCount, qProfile and qExportWig have gained a includeSecondary argument to include/exclude secondary alignments while counting
Changes in version 2.1.1:
handles NA values
upgraded plotting functions
1.2.0: Updates: * Removed dependency from DAVIDQuery package as it will deprected. * Fixed some bugs in DAVIDQuery functions and integrated them into R3CPET. * Updated the Readme.Rd file. * Updated the HPRD.RData and Biogrid.RData to the new igraph class. * some small changes.
Changes in version 1.9.8:
BUG FIXES
Changes in version 1.13.5:
Changes in version 1.13.4:
Changes in version 1.13.3:
add citation of ChIPseeker <2015-07-09, Thu>
add ‘Pathway analysis of NGS data’ section in vignette <2015-06-29, Mon>
convert vignette from Rnw to Rmd <2015-06-29, Mon>
Changes in version 1.13.2:
Changes in version 1.13.1:
Changes in version 1.1.8:
NEW FEATURES
Added new functionality to permTest to use multiple evaluation functions with a single randomization procedure. This gives a significant speedup when comparing a single region set with multiple other features
Created a new function createFunctionsList() that given a function and a list of values, creates a list of curried functions (e.g with one parameter preassigned to each of the given values)
PERFORMANCE IMPROVEMENTS
BUG FIXES
Changes in version 1.3.8:
SIGNIFICANT USER-VISIBLE CHANGES
Changes in version 1.3.7:
NEW FEATURES
Changes in version 1.3.6:
NEW FEATURES
Changes in version 1.3.5:
SIGNIFICANT USER-VISIBLE CHANGES
Merged pull request https://github.com/leekgroup/regionReport/pull/7
Added “template” argument to renderReport and derfinderReport to customize the knitr template used
Wrapped code that works in a temporary directory in with_wd function, which evaluates in the directory but returns to the original directory in the case of a user interrupt or error (with on.exit)
Changes in version 1.3.4:
NEW FEATURES
Changes in version 1.3.3:
NEW FEATURES
Now uses derfinderPlot::vennRegions() to show venn diagram of genomic states. Requires derfinderPlot version 1.3.2 or greater.
derfinderReport() now has a ‘significantVar’ argument that allows users to choose between determining significant regions by P-values, FDR adjusted P-values, or FWER adjusted P-values (if FWER adjusted P-values are absent, then FDR adjusted P-values are used instead, with a warning).
Changes in version 1.3.2:
SIGNIFICANT USER-VISIBLE CHANGES
Changes in version 1.3.1:
BUG FIXES
Changes in version 1.1.6:
Changes in version 1.1.5:
Changes in version 1.1.4:
Changes in version 1.1.3:
error message is extract from GREAT now.
default value of bgChoice
depeneds on gr
Changes in version 1.1.2:
Changes in version 1.1.1:
GreatJob
object are initialized inside
submitGreatJob
Changes in version 2.14.0:
NEW FEATURES
improved handling of error messages: HDF5 error messages are simplified and forwarded to R.
When reading integer valued data, especially 64-integers and unsigned 32-bit integers, overflow values are now replaced by NA’s and a warning is thrown in this case.
When coercing HDF5-integers to R-double, a warning is displayed when integer precision is lost.
New low level general library function H5Dget_storage_size implemented.
BUG FIXES
Memory allocation on heap instead of stack for reading large datasets (Thanks to a patch from Jimmy Jia).
Some bugs have been fixed for reading large 64-bit integers and unsigned 32-bit integers.
A bug was fixed for reading HDF5 files containing soft links.
Changes in version 0.99.7:
Changes in version 0.99.6:
Changes in version 0.99.5:
Added @return for roxygen comment in printPCA.R
Updated packages IRanges and BSgenome.Mmusculus.UCSC.mm10 before check.
Changes in version 0.99.4:
Non-null coverage values define the percentage of best expressed CDSs.
New function: readsToReadStart - it builds the GRanges object of the read start genomic positions
Acronym BAM used instead of bam
Correction of read start coverage (readStartCov) for the reverse strand
Title in Description in Title Case
Typos corrections in vignette.
Style inconsistencies solved: = replaced by <- outside named arguments No space around “=” when using named arguments to functions. This: somefunc(a=1, b=2) spaces around binary operators a space after all commas use of camelCase for both variable and function names ORFrelativePos -> orfRelativePos
Replaced 1:length(x) by seq_len(length(x))
Replaced 1:nrow(x) by seq_len(NROW(x))
Replaced trailing white spaces with this command: ‘find . -type f -path ‘./*R’ -exec perl -i -pe ‘s/ +$//’ {} \;’
countsPlot, histMatchLength, plotSummarizedCov: no longer print directly the graphs. Instead they return a list of graphs.
Replaced ‘class()’ tests by ‘inherits’ or ‘is’.
The codonPCA function no longer prints the PCA graphs sequantially. The 5 PCA graphs are returned, together with the PCA scores.
New function printPCA prints the 5 PCA plots produced by codonPCA.
A BAM file is now available in the inst/extdata ctrl_sample.bam. It is used in the testriboSeqFromBAM testthat
Changes in version 0.99.3:
Changes in version 0.99.2:
Modified the vignette: small corrections of the explanatory text.
Added testthat tests for the following functions: test-aroundPromoter.R, test-riboSeq_fromBAM.R, test-readStartCov.R
Introduced the 4 spaces tabulation
Reduced the percentage of lines > 80 characters to 2%
Added imports in the Namespace for the proposed packages or methods
New R version: 3.2.2 and bioconductor packages update
Changes in version 0.99.1:
Added biocViews: Sequencing, Coverage, Alignment, QualityControl, Software, PrincipalComponent
Added testthat tests for the following functions: test-aroundPromoter.R, test-riboSeq_fromBAM.R, test-readStartCov.R
Introduced the 4 spaces tabulation
Reduced the percentage of lines > 80 characters to 2%
Added imports in the Namespace for the proposed packages or methods v.0.99.0 Initial release.
Changes in version 1.1.2:
BUG FIXES
MISC
Changes in version 1.1.9:
Filtering report fix when no normalization is conducted
Bugfixes for combine(RnBSet, RnBSet) and BigFf matrices
Changes in version 1.1.8:
Corrected coverage statistics in sample summary table: Sites with NA methylation values are no longer considered in the coverage statistics (makes a difference if some coverage threshold is applied)
Improved method for gender prediction. Predicted genders are also included in the exported annotation table
Changes in version 1.1.7:
Improvements to mergeSamples function for RnBiseqSets
Some more memory clean-up
Changes in version 1.1.6:
Differential methylation based on region level only is now supported
Minor updates to the differential methylation report generation
Performance improvements and minor bugfixes for using disk.dump.bigff
Performance improvements (more memory clean-up)
Changes in version 1.1.5:
Changes in version 1.1.4:
Changes in version 1.1.3:
Some fixes in data loading
Fixes in parallel environment setup
Changes in version 1.1.2:
New annotation package format
Support for filtering out cross-reactive probes in Infinium 450k dataset
Improved logging on a Mac
Changes in version 1.11.6:
Changes in version 1.11.5:
add test script <2015-06-30 Tue>
more unit tests <2015-06-30 Tue>
Changes in version 1.11.4:
Changes in version 1.11.3:
Changes in version 1.11.2:
Changes in version 1.11.1:
Changes in version 1.11.0:
Changes in version 1.1.11:
NEW FEATURES
Changes in version 1.1.10:
NEW FEATURES
Changes in version 1.1.9:
NEW FEATURES
opls: default number of permutations set to 10 (instead of 100) as a compromise to enable both quick computation and a first hint at model significance
opls: maximum number of components in automated mode (predI = NA or orthoI = NA) set to 10 (instead of 15)
plot.opls: bug corrected in case of single component model without permutation testing
Changes in version 1.1.8:
SIGNIFICANT USER-VISIBLE CHANGES
Changes in version 1.1.7:
NEW FEATURES
Changes in version 1.1.6:
NEW FEATURES
Changes in version 1.1.5:
NEW FEATURES
Changes in version 1.1.4:
NEW FEATURES
Changes in version 1.1.3:
NEW FEATURES
Changes in version 1.1.2:
BUG FIXES
Changes in version 1.1.1:
SIGNIFICANT USER-VISIBLE CHANGES
The packaging was modified (but not the algorithms) to be consistent with other machine learning packages: ‘opls’ is now a class and the ‘print’, ‘plot’, ‘predict’, ‘summary’, ‘fitted’, ‘coefficients’ and ‘residuals’ methods are available (see the vignette)
renamed method: roplsF -> opls
renamed arguments testVi -> now ‘subset’ which indicates the indices of the training (instead of the testing) observations
values: tMN -> scoreMN pMN -> loadingMN wMN -> weightMN bMN -> coefficients rMN -> rotationMN varVn -> pcaVarVn tOrthoMN -> orthoScoreMN pOrthoMN -> orthoLoadingMN wOrthoMN -> orthoWeightMN
new (S3) methods for objects of class ‘opls’ print summary plot predict fitted coefficients residuals
Changes in version 1.5.1:
unit tests <2015-06-30 Tue>
export and document pxnodes <2015-06-30 Tue>
Changes in version 1.5.0:
Changes in version 1.4:
NEW FEATURES
Custom template support added
Read frequency result and plot (rqcReadFrequencyPlot) added
Per file top represented reads added
Top representated reads added
Per file heatmap plot (rqcFileHeatmap) added
checkpoint function added (experimental)
USER VISIBLE CHANGES
BPPARAM argument replaced by workers argument
File information table added to default report template
Function rqcReadWidthPlot, y-axis changed to proportion (%)
Almost all plots use colorblid scheme
Changes in version 1.21:
SIGNIFICANT USER-VISIBLE CHANGES
pileup adds query_bins arg to give strand-sensitive cycle bin behavior; cycle_bins renamed left_bins; negative values allowed (including -Inf) to specify bins based on distance from end-of-read.
mapqFilter allows specification of a mapping quality filter threshold
PileupParam() now correctly follows samtools with min_base_quality=13, min_map_quality=0 (previously, values were assigned as 0 and 13, respectively)
Support parsing ‘B’ tags in bam file headers.
BUG FIXES
segfault on range iteration introduced 1.19.35, fixed in 1.21.1
BamViews parallel evaluation with BatchJobs back-end requires named arguments
Changes in version 1.20.0:
NEW FEATURES
Fast sorting of input bam files in featureCounts.
Fractional counting of multi-mapping reads in featureCounts.
Detection of complex indels in Subread and Subjunc aligners.
Including more candidate locations in read re-alignment step to improve mapping performance.
New formula for mapping paired-end reads that takes into account paired-end distance, number of subread votes and number of mismatched bases.
Changes in version 1.30:
NEW FEATURES
SIGNIFICANT USER-VISIBLE CHANGES
Changes in version 1.3:
New argument ‘isLog’ to RUV* methods: if counts provided on the log scale, normalizedCounts will also be on the log scale.
Fixed a bug: epsilon is now removed from the corrected counts.
New function makeGroups to make scIdx matrix for RUVs.
Changes in version 1.0.0 (2015-05-01):
Initial version
All the APIs of the SBG platform are supported
First vignette added
Changes in version 1.1.8:
Used Sys.info() rather than sessionInfor() to extract platform information
Avoided the use of “\” in R
Added a parameter “Ontology” to the function FisherTest_GO_BP_MF_CC()
Changes in version 1.1.6:
Corrected the python path for Linux users
Activated the demo code in R help files and vignettes
Changed the maintainer
Changes in version 1.1.4:
Update the Fisher’s exact test used mouse gene background.
Replace the mm10 GENCODE database V3 with V4 in the seq2pathway.data
Changes in version 1.1.2:
Changes in version 1.0.2:
Changes in version 1.10.0:
Changes in version 1.7.9:
Changes in version 1.7.7:
Changes in version 1.7.6:
Changes in version 1.7.5:
Changes in version 1.7.4:
Changes in version 1.7.3:
Add methods for duplicateDiscordance with two datasets
Add alternateAlleleDetection
Changes in version 1.4.0:
Added importTranscripts() for importing annotation from GFF format
Added plotCoverage() for visualization of per-base read coverage and junction read counts
Added predictVariantEffects() for predicting the effect of splice variants on annotated protein-coding transcripts
findSGVariants() is now able to deal with more complex gene models
SGVariants columns closed5p and closed3p now refer to individual splice variants rather than the splice event they belong to
Bug fixes and other improvements
Changes in version 1.27:
SIGNIFICANT USER-VISIBLE CHANGES
fastqFilter allows several input ‘files’ to be written to a single ‘destinations’.
readAligned() for BAM files is defunct. QA and associated methods removed.
srapply removed
Changes in version 1.1.01:
paramether tsne.theta has been added to function sc_DimensionalityReductionObj
function sc_InSilicoCellsReplicatesObj has been expanded to incorporate a forth model of noise generation following the negative binomial (NB) distribution. For each gene, dispersion parameters for the NB can be estimated in three alternative ways allowing different types of estimates (e.g. technical noise provided by the user). See documentation of sc_InSilicoCellsReplicatesObj() function.
Changes in version 0.99.0 (2015-08-07):
Changes in version 1.4.0:
Changes in version 1.3.7:
USER UNVISIBLE CHANGES
Changes in version 1.3.5:
USER UNVISIBLE CHANGES
Changes in version 1.3.4:
USER VISIBLE CHANGES
USER UNVISIBLE CHANGES
read.bibliospec - replaced old code (for loop) by using mcmapply
added time meassurements to read.bibliospec
Changes in version 1.3.3:
USER VISIBLE CHANGES
USER UNVISIBLE CHANGES
.mascot2psmSet buxfix
renamed column name in spectronaut outpu from irt to irt_or_rt
Changes in version 1.3.2:
USER VISIBLE CHANGES
added ssrc (Sequence Specific Retention Calculator) function
added a CITATION file
Changes in version 1.3.1:
USER VISIBLE CHANGES
USER UNVISIBLE CHANGES
Changes in version 1.0.0:
Changes in version 1.7.3:
NEW FEATURES
Changes in version 1.7.2:
NEW FEATURES
Changes in version 1.11.2:
Changes in version 1.11.1:
Changes in version 1.3:
OVERVIEW
systemPipeR is an R/Bioconductor package for building and running automated analysis workflows for a wide range of next generation sequence (NGS) applications. Important features include a uniform workflow interface across different NGS applications, automated report generation, and support for running both R and command-line software, such as NGS aligners or peak/variant callers, on local computers or compute clusters. Efficient handling of complex sample sets and experimental designs is facilitated by a consistently implemented sample annotation infrastructure.
The most important enhancements in the upcoming release of the package are outlined below.
NGS WORKFLOWS
Added new end-to-end workflows for 3 additional NGS application areas: - Ribo-Seq and polyRibo-Seq - ChIP-Seq - VAR-Seq The previous version of systemPipeR included only a complete workflow for RNA-Seq.
Added the data package ‘systemPipeRdata’ to generate systemPipeR workflow environments with a single command (genWorkenvir) containing all parameter files and sample data required to quickly test and run workflows. This change will also allow evaluation of much more code examples in the vignettes during the package build/test process than this was possible in the past.
About 20 new functions have been added to the package. Some examples are: - Read pre-processor function with support for SE and PE reads - Parallelization option of detailed FASTQ quality reports - Read distribution plots across all features available in a genome annotation (see ?featuretypeCounts) - Visualization of coverage trends along transcripts summarized for any number of transcripts (see ?featureCoverage) - Functionalities to predict uORFs/sORFs and to use them for expression profiling - Differential expression/binding analysis includes now DESeq2 as well as edgeR
Added param templates for additional command-line software including, but not limited to: BWA-MEM, GATK, BCFtools, MACS2
Adoption of R Markdown for main vignette. Future plans are to provide for all workflows the report templates in both formats: Latex/PDF and R_Markdown/HTML.
WORFLOW FRAMEWORK
Simplified design of complex analysis workflows. Workflows can now include any number or combination of R and/or command-line steps
Improvements to workflow automation and parallelization on single machines and computer clusters. This also includes now many additional parallelization examples in the workflow vignettes.
Changes in version 1.26.0:
SIGNIFICANT USER-VISIBLE CHANGES
BUG FIXES
Fix potential potencial pearson correlation errors that occur when the standard is deviation zero. If that is the case, replace the resulting NA/NaN by zero.
Fix R check warnings.
Changes in version 0.99.9:
CODE
Modifications in pileupCounts in order to consider stranded counts
Changes in plot methods. arrangeGrob from gridExtra was changed by plot_grid form cowplot package.
Update the package vignette.
Changes in version 0.99.8:
CODE
Modifications in pileupCounts and buildFeaturePanel in order to process overlapped features.
Wrap plotting examples.
Changes in version 0.99.7:
CODE
Modifications in pileupCounts and buildFeaturePanel in order to process overlapped features.
Modifications in bedFile building in order to remove duplicated features based on duplicated start, end and chromosome definitions.
Changes in version 0.99.6:
CODE
Definition of pileupCounts as a function instead a TargetExperiment S4 method.
Adaptation and optimization of pileupCounts and bplapply usage in the buildFeaturePanel method.
Changes in version 0.99.4:
DESCRIPTION file
Changes in version 0.99.3:
CODE
Changes in version 0.99.2:
CODE
Changes in version 0.99.1:
DOCUMENTATION
Changes in version 0.99.0:
DOCUMENTATION
NEWS
file was added.Changes in version 1.9.3:
changed default value. Set ‘test.method = “DESeq2” as default value when analyze multi-group without replicate data.
add ‘makeFCMatrix’ function for generating the foldchange matrix that is used in ‘simulateReadCounts’ funtion.
add function to simulate DEGs using fondchange matrix into ‘simulateReadCounts’ function.
Changes in version 3.9.1:
new parameter ‘plotchroms’ in function ‘chrom.barplot’ that allows to specify the chromosomes (and their desired order) that shall be included in the plot
bug fix regarding use of ‘Offset’ bases in ‘TEQCreport’
Changes in version 1.7.2:
NEW FEATURES
New class TFFMFirst and TFFMDetail for next generation TFBSs.
Novel TFFM sequence logo.
BUG FIXES
Changes in version 1.9.9:
Major update to the CCR-part: It is now possible to fit and plot multiple experiments simultaneously.
It is now possible to perform user-specified comparisons of different experiments. They are specified in the ‘comparison’ column of the config table.
TR-part: Hypothesis testing is now separated from result table creation. Therefore, a new function was introduced (tpptrAnalyzeMeltCurves) -> see vignette.
CCR-part: Curve fitting and plotting are now conducted by separate functions -> see vignette.
Bug fixes
Introduced color coding of the columns belonging to different experiments in the excel output. This requires openxlsx version >= 2.4.0.
The CCR workflow now only returns normalized measurements if normalization was actually performed. Unmodified measurements are always returned and indicated by the suffix ‘unmodified’.
Data import from tab-delimited files now ignores quotes so that protein annotation fields can contain single ‘ or “ characters.
Now enabling arbitrary numbers of plot colors for melting curves or dose response curves.
Changes in version 1.2.5:
CCR-import: Argument nonZeroCols can be NULL if no additional filtering is needed.
CCR output: To make filtering easier, the ‘passed_filter’ column now shows FALSE even if proteins could not be used for fitting (instead of NAs).
CCR output: To make filtering easier, the ‘passed_filter’ column now shows FALSE even if proteins could not be used for fitting (instead of NAs).
CCR output: column with normalization results was renamed from ‘normalized’ to ‘median_normalized’ to distinguish from the newly introduced normalization to value at lowest concentration.
Excel export: Columns are only color-coded by experiment, when the number of experiments is > 1.
Excel export: Columns are only color-coded by experiment when the number of experiments is > 1.
Excel export: Relative paths to the plots work now for TR- and CCR part
Bug fix for data import: Unique identifiers now treated correctly again.
Bug fix for Excel output: Boolean column entries are only transformed to “yes”/”no” for non-missing values.
Bugfix in TR-QC plots: do not attempt to create Tm difference histograms if only one experiment is provided.
Bugfix in TR normalization: fixedReference argument works again
Changes in version 1.1.4:
Changes in version 1.1.3:
Changes in version 1.1.2:
Changes in version 1.1.1:
Changes in version 1.1.0:
Changes in version 1.5.6:
update documentation.
add new feature for optimizing the styles with theme.
Changes in version 1.5.5:
NEW FEATURES
BUG FIXES
Changes in version 1.5.4:
NEW FEATURES
BUG FIXES
Changes in version 1.5.3:
NEW FEATURES
BUG FIXES
Changes in version 1.5.2:
NEW FEATURES
Add GRanges operators: +, -, *, /
export parseWIG function.
BUG FIXES
Changes in version 1.15.1:
Changes in version 2.0.0-16:
Changes in version 0.99.8:
Changes in version 0.99.7:
added new class varPartResults to store results of fitExtractVarPartModel() and fitExtractVarPartModel() - the user will not notice any change, only the backend is different
Allow computation of adjusted ICC in addition to ICC.
add warning when categorical variables are modeled as fixed effects
fix computation of variance fractions for varying coefficient models
add getVarianceComponents() to return variances from lmer() or lm() model fit
showWarnings=FALSE suppresses warning messages
add fxn argument to fitVarPartModel to evaluate any function on the model fit
Changes in version 0.99.6:
Changes in version 0.99.5:
Changes in version 0.99.4:
add documentation for example datasets
convert calcVarPart() to S4 from S3 function call
fix typos in vignette
Changes in version 0.99.3:
Changes in version 0.99.2:
rename sort.varParFrac to sortCols
support ExpressionSet
change options for plotStratifyBy() # Before Bioconductor submission
Changes in version 0.99.0:
Changes in version 1.16.0:
NEW FEATURES
support REF and ALT values “.”, “+” and “-“ in predictCoding()
return non-translated characters in VARCODON in predictCoding() output
add ‘verbose’ option to readVcf() and friends
writeVcf() writes ‘fileformat’ header line always
readVcf() converts REF and ALT values “*” and “I” to ‘’ and ‘.’
MODIFICATIONS
VRanges uses ‘*’ strand by default
coerce ‘alt’ to DNStringSet for predictCoding,VRanges-method
add detail to documentation for ‘ignore.strand’ in predictCoding()
be robust to single requrested INFO column not present in vcf file
replace old SummarizedExperiment class from GenomicRanges with the new new RangedSummarizedExperiment from SummarizedExperiment package
return strand of ‘subject’ for intronic variants in locateVariants()
BUG FIXES
writeVcf() does not duplicate header lines when chunking
remove extra tab after INFO when no FORMAT data are present
filteVcf() supports ‘param’ with ranges
Changes in version 1.6:
USER VISIBLE CHANGES
Update on the scores() method for PhastConsDb objects that enables a 10-fold faster retrieval of mean phastCons scores over genomic intervals.
Added two new annotated regions coded as fiveSpliceSite and threeSpliceSite and the scoring of their binding affyinity, if scoring matrices are provided.
BUG FIXES
Fix on the scores() method for PhastConsDb objects, that was affecting multiple-nucleotide ranges from an input GRanges object with unordered sequence names.
Fix on snpid2maf() method when decoding MafDb variants with AF values whose significant digits start with 95.
Changes in version 1.45.7:
USER VISIBLE CHANGES
Changes in version 1.45.6:
NEW FEATURE
BUG FIXES
Changes in version 1.45.5:
USER VISIBLE CHANGES
The sampclass method for xcmsSet will now return the content of the column “class” from the data.frame in the phenoData slot, or if not present, the interaction of all factors (columns) of that data.frame.
The sampclass<- method replaces the content of the “class” column in the phenoData data.frame. If a data.frame is submitted, the interaction of its columns is calculated and stored into the “class” column.
BUG FIXES
Changes in version 1.45.4:
BUG FIXES
Changes in version 1.45.3:
NEW FEATURE
xcmsSet now allows phenoData to be an AnnotatedDataFrame.
new slots for xcmsRaw: - mslevel: store the mslevel parameter submitted to xcmsRaw. - scanrange: store the scanrange parameter submitted to xcmsRaw.
new slots for xcmsSet: - mslevel: stores the mslevel argument from the xcmsSet method. - scanrange: to keep track of the scanrange argument of the xcmsSet method.
USER VISIBLE CHANGES
show method for xcmsSet updated to display also informations about the mslevel and scanrange.
Elaborated some documentation entries.
rtrange and mzrange for xcmsRaw method plotEIC use by default the full RT and m/z range.
Added arguments “lty” and “add” to plotEIC method for xcmsRaw.
getEIC without specifying mzrange returns the ion chromatogram for the full m/z range (i.e. the base peak chromatogram).
BUG FIXES
Checking if phenoData is a data.frame or AnnotatedDataFrame and throw an error otherwise.
xcmsSet getEIC method for water Lock mass corrected files for a subset of files did not evaluate whether the specified files were corrected.
Changes in version 1.45.2:
BUG FIXES
Changes in version 1.45.1:
NEW FEATURE
plotrt now allows col to be a vector of color definition, same as the plots for retcor methods.
Added $ method to access phenoData columns in a eSet/ExpressionSet like manner.
Allow to use the “parallel” package for parallel processing of the functions xcmsSet and fillPeaks.chrom.
Thanks to J. Rainer!
Changes in version 3.2:
VERSION xps-1.29.1
Changes in version 1.29.1:
No packages were removed in this release.