October 15, 2013
Bioconductors:
We are pleased to announce Bioconductor 2.13, consisting of 749 software packages, 179 experiment data packages, and more than 690 up-to-date annotation packages.
There are 84 new software packages, and many updates and improvements to existing packages; Bioconductor 2.13 is compatible with R 3.0.2, and is supported on Linux, 32- and 64-bit Windows, and Mac OS X. This release includes an updated Bioconductor Amazon Machine Image.
Visit http://bioconductor.org for details and downloads.
To update to or install Bioconductor 2.13:
Install R 3.0.2. Bioconductor 2.13 has been designed expressly for this version of R.
Follow the instructions at http://bioconductor.org/install/
There are 84 new packages in this release of Bioconductor.
AllelicImbalance: Provides a framework for allelic specific expression investigation using RNA-seq data
ampliQueso: The package provides tools and reports for the analysis of amplicon sequencing panels, such as AmpliSeq
ArrayTV: Wave correction for genotyping and copy number arrays
ASSET: An R package for subset-based analysis of heterogeneous traits and subtypes
BADER: For RNA sequencing count data, BADER fits a Bayesian hierarchical model. The algorithm returns the posterior probability of differential expression for each gene between two groups A and B. The joint posterior distribution of the variables in the model can be returned in the form of posterior samples, which can be used for further down-stream analyses such as gene set enrichment.
BAGS: R package providing functions to perform geneset significance analysis over simple cross-sectional data between 2 and 5 phenotypes of interest.
BiGGR: This package provides an interface to simulate metabolic reconstruction from the BiGG database(http://bigg.ucsd.edu/) and other metabolic reconstruction databases. The package aids in performing flux balance analysis (FBA). Metabolic networks and estimated fluxes can be visualized using hypergraphs.
bioassayR: bioassayR provides tools for statistical analysis of small molecule bioactivity data
BiocParallel: This package provides modified versions and novel implementation of functions for parallel evaluation, tailored to use with Bioconductor objects.
BiocStyle: Provides standard formatting styles for Bioconductor documents. The vignette illustrates use and functionality.
BiRewire: Fast functions for bipartite network rewiring through N consecutive switching steps (See References) and for the computation of the minimal number of switching steps to be performed in order to maximise the dissimilarity with respect to the original network. Includes function for the analysis of the introduced randomness across the switching and several other routines to analyse the resulting networks and their natural projections. Extension to undirected networks (not bipartite) is also provided.
CexoR: Strand specific peak-pair calling in ChIP-exo replicates. The cumulative Skellam distribution function (package ‘skellam’) is used to detect significant normalized count differences of opposed sign at each DNA strand (peak-pairs). Irreproducible discovery rate for overlapping peak-pairs across biological replicates is estimated using the package ‘idr’.
ChAMP: The package includes quality control metrics, a selection of normalization methods and novel methods to identify differentially methylated regions and to highlight copy number aberrations.
ChemmineOB: ChemmineOB provides an R interface to a subset of cheminformatics functionalities implemented by the OpelBabel C++ project. OpenBabel is an open source cheminformatics toolbox that includes utilities for structure format interconversions, descriptor calculations, compound similarity searching and mor. ChemineOB aims to make a subset of these utilities available from within R. For non-developers, ChemineOB is primarily intended to be used from ChemmineR as an add-on package rather than used directly.
chipenrich: ChIP-Enrich performs gene set enrichment testing using peaks called from a ChIP-seq experiment. The method empirically corrects for confounding factors such as the length of genes, and the mappability of the sequence surrounding genes.
cleanUpdTSeq: This package uses the Naive Bayes classifier (from e1071) to assign probability values to putative polyadenylation sites (pA sites) based on training data from zebrafish. This will allow the user to separate true, biologically relevant pA sites from false, oligodT primed pA sites.
cleaver: In-silico cleavage of polypeptide sequences. The cleavage rules are taken from: http://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html
clonotypeR: High throughput analysis of T cell antigen receptor sequences The genes encoding T cell receptors are created by somatic recombination, generating an immense combination of V, (D) and J segments. Additional processes during the recombination create extra sequence diversity between the V an J segments. Collectively, this hyper-variable region is called the CDR3 loop.
The purpose of this package is to process and quantitatively analyse millions of V-CDR3-J combination, called clonotypes, from multiple sequence libraries.
CNVrd2: CNVrd2 uses next-generation sequencing data to measure human gene copy number for multiple samples, identify SNPs tagging copy number variants and detect copy number polymorphic genomic regions.
cobindR: Finding and analysing co-occuring motifs of transcription factor binding sites in groups of genes
CSSP: Power computation for ChIP-Seq data based on Bayesian estimation for local poisson counting process.
customProDB: Generate customized protein sequence database from RNA-Seq data for proteomics search
dagLogo: Visualize significant conserved amino acid sequence pattern in groups based on probability theory
DNaseR: Strand-specific digital genomic footprinting in DNase-seq data. The cumulative Skellam distribution function (package ‘skellam’) is used to detect significant normalized count differences of opposed sign at each DNA strand. This is done in order to determine the protein-binding footprint flanks. Preprocessing of the mapped reads is recommended before running DNaseR (e.g., quality checking and removal of sequence-specific bias).
EBSeq: Differential Expression analysis at both gene and isoform level using RNA-seq data
epivizr: This package provides Websocket communication to the epiviz web app (http://epiviz.cbcb.umd.edu) for interactive visualization of genomic data. Objects in R/bioc interactive sessions can be displayed in genome browser tracks or plots to be explored by navigation through genomic regions. Fundamental Bioconductor data structures are supported (e.g., GenomicRanges and SummarizedExperiment objects), while providing an easy mechanism to support other data structures. Visualizations (using d3.js) can be easily added to the web app as well.
exomePeak: The package is developed for the analysis of affinity-based epitranscriptome shortgun sequencing data from MeRIP-seq (maA-seq). It was built on the basis of the exomePeak MATLAB package (Meng, Jia, et al. “Exome-based analysis for RNA epigenome sequencing data.” Bioinformatics 29.12 (2013): 1565-1567.) with new functions for differential analysis of two experimental conditions to unveil the dynamics in post-transcriptional regulation of the RNA methylome. The exomePeak R-package accepts and statistically supports multiple biological replicates, internally removes PCR artifacts and multi-mapping reads, outputs exome-based binding sites (RNA methylation sites) and detects differential post-transcriptional RNA modification sites between two experimental conditions in term of percentage rather the absolute amount. The package is still under active development, and we welcome all biology and computation scientist for all kinds of collaborations and communications. Please feel free to contact Dr. Jia Meng jia.meng@hotmail.com if you have any questions.
FGNet: Build and visualize functional gene networks from clustering of enrichment analyses in multiple annotation spaces. The package includes an interface to perform the analysis through David and GeneTerm Linker.
flipflop: Flipflop discovers which isoforms of a gene are expressed in a given sample together with their abundances, based on RNA-Seq read data.
flowBeads: This package extends flowCore to provide functionality specific to bead data. One of the goals of this package is to automate analysis of bead data for the purpose of normalisation.
flowFit: This package estimate the proliferation of a cell population in cell-tracking dye studies. The package uses an R implementation of the Levenberg-Marquardt algorithm (minpack.lm) to fit a set of peaks (corresponding to different generations of cells) over the proliferation-tracking dye distribution in a FACS experiment.
flowMap: This package provides an algorithm to compare and match cell populations across multiple flow cytometry samples. The method is based on the Friedman-Rafsky test, a nonparametric multivariate statistical test, where two cell distributions match if they occupy a similar feature space. The algorithm allows the users to specify a reference sample for comparison or to construct a reference sample from the available data. The output of the algorithm is a set of text files where the cell population labels are replaced by a metaset of population labels, generated from the matching process.
GOSim: This package implements several functions useful for computing similarities between GO terms and gene products based on their GO annotation. Moreover it allows for computing a GO enrichment analysis
h5vc: This package contains functions to interact with tally data from NGS experiments that is stored in HDF5 files. For detail see the webpage at http://www.ebi.ac.uk/~pyl/h5vc.
intansv: This package provides efficient tools to read and integrate structural variations predicted by popular softwares. Annotation and visulation of structural variations are also implemented in the package.
interactiveDisplay: The interactiveDisplay package contains the methods needed to generate interactive Shiny based display methods for Bioconductor objects.
maPredictDSC: This package implements the classification pipeline of the best overall team (Team221) in the IMPROVER Diagnostic Signature Challenge. Additional functionality is added to compare 27 combinations of data preprocessing, feature selection and classifier types.
metaSeq: The probabilities by one-sided NOISeq are combined by Fisher’s method or Stouffer’s method
methylMnM: To give the exactly p-value and q-value of MeDIP-seq and MRE-seq data for different samples comparation.
mitoODE: The package contains the methods to fit a cell-cycle model on cell count data and the code to reproduce the results shown in the paper “Dynamical modelling of phenotypes in a genome-wide RNAi live-cell imaging assay” (submitted).
msmsEDA: Exploratory data analysis to assess the quality of a set of LC-MS/MS experiments, and visualize de influence of the involved factors.
msmsTests: Statistical tests for label-free LC-MS/MS data by spectral counts, to discover differentially expressed proteins between two biological conditions. Three tests are available: Poisson GLM regression, quasi-likelihood GLM regression, and the negative binomial of the edgeR package.The three models admit blocking factors to control for nuissance variables.To assure a good level of reproducibility a post-test filter is available, where we may set the minimum effect size considered biologicaly relevant, and the minimum expression of the most abundant condition.
MSstats: A set of tools for protein significance analysis in label-free or LC-MS, SRM and DIA experiments.
mzID: A parser for mzIdentML files implemented using the XML package. The parser tries to be general and able to handle all types of mzIdentML files with the drawback of having less ‘pretty’ output than a vendor specific parser. Please contact the maintainer with any problems and supply an mzIdentML file so the problems can be fixed quick.
neaGUI: neaGUI is an easy to use R package developed to perform the network enrichment analysis (NEA) proposed by Alexeyenko et al. (2012). The NEA method extends the overlap statistics in GSEA to network links between genes in the experimental set and those in the functional categories by exploiting biological information in terms of gene interaction network. The neaGUI requires the following R packages: tcltk, KEGG.db, GO.db, reactome.db, org.Hs.eg.db, AnnotationDbi, and hwriter.
NetSAM: The NetSAM (Network Seriation and Modularization) package takes an edge-list representation of a network as an input, performs network seriation and modularization analysis, and generates as files that can be used as an input for the one-dimensional network visualization tool NetGestalt (http://www.netgestalt.org) or other network analysis.
omicade4: Multiple co-inertia analysis of omics datasets
OmicCircos: OmicCircos is an R application and package for generating high-quality circular maps for omic data
openCyto: This package is designed to facilitate the automated gating methods in sequential way to mimic the manual gating strategy.
paircompviz: This package provides visualization of the results from the multiple (i.e. pairwise) comparison tests such as pairwise.t.test, pairwise.prop.test or pairwise.wilcox.test. The groups being compared are visualized as nodes in Hasse diagram. Such approach enables very clear and vivid depiction of which group is significantly greater than which others, especially if comparing a large number of groups.
pathifier: Pathifier is an algorithm that infers pathway deregulation scores for each tumor sample on the basis of expression data. This score is determined, in a context-specific manner, for every particular dataset and type of cancer that is being investigated. The algorithm transforms gene-level information into pathway-level information, generating a compact and biologically relevant representation of each sample.
plethy: This package provides the infrastructure and tools to import, query and perform basic analysis of whole body plethysmography and metabolism data. Currently support is limited to data derived from Buxco respirometry instruments as exported by their FinePointe software.
ProCoNA: Protein co-expression network construction using peptide level data, with statisical analysis. (Journal of Clinical Bioinformatics 2013, 3:11 doi:10.1186/2043-9113-3-11)
prot2D: The purpose of this package is to analyze (i.e. Normalize and select significant spots) data issued from 2D GEl experiments
PSICQUIC: PSICQUIC is a project within the HUPO Proteomics Standard Initiative (HUPO-PSI). It standardises programmatic access to molecular interaction databases.
qcmetrics: The package provides a framework for generic quality control of data. It permits to create, manage and visualise individual or sets of quality control metrics and generate quality control reports in various formats.
qusage: This package is an implementation the Quantitative Set Analysis for Gene Expression (QuSAGE) method described in (Yaari G. et al, Nucl Acids Res, 2013). This is a novel Gene Set Enrichment-type test, which is designed to provide a faster, more accurate, and easier to understand test for gene expression studies. qusage accounts for inter-gene correlations using the Variance Inflation Factor technique proposed by Wu et al. (Nucleic Acids Res, 2012). In addition, rather than simply evaluating the deviation from a null hypothesis with a single number (a P value), qusage quantifies gene set activity with a complete probability density function (PDF). From this PDF, P values and confidence intervals can be easily extracted. Preserving the PDF also allows for post-hoc analysis (e.g., pair-wise comparisons of gene set activity) while maintaining statistical traceability. Finally, while qusage is compatible with individual gene statistics from existing methods (e.g., LIMMA), a Welch-based method is implemented that is shown to improve specificity. For questions, contact Chris Bolen (cbolen1@gmail.com) or Steven Kleinstein (steven.kleinstein@yale.edu)
Rchemcpp: The Rchemcpp package implements the marginalized graph kernel and extensions, Tanimoto kernels, graph kernels, pharmacophore and 3D kernels suggested for measuring the similarity of molecules.
RDAVIDWebService: Tools for retrieving data from the Database for Annotation, Visualization and Integrated Discovery (DAVID) using Web Services into R objects. This package offers the main functionalities of DAVID website including: i) user friendly connectivity to upload gene/background list/s, change gene/background position, select current specie/s, select annotations, etc. ii) Reports of the submitted Gene List, Annotation Category Summary, Gene/Term Clusters, Functional Annotation Chart, Functional Annotation Table
rfPred: Based on external numerous data files where rfPred scores are pre-calculated on all genomic positions of the human exome, the package gives rfPred scores to missense variants identified by the chromosome, the position (hg19 version), the referent and alternative nucleotids and the uniprot identifier of the protein. Note that for using the package, the user has to be connected on the Internet or to download the TabixFile and index (approximately 3.3 Go).
Roleswitch: Infer Probabilities of MiRNA-mRNA Interaction Signature (ProMISe) using paired expression data from a single sample. Roleswitch operates in two phases by inferring the probability of mRNA (miRNA) being the targets (“targets”) of miRNA (mRNA), taking into account the expression of all of the mRNAs (miRNAs) due to their potential competition for the same miRNA (mRNA). Due to dynamic miRNA repression in the cell, Roleswitch assumes that the total transcribed mRNA levels are higher than the observed (equilibrium) mRNA levels and iteratively updates the total transcription of each mRNA targets based on the above inference.
RRHO: The package is aimed at inference on the amount of agreement in two sorted lists using the Rank-Rank Hypergeometric Overlap test.
RTN: This package provides classes and methods for transcriptional network inference and analysis. Modulators of transcription factor activity are assessed by conditional mutual information, and master regulators are mapped to phenotypes using different strategies, e.g., gene set enrichment, shadow and synergy analyses.
rTRM: rTRM identifies transcriptional regulatory modules (TRMs) from protein-protein interaction networks.
rTRMui: This package provides a web interface to compute transcriptional regulatory modules with rTRM.
seqCNA: Copy number analysis of high-throughput sequencing cancer data with fast summarization, extensive filtering and improved normalization
SeqVarTools: An interface to the fast-access storage format for VCF data provided in SeqArray, with tools for common operations and analysis.
shinyTANDEM: This package provides a GUI interface for rTANDEM. The GUI is primarily designed to visualize rTANDEM result object or result xml files. But it also provides an interface for creating parameter objects, launching searches or performing conversions between R objects and xml files.
SigFuge: Algorithm for testing significance of clustering in RNA-seq data.
SimBindProfiles: SimBindProfiles identifies common and unique binding regions in genome tiling array data. This package does not rely on peak calling, but directly compares binding profiles processed on the same array platform. It implements a simple threshold approach, thus allowing retrieval of commonly and differentially bound regions between datasets as well as events of compensation and increased binding.
SpacePAC: Identifies clustering of somatic mutations in proteins via a simulation approach while considering the protein’s tertiary structure.
spliceR: An R package for classification of alternative splicing and prediction of coding potential from RNA-seq data.
spliceSites: Align gap positions from RNA-seq data
sRAP: This package provides a pipeline for gene expression analysis (primarily for RNA-Seq data). The normalization function is specific for RNA-Seq analysis, but all other functions (Quality Control Figures, Differential Expression and Visualization, and Functional Enrichment via BD-Func) will work with any type of gene expression data.
sSeq: The purpose of this package is to discover the genes that are differentially expressed between two conditions in RNA-seq experiments. Gene expression is measured in counts of transcripts and modeled with the Negative Binomial (NB) distribution using a shrinkage approach for dispersion estimation. The method of moment (MM) estimates for dispersion are shrunk towards an estimated target, which minimizes the average squared difference between the shrinkage estimates and the initial estimates. The exact per-gene probability under the NB model is calculated, and used to test the hypothesis that the expected expression of a gene in two conditions identically follow a NB distribution.
STRINGdb: The STRINGdb package provides a user-friendly interface to the STRING protein-protein interactions database ( http://www.string-db.org ).
supraHex: A supra-hexagonal map is a giant hexagon on a 2-dimensional grid seamlessly consisting of smaller hexagons. It is supposed to train, analyse and visualise a high-dimensional omics data. The supraHex is able to carray out gene/meta-gene clustering and sample correlation, plus intuitive visualisations to facilitate exploratory analysis. Uniquely to this package, users can simultaneously understand their own omics data in a sample-specific fashion but without loss of information on large genes.
SwimR: SwimR is an R-based suite that calculates, analyses, and plots the frequency of C. elegans swimming behavior over time. It places a particular emphasis on identifying paralysis and quantifying the kinetic elements of paralysis during swimming. Data is input to SwipR from a custom built program that fits a 5 point morphometric spine to videos of single worms swimming in a buffer called Worm Tracker.
TargetScore: Infer the posterior distributions of microRNA targets by probabilistically modelling the likelihood microRNA-overexpression fold-changes and sequence-based scores. Variaitonal Bayesian Gaussian mixture model (VB-GMM) is applied to log fold-changes and sequence scores to obtain the posteriors of latent variable being the miRNA targets. The final targetScore is computed as the sigmoid-transformed fold-change weighted by the averaged posteriors of target components over all of the features.
TCC: This package provides a series of functions for performing differential expression analysis from RNA-seq count data using robust normalization strategy (called DEGES). The basic idea of DEGES is that potential differentially expressed genes or transcripts (DEGs) among compared samples should be removed before data normalization to obtain a well-ranked gene list where true DEGs are top-ranked and non-DEGs are bottom ranked. This can be done by performing a multi-step normalization strategy (called DEGES for DEG elimination strategy). A major characteristic of TCC is to provide the robust normalization methods for several kinds of count data (two-group with or without replicates, multi-group/multi-factor, and so on) by virtue of the use of combinations of functions in other sophisticated packages (especially edgeR, DESeq, and baySeq).
TFBSTools: Software package for TFBS.
tRanslatome: Detection of differentially expressed genes (DEGs) from the comparison of two biological conditions (treated vs. untreated, diseased vs. normal, mutant vs. wild-type) among different levels of gene expression (transcriptome ,translatome, proteome), using several statistical methods: Rank Product, t-test, SAM, Limma, ANOTA, DESeq, edgeR. Possibility to plot the results with scatterplots, histograms, MA plots, standard deviation (SD) plots, coefficient of variation (CV) plots. Detection of significantly enriched post-transcriptional regulatory factors (RBPs, miRNAs, etc) and Gene Ontology terms in the lists of DEGs previously identified for the two expression levels. Comparison of GO terms enriched only in one of the levels or in both. Calculation of the semantic similarity score between the lists of enriched GO terms coming from the two expression levels. Visual examination and comparison of the enriched terms with heatmaps, radar plots and barplots.
trio: Testing SNPs and SNP interactions with a genotypic TDT. This package furthermore contains functions for computing pairwise values of LD measures and for identifying LD blocks, as well as functions for setting up matched case pseudo-control genotype data for case-parent trios in order to run trio logic regression, for imputing missing genotypes in trios, for simulating case-parent trios with disease risk dependent on SNP interaction, and for power and sample size calculation in trio data.
vtpnet: variant-transcription factor-phenotype networks, inspired by Maurano et al., Science (2012), PMID 22955828
XVector: Memory efficient S4 classes for storing sequences “externally” (behind an R external pointer, or on disk).
Package maintainers can add NEWS files describing changes to their packages. The following package NEWS is available:
Changes in version 2.1.6 (2013-09-23):
Started testing against R beta 3.0.2. Fixed Imports and Depends.
chromData: using “short”, not “ushort”, to catch more user errors.
pSegmentGLAD: using a custom daglad that minimizes unneeded calls, specially sorting, that can be very expensive.
Added “certain_noNA” to segmentation methods.
Started testing against R-devel (to become R-3.1.0).
Changes in version 2.1.5 (2013-09-16):
Fixed typos.
Minimized usage of “:::”, removed unused functions for Ansari, and some assignemts that no longer made sense (all packages now have namespaces).
Minimize “Depends” and use “Suggests” and “Imports” in DESCRIPTION with “importFrom” in NAMESPACE.
No longer using our own mergeLevels, since identical to the ones in aCGH package.
GLAD uses now the recommended fastest option (smoothfunc=haarseg).
Changes in version 2.1.4 (2013-07-01):
Changes in version 2.1.3 (2013-06-20):
Default merging of pSegmentDNAcopy changed to “MAD”, to reflect our usage.
Added more benchmarking results and recommendations to the vignette, and fixed some typos.
Changes in version 2.1.2 (2013-06-17):
More changes in cutFile to try and get it to run under Mac.
Fixed names in long examples that were leading to mistakenly reporting results as different.
Added new benchmarking results.
Changes in version 2.1.1 (2013-06-16):
Many small changes and adaptations in vignette and help to get it to work unded Win and Mac.
Changes in cutFile to try and get it to run under Mac.
Changes in version 2.1.0 (2013-05-30):
This is a major rewrite of a most of the code, has new functions, major changes in existing functions, new vignettes, etc.
We no longer use snowfall.
Major changes in parallelization, using forking.
Reading of data: many more options, parallelized reading.
Changes in version 1.34.0 (2012-10-14):
Changes in version 1.33.4 (2013-09-23):
Changes in version 1.33.3 (2013-06-29):
Changes in version 1.33.2 (2013-05-25):
Changes in version 1.33.1 (2013-05-20):
Changes in version 1.33.0 (2013-04-03):
The version number was bumped for the Bioconductor devel version.
No updates.
Changes in version 1.32.3 (2013-06-29):
BUG FIX: Since affxparser v1.30.2/1.31.2 (r72352; 2013-01-08), writeCdf() would incorrectly encode the unit types, iff the input ‘cdf’ argument specified them as integers, e.g. as done by writeCdf() for AffyGenePDInfo in aroma.affymetrix. More specifically, the unit type index would be off by one, e.g. an ‘expression’ unit (1) would be encoded as an ‘unknown’ unit (0) and so on. On the other hand, if they were specified by their unit-type names (e.g. ‘expression’) the encoding should still be correct, e.g. if input is constructed from readCdf() of affxparser. Thanks to Guido Hooiveld at Wageningen UR (The Netherlands) for reporting on this.
BUG FIX: Similarily, writeCdf() has “always”, at least affxparser v1.7.4 since (r21888; 2007-01-09), encoded unit directions and QC unit types incorrectly, iff they were specified as integers.
Changes in version 1.32.2 (2013-05-25):
SPEEDUP: Removed all remaining gc() calls.
SPEEDUP: Replaced all rm() calls with NULL assignments.
Changes in version 1.32.1 (2013-05-20):
Changes in version 1.2.1:
Changes in version 1.2.0:
NEW FEATURES
BUG FIXES
Changes in version 1.32.0 (2012-10-14):
Changes in version 1.31.10 (2013-10-08):
Added averageQuantile() for matrices in addition to lists.
SPEEDUP: Now normalizeQuantileSpline(…, sortTarget=TRUE) sorts the target only once for lists of vectors just as done for matrices.
DOCUMENTATION: Merged the documentation for normalizeQuantileSpline() for all data types into one help page. Same for plotXYCurve().
BUG FIX: Argument ‘lwd’ of plotXYCurve(X, …) was ignored if ‘X’ was a matrix.
Bumped up package dependencies.
Changes in version 1.31.9 (2013-10-07):
Now library(aroma.light, quietly=TRUE) attaches the package completely silently without any messages.
Now the ‘aroma.light’ Package object is also available when the package is only loaded (but not attached).
DOCUMENTATION: Merged the documentation for normalizeQuantileRank() for numeric vectors and lists.
DOCUMENTATION: Now documention S3 methods under their corresponding generic function.
Changes in version 1.31.8 (2013-10-02):
Changes in version 1.31.7 (2013-09-27):
SPEEDUP: Now all package functions utilizes ‘matrixStats’ functions where possible, e.g. anyMissing(), colMins(), and rowWeightedMedians().
Bumped up package dependencies.
Changes in version 1.31.6 (2013-09-25):
Changes in version 1.31.5 (2013-09-23):
ROBUSTNESS: Now properly declaring all S3 methods in the NAMESPACE file.
SPEEDUP/CLEANUP: normalizeTumorBoost() now uses which() instead of whichVector() of ‘R.utils’. Before R (< 2.11.0), which() used to be 10x slower than whichVector(), but now it’s 3x faster.
CLEANUP: Now only using ‘Authors@R’ in DESCRIPTION, which is possible since R (>= 2.14.0). Hence the new requirement on the version of R.
Bumped up package dependencies.
Changes in version 1.31.4 (2013-09-10):
CLEANUP: Now package explicitly imports what it needs from matrixStats.
Bumped up package dependencies.
Changes in version 1.31.3 (2013-05-25):
SPEEDUP: Removed all remaining gc() calls, which were in normalizeQuantileSpline().
SPEEDUP: Replaced all rm() calls with NULL assignments.
Updated the package dependencies.
Changes in version 1.31.2 (2013-05-20):
Changes in version 1.31.1 (2011-04-18):
Changes in version 1.31.0 (2013-04-03):
Changes in version 1.30.5 (2013-09-25):
Backport from v1.31.5: Declaring all S3 methods in NAMESPACE.
Backport from v1.31.5: normalizeTumorBoost() now uses which(), which also removes one dependency on ‘R.utils’.
Changes in version 1.30.4 (2013-09-25):
Changes in version 1.30.3 (2013-09-25):
Backport from v1.31.3: Removal of all gc() calls and removal of variables is now faster.
Removed one stray str() debug output in robustSmoothSpline().
Changes in version 1.30.2 (2013-05-20):
Changes in version 1.30.1 (2013-04-18):
Now backtransformPrincipalCurve() preserves dimension names.
BUG FIX: backtransformPrincipalCurve() gave an error if the pricipal curve was fitted using data with missing values.
BUG FIX: fitPrincipalCurve() would not preserve dimension names if data contain missing values.
Changes in version 1.0:
USER VISIBLE CHANGES
BUG FIXES
PLANS
Changes in version 2.1:
Changes in version 1.1:
NEW FEATURES
New high level function performOAuth() makes the App authentication easier.
initializeAuth() now fires up a browser window and starts the OAuth v2 process. Users can use ‘useBrowser’ parameter to control this behaviour.
SIGNIFICANT USER-VISIBLE CHANGES
BUG FIXES
Added end of line character to some messages.
fileItem$Size is now stored as a numeric, thus allowing for file larger than 2GB.
Changes in version 0.99.3:
1.3.1: # Thu 06-20-2013 - 11:29
1.4.0: # Wed 06-26-2013 - 19:56
1.4.1:
Changes in version 1.0.0 (2013-10-15):
NEW FEATURES
NEW FEATURES
NEW FEATURES
NEW FEATURES
Changes in version 2.21:
USER VISIBLE CHANGES
USER VISIBLE CHANGES
Changes in version 0.99.0:
NEW FEATURES
mclapply(), pvec() require only length, [, and (for mclapply) [[.
pvectorize() creates a parallel version of its vectorized function argument.
MulticoreParam, SnowParam, DoparParam (foreach-derived), SerialParam to parameterize back-ends.
bplapply, bpvec as parallel evaluation models.
bpstart, bpstop, bpisup for back-end management.
bpvec has a new argument AGGREGATE, a function to specify how results are to be combined.
SIGNIFICANT USER-VISIBLE CHANGES
BPPARM is now used as the argument name for passing BiocParallelParam instances to functions.
bplapply and bpvec now only dispatch on X and BPPARAM.
Changes in version 1.0.0:
USER VISIBLE CHANGES
BUG FIXES
Changes in version 1.1.9:
BUG FIXES
BUG FIXES
Changes in version 1.1.8:
NEW FEATURES
BUG FIXES
NEW FEATURES
BUG FIXES
Changes in version 1.1.7:
NEW FEATURES
NEW FEATURES
Changes in version 1.1.6:
BUG FIXES
Changes in version 1.1.5:
NEW FEATURES
BUG FIXES
Changes in version 1.1.4:
NEW FEATURES
update biomvRGviz to plot multiple samples in one, and more param
plot method now defaults to multiple samples in one, sampleInOne=T
BUG FIXES
Changes in version 1.1.3:
NEW FEATURES
NEW FEATURES
Changes in version 1.1.2:
NEW FEATURES
add a new clustering method for emission prior estimation
add a new example section of DMR detection in the vignette
BUG FIXES
Changes in version 1.1.1:
NEW FEATURES
BUG FIXES
Changes in version 1.5.5 (2013-10-12):
BUG FIXES
BUG FIXES
BUG FIXES
Changes in version 1.5.2 (2013-10-09):
BUG FIXES
fixed force option in estimateHyperPar (it worked the wrong way around)
fixed problem with effective lengths being too small
NEW FEATURES
Changes in version 1.4.3 (2013-07-08):
BUG FIXES
NEW FEATURES
BUG FIXES
NEW FEATURES
BUG FIXES
NEW FEATURES
Changes in version 0.9:
Fixed a problem with “width” in the title of bsseq plots.
plot.BSseqTstat now allows for BSseqTstat objects computed without correction.
validObject(BSseq) has been extended to also check for sampleNames consistency.
Fixed a bug related to validity checking.
Increased maxk from 10,000 to 50,000 in calls to locfit, to allowing fitting the model on genomes with unusally long chromosomes (Thanks to Brian Herb for reporting).
The class representation for class ‘BSseq’ has changed completely. The new class is build on ‘SummarizedExperiment’ from GenomicRanges instead of ‘hasGRanges’. Use ‘x <- updateObject(x)’ to update serialized (saved) objects.
Fixing a problem in orderBSseq related to chromosome names.
Allowed user specification of maxk, with a default of 10,000 in BSmooth.
Many bugfixes made necessary by the new class representation.
Better argument checking in BSmooth.tstat.
A few undocumented functions are now documented.
Rewrote orderBSseq
Changes in version 1.1:
Added NEWS file.
Fixed a bug related to >= for numerics.
Added smoothing using a gaussian kernal as implemented in the locfit package through the function locfitByCluster.
Added closeSockets for cleanup for doParallel on Windows.
More bugfixes for windows; now using foreachCleanup().
Added a ‘bumps’ class and print method.
annotateNearest / regionMatch now give NA annotations for queries with no nearest subject (perhaps because the seqname is missing from the subject). Previously this was taken to be mistaken input and a hard error raised.
Speedup of fwer computations using foreach.
Added boundedClusterMaker.
bug fix to internal function .getModT (which are not used in the main bumphunter functions). Now the t-statistics returned a correct.
Changes in version 2012-06-12:
Changes in version 2012-06-11:
Version 1.13.4
Add ByteCompile: TRUE
Bugfix for findIsotopes, clears subscript out of bound error
Changes in version 2012-05-25:
Version 1.13.2
First changes for improved isotope detection
Changes in version 2012-04-12:
Version 1.13.1
Bugfix for findIsotopes to fix not consecutive isotope label like [M]+,[M+2]+ without [M+1]+
Changes in version 2012-03-19:
Version 1.11.10
Bugfix in groupCorr, where the function throws an error if argument xraw is not null
Version 1.11.9
Bugfix in findAdducts, where adduct annotation filtering was to stringent, if ips score is higher 1.5
Changes in version 2012-02-29:
Version 1.11.8
Bugfix in findAdducts parallel mode, where wrong psgrp indices were stored in annoGrp
Changes in version 2012-02-17:
Version 1.11.7
Bugfix in findAdducts, where the ruleset is not saved within a xsAnnotate object with user defined rules
Changed a general groupCorr behaviour. If no edge is above correlation threshold, all peaks are seperated in pspecs of size 1
Changes in version 2012-02-15:
Version 1.11.6
Fix error in groupCorr: If sample is set to something other than 1 or NA, it result in a crash
Changes in version 2012-02-10:
Version 1.11.5
Bugfix in groupCorr where parameter cor_eic_th doesn’t influence correlation across samples
Add new parameter for groupCorr cor_exp_th
Changes in version 2011-29-11:
Version 1.11.3
Add new function combinexsAnnos. It allows checking and reannotation of sample with a coressponding sample from the opposite ion mode
Changes in version 2011-28-04:
Changes in version 2011-24-11:
Version 1.11.2
Bugfix in annotateDiffreport: Since 1.7.7 mismatch of the peaklist from CAMERA and the diffreport function results in false ordered peaktable
Changes in version 2011-24-05:
Changes in version 2011-23-09:
Version 1.9.7
Bugfix in calcIsotopes, causes groupCorr with calcIso to crash with (Error in rbind(resMat …)
Bugfix in groupCorr with given xcmsRaw
Changes in version 2011-22-08:
Version 1.9.6
Bugfix in plotEICs (Error in pks[, 1] : incorrect number of dimensions)
Changes in version 2011-20-25:
Version 1.9.9
added some “drop=FALSE” to fix “Error in isomatrix[, 1] : incorrect number of dimensions” error
Changes in version 2011-20-10:
Version 1.9.8
Correct rule table extended_adducts_pos.csv (typo in proton mass)
Changes in version 2011-12-12:
Version 1.11.4
Add missing Rd page combinexsAnnos
Changes in version 2011-12-05:
Changes in version 2011-10-11:
Version 1.11.1
add the possibility to extract multiple isotope intensity from different samples with getIsotopeCluster
Changes in version 2011-04-04:
Changes in version 2011-02-08:
Version 1.9.5
Bugfix for findIsotopes if ppm was very high it could occur that one peak is assigned as two or more isotope peaks
Version 1.9.4
Add parameter polarity to xsAnnotate constructor
getPeaklist and getpspectra returns now correct annotation of negative charged ions [M]-
Add snow as additonal possibilty for parallel processing
Add function cleanParallel to clean up with spawned slave processes
Changes in version 2010-29-09:
Changes in version 2010-23-11:
Changes in version 2010-20-09:
Changes in version 2010-11-10:
Changes in version 2010-11-06:
Speed up in findAdducts
Fix unit tests
Changes in version 2010-08-11:
Add intval parameter to groupFWHM and findIsotopes
Change getPeaklist to S4 Methods.
Add getPeaklist parameter intval, where the intensity value can be selected
Additional bugfix for findIsotopes. Could occur with 1.7.1, that all isotopes will be deleted.
Changes in version 2010-05-03:
Changes in version 2010-04-20:
Changes in version 2010-04-19:
Last changes for the next BioC release
Rewrite of the vignette
Changes in version 2010-03-17:
Hugh changes in CAMERA for working with multiple sample
Add check constrains in groupCorr for isotopes and primary adducts
Changes in version 2010-01-11:
Fix bug in findIsotopes. Occurs if the first isotope peak, could be assigned from two different monoisotopic peaks.
Reduce slightly the number of found isotopes
Changes in version 2009-11-24:
Changes in version 2009-11-20:
Changes in version 2009-08-26:
Changes in version 2009-08-24:
small bugfixes in getPeaklist
add neutral losses to rule set
Changes in version 2009-08-12:
Changes in version 2009-08-04:
Changes in version 2009-06-03:
Add adduct labels to plotPeaks()
Add adduct labels to plotEICs()
Changes in version 2009-05-22:
Changes in version 2009-05-06:
Changes in version 2009-03-30:
add combine_xsanno
small refactoring
changes in scoring schemata
Changes in version 2009-03-18:
after groupCorr every peak is now member of a group
bugfix: remove xM-xH clones
remove dependency on Hmisc
Changes in version 2009-03-10:
Changes in version 2009-02-24:
refactoring findAdducts
add methods for pos/neg polarity comparison
Changes in version 2009-02-20:
Changes in version 2009-02-18:
add neutral losses into ruleset
other bugfixes
Changes in version 2009-01-19:
Change isotope nomination
add lists for fragments, ions and neutral losses
Changes in version 2008-10-15:
Changes in version 2008-10-13:
Changes in version 2007-10-12:
1.5.1:
Changes in version 1.8.0 (2013-08-28):
BUG FIX
readMIDAS: DV, DA and TR can now be in the specy name
prep4sim can read self loop
plotOptimResultsPan: fix special cases with one or no inhibitors/stimuli
fix bug in cutNONC: notMat was not populated
readSIF: can read and gates coded in big caps as well as small ones
writeMIDAS: manages absence of inhibitors
CHANGES
CNOlist: subfield parameter has been removed. Subfield are automatically found from the header
expandAndGates are not limited to 4 inputs anymore
normaliseCNOlist: EC50 is set to 1 by default
NEW FEATURES
readSBMLQual: a function to read prior knowledge network in SBMLqual format. !! This is a prototype. use with care for now.
cutCNOlist function can cut a MIDAS file over time
Changes in version 1.0.0:
NEW FEATURES
NEW FEATURES
NEW FEATURES
Changes in version 1.3.15:
NEW FEATURES
Changes in version 1.3.12:
NEW FEATURES
NEW FEATURES
NEW FEATURES
Changes in version 1.3.9:
NEW FEATURES
Changes in version 1.3.3:
NEW FEATURES
NEW FEATURES
NEW FEATURES
NEW FEATURES
Changes in version 1.0:
PKG FEATURES
PKG FEATURES
PKG FEATURES
PKG FEATURES
PKG FEATURES
PKG FEATURES
PKG FEATURES
PKG FEATURES
PKG FEATURES
Changes in version 0.99.2:
USER-VISIBLE CHANGES
Updated examples for various functions to be runnable (removed donttest)
Updated DESCRIPTION to use Imports: rather than Depends:
Updated license to GPL-3
Updated NEWS file for bioconductor guidelines
BUG FIXES
Changes in version 0.99.1:
USER-VISIBLE CHANGES
Changes in version 0.99.0:
NEW FEATURES
Changes in version 0.9.6:
NEW FEATURES
Changes in version 0.9.5:
BUG FIXES
USER-VISIBLE CHANGES
Changes in version 0.9.4:
USER-VISIBLE CHANGES
Changes in version 0.9.3:
NEW FEATURES
BUG FIXES
Changes in version 0.9.2:
NEW FEATURES
Added ability for user to input their own locus definition file (pass the full path to a file as the locusdef argument)
Added a data frame to the results object that gives the arguments/values passed to chipenrich, also written to file *_opts.tab
For FET and chipenrich methods, the outcome variable can be recoded to be >= 1 peak, 2 peaks, 3 peaks, etc. using the num_peak_threshold parameter
Added a parameter to set the maximum size of gene set that should be tested (defaults to 2000)
USER-VISIBLE CHANGES
Previously only peak midpoints were given in the peak –> gene assignments file, now the original peak start/ends are also given
Updated help/man with new parameters and more information about the results
BUG FIXES
Changes in version 0.9.1:
NEW FEATURES
NEW FEATURES
NEW FEATURES
Changes in version 0.9:
NEW FEATURES
BUG FIXES
Changes in version 0.8:
BUG FIXES
Changes in version 0.7:
USER-VISIBLE CHANGES
Updated binomial test to sum gene locus lengths to get genome length and remove genes that are not present in the set of genes being tested
Updated spline fit plot to take into account mappability if requested (log mappable locus length plotted instead of simply log locus length)
Removed SAMPLEABLE_GENOME* constants since they are no longer needed
Updated help files to reflect changes to plot_spline_length and chipenrich functions
BUG FIXES
Changes in version 0.6:
BUG FIXES
Changes in version 0.5:
USER-VISIBLE CHANGES
USER-VISIBLE CHANGES
Changes in version 2.9.6:
BUG FIXES
Changes in version 2.9.5:
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:
Changes in version 1.1.2:
Changes in version 1.1.1:
Changes in version 0.99.5 (2013-07-24):
vignette:
remove duplicated sessionInfo entries.
Changes in version 0.99.4 (2013-07-23):
vignette:
use BiocStyle.
add sessionInfo() and TOC.
Changes in version 0.99.3 (2013-07-08):
Changes in version 0.99.2 (2013-06-17):
Replace own AAStringSetList constructor by Biostrings::AAStringSetList.
man/cleaver-package.Rd: remove static date.
vignette: add dynamic date and don’t load Biostrings manually anymore.
NAMESPACE: don’t import from Biostrings and IRanges.
Changes in version 0.99.1 (2013-05-30):
Add S4-methods for character, AAString, AAStringSet.
man/cleave-methods.Rd: split table of cleavage rules to reduce table width.
Extend vignette (add BRAIN and UniProt.ws based examples).
Changes in version 0.99.0 (2013-04-27):
Changes in version 2013-10-07:
Commited 0.99.6 to Bioconductor.
Added unit tests for yassai_identifier().
Changes in version 2013-08-01:
Changes in version 2013-05-07:
Resubmitted 0.99.5 to Bioconductor.
Distribute a copy of the clonotypes extracted from example_data.
Execute all examples in the vignette.
Changes in version 2013-05-01:
Resubmitted 0.99.4 to Bioconductor
Moved the Markdown vignette to ‘/vignettes’.
Added executable example with test data to the vignette.
Changes in version 2013-04-26:
Resubmitted 0.99.3 to Bioconductor
Moved extra data to ‘inst/extdata’.
Moved the Markdown vignette to ‘inst/vignettes’.
Changes in version 2013-04-15:
Changes in version 2013-01-08:
Leaner Bioconductor package, without the wiki documentation. 2012-….. Charles Plessy plessy@riken.jp
Many entries missing.
Changes in version 2012-10-10:
Changes in version 2012-09-06:
Changes in version 1.9.4:
Changes in version 1.9.3:
extend enrichGO to support 20 species <2013-07-09, Mon>
update vignettes. <2013-07-09, Mon>
Changes in version 1.9.1:
enrichGO and enrichKEGG support rat organism <2013-05-20, Mon>
change some code according to DOSE <2013-03-27, Wed>
modify enrichGO and enrichKEGG according to the change of enrich.internal, remove qvalueCutoff parameter, add pAdjustMethod, add universe paramter for user to specify background. <2013-05-29, Wed>
add function viewKEGG for visualizing KEGG pathway and update vignette. <2013-06-14, Fri>
1.7.1:
Changes in version 1.4.0:
cSimulator handles non integers values for the ihibitors and stimuli
gaDiscreteT1.R: fix issue when only 1 model was returned within tolerance
reduceFuzzy.R fix bug that causes seg faut (model was not cut properly)
defaultParametersFuzzy.R: added nTF to set number of TF to arbitrary value (not tested)
CNORwrapFuzzy.R: fixed pMutation argument that was not populated
gaDiscrete functions return best score as well in the dataframe.
output names of the fields returned by gaDiscrete are now using camel lower case so that plotFit from CellNoptR can be used
add C simulator
Changes in version 1.30.0:
The most visible change is that the CodelinkSet interface has been adopted as the official supported system. Documentation of these topic has been improved, and a new vignette describing the CodelinkSet system is available (Codelink_Introduction). Documentation to the old Codelink class has moved to the Codelink_Legacy vignette.
Before, readCodelink() would assign NA values to spots flagged as M (MSR spot), I (Irregular) and C (Contaminated). This could cause in large datasets that many spots would have at least one sample with NA at random, reducing drastically the number of de facto spots/probes used during normalization. Many thanks to Emmanuelle Dantony for spotting this problem and subsequent feedback. Because of this and other problems implementing and appropriate method to deal with this, automatic assigment of NA values is not performed anymore. The only exception are M flagged spots, which have intensity values of -9999, and hence do not represent any measure of intensity. Also, background and normalization methods are applied calling the appropriate functions in the limma package. Support for type- and flag-based weights has been included, and weights are automatically created by readCodelinkSet(). Weights can be used to modulate the contribution of some probes to normalization and during linear modeling more efficiently. Examples on how to use these approaches are documented in the vignette Codelink_Introduction.
Added generic method normalize() for Codelink and CodelinkSet classes.
Changes in version 1.7.1:
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
Bugfixes
Updates
Bugfixes
Changes in version 1.99.0 (2013-04-30):
Updates
Updates
Changes in version 1.7.4 (2013-09-28):
Updates
Updates
Changes in version 1.1.3:
corrected errors generated in denoiseSegments when segments are too small
refined plotting with data that has many subpopulations (>10)
more robust argument selection in functions
Changes in version 1.1.32:
By default, use QR decomposition on the design matrix X. This stabilizes the GLM fitting. Can be turned off with the useQR argument of nbinomWaldTest() and nbinomLRT().
Allow for “frozen” normalization of new samples using previous estimated parameters for the functions: estimateSizeFactors(), varianceStabilizingTransformation(), and rlogTransformation(). See manual pages for details and examples.
Changes in version 1.1.31:
Changes in version 1.1.24:
Changes in version 1.1.23:
Changes in version 1.1.21:
Changes in version 2013-09-12:
Major changes to vignette to provide more of an end-to-end description of the work flow.
Major changes to function names to now make TRT rather than BM the default; changed vignette to reflect this.
Added apepndix explaining TRT to vignette.
Changes in version 2013-02-27:
Changes in version 2012-11-28:
Changes in version 2012-06-26:
Changes in version 2012-05-21:
Changes in version 2011-10-03:
Changes in version 2011-07-12:
Changes in version 2011-07-01:
Changes in version 1.8.0:
Add support for DESeq2:
New: Add DBA_DESEQ2, DBA_ALL_METHODS and DBA_ALL_BLOCK method constants
Change: dba.analyze can analyze using DESeq2
Change: all reporting and plotting functions support DESeq2 results
Change: vignette includes comparison of edgeR, DESeq, and DESeq2
Changes to counting using dba.count:
Change: optimize built-in counting code to use much less memory and run faster
Change: deprecate bLowMem, replaced with bUseSummarizeOverlaps
New: add readFormat parameter to specify read file type (instead of using file suffix)
New: generation of result-based DBA object using dba.report (makes it easier to work with differentially bound peaksets)
Changes to defaults:
Change: default score is now DBA_SCORE_TMM_MINUS_FULL instead of DBA_SCORE_TMM_MINUS_EFFECTIVE in dba.count
Change: default value for bFullLibrarySize is now TRUE in dba.analyze
New: add bCorPlot option to DBA$config to turn off CorPlot by default
Various bugfixes, improved warnings, updated documentation
Changes in version 1.99.6:
Changes in version 1.99.5:
Changes in version 1.99.4:
Changes in version 1.99.3:
extend EXTID2NAME to support 20 species <2013-07-09, Tue>
update vignette. <2013-07-09, Tue>
Changes in version 1.99.1:
Changes in version 1.99.0:
extent ggplot to support enrichResult by implementing fortify method. <2013-05-22, Wed>
re-implement barplot.enrichResult. <2013-05-23, Thu>
enrich.internal support user specifiy background by parameter universe. <2013-05-24, Fri>
implement Gene Set Enrichment Analysis algorithm. <2013-05-29, Wed>
change setReadable to support groupGO of clusterProfiler. <2013-05-29, Wed>
fixed mclapply not support Windows platform issue. <2013-05-30, Fri>
rename logFC parameter to foldChange. <2013-06-13, Thu>
Changes in version 1.7.1:
use geom_bar(stat=”identity”) instead of geom_bar() in barplot for explicitly mapping y value. <2013-05-08, Wed>
bug fixed when qvalue can’t calculated. <2013-05-02, Thu>
bug fixed of enrich.internal, drop those genes that without annotation when calculating sample gene number. <2013-05-02, Thu>
change some code to satisfy ReactomePA <2013-03-27, Wed>
Changes in version 1.7.0:
Changes in version 1.6.0:
Changes in version 4.4.0:
NEW FEATURES
New colorLabels function color-coding labels of object masks by a random permutation (Bernd Fisher)
Additional argument inputRange to normalize allowing presetting a limited input intensity range
Additional argument thick to paintObjects controlling the thickness of boundary contours
SIGNIFICANT USER-VISIBLE CHANGES
normalize and combine use the generics from BiocGenerics
removed the along argument from combine
Re-introduced calculation of ‘s.radius.sd’ (standard deviation of the mean radius) in cell features
BUG FIXES
Changes in version 3.3.8:
Changes in version 3.3.5:
Refinement to cutWithMinN() to make the bin numbers more equal in the worst case.
estimateDisp() now creates the design matrix correctly when the design matrix is not given as an argument and there is only one group. Previously this case gave an error.
Minor edit to glm.h code.
Changes in version 3.3.4:
Changes in version 3.3.3:
Changes in version 3.3.2:
Update to cutWithMinN() so that it does not fail even when there are many repeated x values.
Refinement to computation for nbins in dispBinTrend. Now changes more smoothly with the number of genes. trace argument is retired.
Fixes to calcNormFactors with method=”TMM” so that it takes account of lib.size and refCol if these are preset.
Updates to help pages for the data classes.
Changes in version 3.3.1:
Changes in version 1.2.0:
NEW FEATURES
NEW FEATURES
NEW FEATURES
NEW FEATURES
Changes in version 2.6.1:
NEW FEATURES
NEW FEATURES
Changes in version 1.0.0:
NEW FEATURES
Changes in version 2.0.0:
NEW FEATURES
NEW FEATURES
Changes in version 1.4.0:
NEW FEATURES
NEW FEATURES
Changes in version 2.11.3:
add secondary vignette, “RNA-Seq Data Pathway and Gene-set Analysis Workflows”.
add function kegg.gsets, which generates up-to-date KEGG pathway gene sets for any specified KEGG species.
Changes in version 1.5.4:
Changes in version 1.5.3:
Changes in version 1.5.2:
Changes in version 1.5.1:
Changes in version 1.1.7:
Changes in version 1.1.6:
Changes in version 1.1.2:
Changes in version 1.1.1:
Changes in version 1.1.1:
BUG FIXES
Changes in version 2007-09-12:
Added prune function for pruning/trimming the pedigree. It does not work on pedigree, but assumes a data.frame with defined structure. Adaption needed.
We depend on genetics package since gpLong2Wide and hwp assume that input is of genotype class.
Added two utility functions (gpLong2Wide and hwp) for work with gpi(). There is also a separate help page for them.
Internal fixes in gpi - no need to transpose inputs for Fortran call anymore - check that there are no NA values in gp and hwp
Changes in version 2007-04-25:
Changes in version 2007-04-19:
Changes in version 2007-04-18:
R CMD check should now fail also when R error (usually call to stop()) occurs in unit testing.
Added unit tests for sort, examples in help page and clarified sort help page.
Changes in version 2007-04-06:
New small dataset Falconer5.1.
Added sex(), sex<-(), ascendantSex() and ascendantSex<-() functions.
Added some more tests for relationshipAdditive, inverseAdditive and inbreeding. # 0.1.2
Changes in version 2007-04-01:
Now we are more rigorous for value of ascendantSex argument in Pedigree(). It must accord to values in sex column, if that one is passed of course.
MASS added to depends due to use of fractions() in many places in documnetation.
Added vignette on quantitative genetic (animal) model and model.matrix.Pedigree() functions for educational purposes.
Created data directory and added pedigree example Mrode2.1 and Mrode3.1.
Added unit tests for genetic relationship matrices that should test all related functions - mainly against Mrode’s book examples - runit.genRelMatrix.R.
Added arguments sort and names to inverseAdditive(), relationshipAdditive() and inbreeding().
Reworked core for relationshipAdditive() into vectorized form.
Added geneFlowT(), geneFlowTinv(), geneFlowM() and mendelianSamplingD() functions.
Changes in version 2007-04:
Changes in version 2007-03-02:
Registration of native routines - src/register.cc.
Added gpi() function. # 0.1.1
Temporarily removed unknown funcs, due to planned move to BioC and change to S4.
All depends are now in gdata –> removing ggmisc.
Changes in version 2006-03-29:
codeUnit to get internal codes for subject and ascendants if factors are used.
Handled unused levels in nlevels.pedigree and summary.pedigree now produces a simple summary
Started to implement checks in check.pedigree and friends
Proper factor handling
Changes in version 2006-03-16:
Playing around with NA/unknown representation - it is very likely that I messed up some things with factors –> subject to changes. # Version 0.1
Initial version # NEWS ends here
Changes in version 1.14:
NEW FEATURES
keys method now has new arguments to allow for more sophisticated filtering.
adds genes() extractor
makeTranscriptDbFromGFF() now handles even more different kinds of GFF files.
BUG FIXES
better argument checking for makeTranscriptDbFromGFF()
cols arguments and methods will now be columns arguments and methods
Changes in version 1.14.0:
NEW FEATURES
Add coercion from GenomicRangesList to RangedDataList.
Add “c” method for GAlignmentsPairs objects.
Add coercion from GAlignmentPairs to GAlignmentsList.
Add ‘inter.feature’ and ‘fragment’ arguments to summarizeOverlaps().
Add seqselect,GAlignments-method.
Add CIGAR utilities: explodeCigarOps(), explodeCigarOpLengths() cigarRangesAlongReferenceSpace(), cigarRangesAlongQuerySpace() cigarRangesAlongPairwiseSpace(), extractAlignmentRangesOnReference() cigarWidthAlongReferenceSpace(), cigarWidthAlongQuerySpace() cigarWidthAlongPairwiseSpace().
Add seqlevels0() and restoreSeqlevels().
Add seqlevelsInUse() getter for GRanges, GRangesList, GAlignments GAlignmentPairs, GAlignmentsList and SummarizedExperiment objects.
Add update,GAlignments method.
Add GIntervalTree class.
Add coercion from GAlignmentPairs to GAlignments.
Add sortSeqlevels().
Add tileGenome().
Add makeGRangesFromDataFrame() and coercion from data.frame or DataFrame to GRanges.
SIGNIFICANT USER-LEVEL CHANGES
Renaming (with aliases from old to new names): - classes GappedAlignments -> GAlignments GappedAlignmentPairs -> GAlignmentPairs - functions GappedAlignments() -> GAlignments() GappedAlignmentPairs() -> GAlignmentPairs() readGappedAlignments() -> readGAlignments() readGappedAlignmentPairs() -> readGAlignmentPairs()
Remove ‘asProperPairs’ argument to readGAlignmentsList().
Modify “show” method for Seqinfo object to honor showHeadLines and showTailLines global options.
50x speedup or more when merging 2 Seqinfo objects, 1 very small and 1 very big.
Add dependency on new XVector package.
Enhanced examples for renaming seqlevels in seqlevels-utils.Rd.
More efficient reference class constructor for ‘assays’ slot of SummarizedExperiment objects.
‘colData’ slot of SummarizedExperiment produced from call to summarizedOverlaps() now holds the class type and length of ‘reads’.
4x speedup to cigarToRleList().
Relax SummarizedExperiment class validity.
Renaming (with aliases from old to new names): cigarToWidth() -> cigarWidthOnReferenceSpace(), and cigarToQWidth() -> cigarWidthOnQuerySpace().
Improvements to summarizeOverlaps(): - mode ‘Union’: 1.5x to 2x speedup - mode ‘IntersectionNotEmpty’: 2x to 8x speedup + memory footprint reduced by ~ half
Change default ‘use.names’ to FALSE for readGAlignmentsList().
Implement ‘type=”equal”’ for findOverlaps,SummarizedExperiment methods.
Modify summarizeOverlaps() examples to use ‘asMates=TRUE’ instead of ‘obeyQname=TRUE’.
Remove unneeded “window” method for GenomicRanges objects.
Speed up seqinfo() getter and setter on SummarizedExperiment objects and derivatives (e.g. VCF) by using direct access to ‘rowData’ slot.
coverage,GenomicRanges method now uses .Ranges.coverage() when using the defaults for ‘shift’ and ‘width’.
Remove restriction that metadata column names must be different on a GRangesList and the unlisted GRanges.
GenomicRangesUseCases vignette has been redone and renamed to GenomicRangesHOWTOs
DEPRECATED AND DEFUNCT
Defunct all “match” and “%in%” methods in the package except for those with the GenomicRanges,GenomicRanges signature.
Deprecate GappedAlignment*: - GappedAlignments and GappedAlignmentPairs classes - GappedAlignments() and GappedAlignmentPairs() constructors - readGappedAlignments() and readGappedAlignmentPairs() functions
Deprecate cigar util functions: cigarToWidth(), cigarToQWidth(), cigarToIRanges() splitCigar(), cigarToIRanges(), cigarToIRangesListByAlignment() cigarToIRangesListByRName(), cigarToWidth(), cigarToQWidth() cigarToCigarTable(), summarizeCigarTable()
Deprecate seqselect().
BUG FIXES
Fix bug in c,GAlignments for case when objects were unnamed.
Fix bug in flank,GenomicRanges (when ‘ignore.strand=TRUE’ ‘start’ was being set to TRUE).
Fix bug in behavior of summarizeOverlaps() count mode ‘IntersectionNotEmpty’ when ‘inter.features=FALSE’. Shared regions are now removed before counting.
Fix bug in cigarToIRangesListByAlignment() when ‘flag’ is supplied and indicates some reads are unmapped.
Fix bug in summarizeOverlaps(…, mode=’IntersectionNotEmpty’) when ‘features’ has ‘-‘ and ‘+’ elements and ‘ignore.strand=TRUE’.
match,GenomicRanges,GenomicRanges method now handles properly objects with seqlevels not in the same order.
Changes in version 4.10:
Changes in version 4.9:
Changes in version 1.4.0:
NEW FEATURES
Add desired_read_group to BamTallyParam; will limit tallies to that specific read group (useful for multi-amplicon sequencing, like Fluidigm)
Add keep_ref_rows argument to variantSummary() for keeping rows for positions where no alt is detected (the rows where ref == alt).
gsnap() will now output a GsnapOutputList when there are multiple input files
Support ‘terminal_threshold’ and ‘gmap_mode’ parameters in GsnapParam, and use different defaults for DNA vs. RNA. This means a big improvement in alignment quality for DNA.
GmapGenome now accepts a direct path to the genome as its first argument
USER-VISIBLE CHANGES
Renamed summarizeVariants to variantSummary
The ‘which’ in GsnapParam is now a GenomicRanges instead of a RangesList
Refactor bam_tally, so that bam_tally returns a TallyIIT object, which is then summarized via summarizeVariants; this allows computing tallies once and summarizing them in different ways (like maybe get the coverage). The summarizeVariants function yields a VRanges.
BUG FIXES
fix minimum quality cutoff check to >=, instead of >
fix asBam,GsnapOutput for when unique_only is TRUE
package created by makeGmapGenomePackage now have a GmapGenome with the correct name
Changes in version 1.19.3:
Changes in version 1.19.2:
export getDb and loadGOMap <2013-07-09, Mon>
update vignettes <2013-07-9, Mon>
Changes in version 1.19.1:
Changes in version 1.23:
SIGNIFICANT USER-VISIBLE CHANGES
SIGNIFICANT USER-VISIBLE CHANGES
Changes in version 1.7.8:
Added gdsSetMissingGenotypes, updated argument names in ncdfSetMissingGenotypes.
Changed colorscheme in manhattanPlot.R.
Bug fix in ibdPlot - diagonal orange bars are back.
Bug fix in plinkWrite for writing just one sample.
Bug fix in printing pedigreeCheck error message.
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:
Changed labeling of IBD plots from “HS” to “Deg2” and “FC” to “Deg3.”
Bug fix in pedigreePairwiseRelatedness - no more warning about multiple values passed to stringsAsFactor.
pedigreeClean and pedigreeFindDuplicates are now defunct. Use pedigreeCheck instead.
Changes in version 1.2.2:
bug fix split_sparse_matrix
plot functions with other arguments ‘…’
plot arguments grid and pairs
new function ‘plotLarger’ (add samples without IBD and borders)
vcftoFABIA with command line options -s (SNVs_) and -o (output file)
vcftoFABIA in R with output file name
Changes in version 1.5.2:
NEW FEATURES
Efficient memory matrix representation using the Matrix package. The memory usage for big sparse matrix is improved by a factor 7. However, some operation are much slower based on the Matrix implementation. Thus, for some task as the plotting function, the Matrix are converted in standard matrix based object
‘show’ and ‘detail’ method for HTClist object
‘c(x, …)’ method for HTCexp and HTClist objects
SIGNIFICANT USER-VISIBLE CHANGES
The option mask.data from the mapC function is deprecated
Update of parallel computation for some functions (import, normalize)
BUG FIXES
Changes in version 1.5.1:
BUG FIXES
BUG FIXES
BUG FIXES
BUG FIXES
BUG FIXES
Changes in version 1.3.1:
Changes in version 1.3.0:
Changes in version 3.11.10:
Changes in version 3.11.9:
Changes in version 3.11.8:
Changes in version 3.11.7:
Changes in version 3.11.6:
Changes in version 3.11.5:
Changes in version 3.11.4:
update variant calling code to work with VariantTools 1.3.6
include Jens’ minlength=1 modification to handle reads fully trimmed
Changes in version 3.11.3:
exports loginfo, logdebug, logwarn, logerror
uses TallyVariantsParam and as(,”VRanges”) to fix a bug preventing compilation on BioC
the number of threads used during processChunks is divided by 2 due to an erroneous extra mcparallel(…) step in sclapply/safeExecute
use a maximum of 12 cores in preprocessReads
Changes in version 3.11.2:
Changes in version 3.11.1:
Changes in version 3.11.0:
Changes in version 3.10.1:
Changes in version 1.7.1:
Changes in version 1.0.1:
Changes in version 1.13.1:
Node labels were ignoring the ‘cex’ node data value (reported by Hannes Hettling)
Added “start” and “both” options for “arrowLoc” graph attribute (which will draw arrowhead at both ends of hyper edges)
Bug fix for converting Hypergraph to graphBPH so that hyperedge names are used as edge labels (reported by Hannes Hettling)
Update the R version check in drawEdge() to cope properly with major versions greater than 2 (!)
Changes in version 0.3.9:
Changes in version 0.3.8:
Changes in version 0.3.6:
Changes in version 0.3.5 (2013-08-02):
Cleaned up internal code of readBPM().
ROBUSTNESS: Added unit tests for readBPM(). Note that these are only run if environment variable ‘R_CHECK_FULL’ is set, i.e. they will not be perfomed on the Bioconductor servers.
Changes in version 1.12.0:
NEW FEATURES
SIGNIFICANT USER-VISIBLE CHANGES
Changes in version 0.99.3:
Notes
Notes
Changes in version 1.5.2:
09-29-2010:
01-12-2011:
01-17-2012:
Changes in version 1.20.0:
NEW FEATURES
Add IntervalForest class from Hector Corrada Bravo.
Add a FilterMatrix class, for holding the results of multiple filters.
Add selfmatch() as a faster equivalent of ‘match(x, x)’.
Add “c” method for Views objects (only combine objects with same subject).
Add coercion from SimpleRangesList to SimpleIRangesList.
Add an %outside%
that is the opposite of %over%
.
Add validation of length() and names() of Vector objects.
Add “duplicated” and “table” methods for Vector objects.
Add some split methods that dispatch to splitAsList() even when only ‘f’ is a Vector.
SIGNIFICANT USER-VISIBLE CHANGES
All functionalities related to XVector objects have been moved to the new XVector package.
Refine how isDisjoint() handles empty ranges.
Remove ‘keepLength’ argument from “window<-“ methods.
unlist( , use.names=FALSE) on a CompressedSplitDataFrameList object now preserves the rownames of the list elements, which is more consistent with what unlist() does on other CompressedList objects.
Splitting a list by a Vector just yields a list, not a List.
The rbind,DataFrame method now handles the case where Rle and vector columns need to be combined (assuming an equivalence between Rle and vector). Also the way the result DataFrame is constructed was changed (avoids undesirable coercions and should be faster).
as.data.frame.DataFrame now passes ‘stringsAsFactors=FALSE’ and ‘check.names=!optional’ to the underlying data.frame() call. as(x,”DataFrame”) sets ‘optional=TRUE’ when delegating. Most places where we called as.data.frame(), we now call ‘as(x,”data.frame”)’.
The [<-,DataFrame method now coerces column sub-replacement value to class of column when the column already exists.
DataFrame() now automatically derives rownames (from the first argument that has some). This is a fairly significant change in behavior, but it probably does better match user behavior.
Make sure that SimpleList objects are coerced to a DataFrame with a single column. The automatic coecion methods created by the methods package were trying to create a DataFrame with one column per element, because DataFrame extends SimpleList.
Change default to ‘compress=TRUE’ for RleList() constructor.
tapply() now handles the case where only INDEX is a Vector (e.g. an Rle object).
Speedup coverage() in the “tiling case” (i.e. when ‘x’ is a tiling of the [1, width] interval). This makes it much faster to turn into an Rle a coverage loaded from a BigWig, WIG or BED as a GRanges object.
Allow logical Rle return values from filter rules.
FilterRules no longer requires its elements to be named.
The select,Vector method now returns a DataFrame even when a single column is selected.
Move is.unsorted() generic to BiocGenerics.
DEPRECATED AND DEFUNCT
Deprecate seqselect() and subsetByRanges().
Deprecate ‘match.if.overlap’ arg of “match” method for Ranges objects.
“match” and “%in%” methods that operate on Views, ViewsList, RangesList, or RangedData objects (20 methods in total) are now defunct.
Remove previously defunct tofactor().
BUG FIXES
The subsetting code for Vector derivatives was substancially refactored. As a consequence, it’s now cleaner, simpler, and [ and [[ behave more consistently across Vector derivatives. Some obscure long-standing bugs have been eliminated and the code can be slightly faster in some circumstances.
Fix bug in findOverlaps(); zero-width ranges in the query no longer produce hits ever (regardless of ‘maxgap’ and ‘minoverlap’ values).
Correctly free memory allocated for linked list of results compiled for findOverlap(select=”all”).
Various fixes for AsIs and DataFrames.
Allow zero-row replacement values in [<-,DataFrame.
Fix long standing segfault in “[” method for Rle objects (when doing Rle()[0]).
“show” methods now display its most specific class when a column or slot is an S3 object for which class() returns more than one class.
“show” methods now display properly cells that are arrays.
Fix the [<-,DataFrame method for when a value DataFrame has matrix columns.
Fix ifelse() for when one or more of the arguments are Rle objects.
Fix coercion from SimpleList to CompressedList via AtomicList constructors.
Make “show” methods robust to “showHeadLines” and “showTailLines” global options set to NA, Inf or non-integer values.
Fix error condition in eval,FilterRules method.
Corrected an error formatting in eval,FilterRules,ANY method.
Changes in version 1.7.6:
added TMT 10plex (contribution from Florent Gluck)
fixed bugs with system.file not working on R < 2.11 (contribution from Florent Gluck)
fixed bug in isobar-qc which was not working without normalize=TRUE
added writeHscoreData for usage with Hscorer.py (MM Savitski, 2010)
shQuote commands correctly - should fix issues running report generation on Windows
added calculations and XLS tab for peptides with unsure localization of the modification site
updated scripts for creating multi-sample reports (create.meta.reports)
Changes in version 1.7.5:
fixed critical bugs: Excel report output had wrong ordering, ie ratios did not correspond to the meta information [introduced in version 1.7.3].
fix of real peptide names: Reexport I/L peptides in reports
Changes in version 1.7.4:
improved MSGF+ search result import
refactored report properties: all properties can now be defined in in the properties.R
speed and memory usage improvements when creating wide XLS report
ratio p-value adjustment now works per comparision instead of globally
Changes in version 1.7.3:
fix wide XLS report format
novel plot for ratio combinations in QC report showing individual ratio distributions and significant ratios
Changes in version 1.7.2:
added TMT 6plex masses to phosphoRS export script
fixed mascot parsers
MzIdentML version 1.1.0 support implemented [not fully tested]
Changes in version 1.7.1:
Changes in version 1.3.1:
BUGS FIXED
Changes in version 1.3.0:
MINOR CHANGES
Changes in version 2013-07-03 (2013-07-03):
Replaced calls to ‘exit’, ‘fprintf’ which now raise a WARNING upon check.
Iteration index not printed anymore in ‘nem’ (raised an error when compiling the vignette).
Changes in version 2011-03-18 (2011-03-18):
Changes in version 2010-10-01 (2010-10-01):
Cleaned ‘data/flags.RData” which contained objects from an old ‘globalenv’.
Updated maintainer’s email address.
Changes in version 2010-01-24 (2010-01-24):
Changes in version 2009-01-15 (2009-01-15):
Changes in version 2009-01-13 (2009-01-13):
updated references in .Rd files.
fixed warnings due to incorrect use of \item in .Rd files.
Changes in version 2009-01-06 (2009-01-06):
Changes in version 2009-01-04 (2009-01-04):
(almost) one file per function in R/
removed empty section \details in man/qscore.Rd
added a NAMESPACE
removed inst/doc/Makefile (not needed anymore because no html output required)
Changes in version 2009-01-02 (2009-01-02):
Changes in version 2009-01-01 (2009-01-01):
Changes in version 2008-12-31 (2008-12-31):
now use standard “keyword”s
changed \link{\code{stuff}} into \code{\link{stuff}}
Changes in version 2008-11-26 (2008-11-26):
filled in “keyword” sections in .Rd files.
removed empty “examples” sections from .Rd files.
initialized a few variables upon declaration in C code to prevent warnings in R CMD CHECK.
Changes in version 2008-09-23 (2008-09-23):
modification de la fonction cv pour retourner NA lorsque toutes la valeurs du vecteur sont <e0> NA
modification de la function getChromosomeArm pour que cytoband ne soit pas positionn<e9>e <e0> NULL
Changes in version 2008-09-04 (2008-09-04):
added a CHANGELOG
updated outdated reference in the .bib file
changed the definition of flag “rep.flag” to avoid the error now caused by sd(NA, na.rm=TRUE)
Changes in version 1.2 (2013-08-20):
Our paper got accepted and is available!
Added methods for MRexperiment objects (colSums,colMeans,rowSums,rowMeans, usage is for example colSums(obj) or colSums(obj,norm=TRUE)) (09-25)
Added two new functions, plotOrd and plotRare - a function to plot PCA/MDS coordinates and rarefaction effect (09-04,09-18)
Updated MRfisher to include thresholding for presence-absence testing (08-19)
Updated comments (roxygen2) style for all the functions using the Rd2roxygen package (07-13)
Updated plotCorr and plotMRheatmap to allow various colors/not require trials(07-13)
Rewrote vignette (and switched to knitr)
Changes in version 1.1 (2013-06-25):
Rewrote load_meta and load_metaQ to be faster/use less memory
Modified cumNormStat to remove NA samples from calculations (example would be samples without any counts)
Re-added plotGenus’ jitter
Fixed uniqueNames call in the MR tables
Changed thanks to Kasper Daniel Hansen’s suggestions the following: plotOTU and plotGenus both have much better auto-generated axis MRtable, MRfulltable, MRcoefs have a sort by p-value option now MRtable, MRfulltable, MRcoefs now have an extra option to include unique numbers for OTU features (default would automatically add them previously) cumNorm.R - now returns the object as well - not just replacing the environment 0 Still need to turn the fitZig output to S3, consider subsetting function address low p-values
Changes in version 1.7:
Added getMethSignal(), a convenience function for programming.
Changed the argument name of “type” to “what” for getMethSignal().
Added the class “RatioSet”, like “GenomicRatioSet” but without the genome information.
Bugfixes to the “GenomicRatioSet()” constructor.
Added the method ratioConvert(), for converting a “MethylSet” to a “RatioSet” or a “GenomicMethylSet” to a “GenomicRatioSet”.
Fixed an issue with GenomicMethylSet() and GenomicRatioSet() caused by a recent change to a non-exported function in the GenomicRanges package (Reported by Gustavo Fernandez Bayon gbayon@gmail.com).
Added fixMethOutliers for thresholding extreme observations in the [un]methylation channels.
Added getSex, addSex, plotSex for estimating sex of the samples.
Added getQC, addQC, plotQC for a very simple quality control measure.
Added minfiQC for a one-stop function for quality control measures.
Changed some verbose=TRUE output in various functions.
Added preprocessQuantile.
Added bumphunter method for “GenomicRatioSet”.
Handling signed zero in minfi:::.digestMatrix which caused unit tests to fail on Windows.
addSex and addQC lead to sampleNames() being dropped because of a likely bug in cbind(DataFrame, DataFrame). Work-around has been implemented.
Re-ran the test data generator.
Fixed some Depends and Imports issues revealed by new features of R CMD check.
Added blockFinder and cpgCollapse.
(internal) added convenience functions for argument checking.
Exposed and re-wrote getAnnotation().
Changed getLocations() from being a method to a simple function. Arguments have been removed (for example, now the function always drops non-mapping loci).
Implemented getIslandStatus(), getProbeType(), getSnpInfo() and addSnpInfo(). The two later functions retrieve pre-computed SNP overlaps, and the new annotation object includes SNPs based on dbSNP 137, 135 and 132.
Changed the IlluminaMethylatioAnnotation class to now include genomeBuild information as well as defaults.
Added estimateCellCounts for deconvolution of cell types in whole blood. Thanks to Andrew Jaffe and Andres Houseman.
Changes in version 0.99.6:
Changes in version 0.99.5:
Changes in version 0.99.2:
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
BUG FIXES
Changes in version 1.5.1:
NEW FEATURES
BUG FIXES
Changes in version 1.9.12:
fix MSnSet -> ExpressionSet <2013-10-13 Sun>
MSnSet -> ExpressionSet unit test <2013-10-13 Sun>
Changes in version 1.9.11:
MIAPE to MIAME conversion <2013-10-11 Fri>
proper MIAME when MSnSet -> ExpressionSet <2013-10-11 Fri>
Changes in version 1.9.10:
faster plotMzDelta <2013-09-28 Sat>
faster plotMzDelta for mzRramp instances <2013-09-29 Sun>
chromatogram method <2013-10-04 Fri>
plotMzDelta has subset arg <2013-10-04 Fri>
xic method <2013-10-04 Fri>
suggesting msdata for chromatogram example <2013-10-04 Fri>
renamed plotting arg ‘centroided.’ <2013-10-04 Fri>
Changes in version 1.9.9:
typo in filterNA Rd <2013-09-18 Wed>
writeMgfData now has a progress bar <2013-09-24 Tue>
centroided(MSnExp) <- TRUE now allowed <2013-09-24 Tue>
Changes in version 1.9.8:
using new.env(parent=emptyenv()) to get rid of enclosing env when creating new MSnExps <2013-09-17 Tue>
new (private) MSnExp.size function <2013-09-17 Tue>
Changes in version 1.9.7:
Passing … to read.table in MSnbase:::readIspy[Silac|15N]Data <2013-09-16 Mon>
QualityControl biocView <2013-09-16 Mon>
Changes in version 1.9.6:
new as.data.frame.MSnSet method <2013-08-16 Fri>
new ms2df function <2013-08-16 Fri>
new getEcols and grepEcols helpers for readMSnSet2 <2013-08-16 Fri>
Changes in version 1.9.5:
Changes in version 1.9.4:
Changes in version 1.9.3:
Using knitr as VignetteEngine <2013-04-29 Mon>
Remove LazyLoad from DESCRIPTION, which is default nowadays <2013-04-29 Mon>
knitr dependency > 1.1.0 for VignetteBuilder <2013-04-29 Mon>
Adding MSnSet creating sections in io vignette <2013-04-29 Mon>
new readMSnSet2 function <2013-04-30 Tue>
Changes in version 1.9.2:
clean has now a all param (default FALSE is retain original behavious) to remove all 0 intensity values <2013-04-17 Wed>
using BiocGenerics::normalize <2013-04-25 Thu>
Changes in version 1.9.1:
new logging utility function to update an MSnSet’s processingData(object)$processing <2013-03-29 Fri>
Proper logging in t.MSnSet <2013-03-29 Fri>
Changes in version 1.9.0:
Changes in version 1.99.1:
fixed several NOTES, added .Rbuildignore, compacted vignettes
TODO: check remaining ‘no visible binding for global variable’ NOTES
removed warn -1
added validity check when returning MSnSet
used inherits/is. for class testing
TODO fix if conditions syntax
Changes in version 1.99.0:
improve efficiency for computing groupComparison and quantification <2012-12-21>
add .rnw <2012-12-03>
update groupComparision for label-free time-course experiment with single Feature and with or without technical replicates <2013-04-08>
add option for saving QQ plot and Residual plot in order to checkin the normality assumption in groupComparison function. <2013-04-08>
use ggplot2 package for all plots. <2013-07-11>
fix bug for volcano plot : different color labeling <2013-07-12>
add power plot in sample size calculation plot <2013-07-12>
add ‘interference=TRUE or FALSE’ in sample size calculation <2013-07-15>
add ‘legend.size=7’for size of feature name legends in dataProcessPlots <2013-07-23>
add ‘text.angle=0’for angle of condition labeling in dataProcessPlots <2013-07-23>
fix bug for quantification : when there are missing values in endogenous intensities, but values in reference intensities. <2013-07-24>
fix bug for groupComparison : when there are missing values in endogenous intensities, but values in reference intensities, .make.constast.based or .free sub function were changed. <2013-07-25>
two function for transformation between required input for MSstats and MSnSet class <2013-09-04>
flexibility for visualization : save as pdf files or show in window with selected proteins or all proteins. <2013-09-04>
handle unequal variance for feature in groupComparison function with featureVar=TRUE <2013-09-04>
Add ‘missing.action’ for impute missing values in group comparison stage. <2013-09-20>
Changes in version 0.3.1:
Comment unused functions <2013-07-05 Fri>
Minor typos in vignette <2013-07-05 Fri>
Changes in version 0.3.0:
NEW FEATURES AND FUNCTIONS
Changes in version 0.2.1:
NEW FEATURES AND FUNCTIONS
NEW FEATURES AND FUNCTIONS
NEW FEATURES AND FUNCTIONS
Changes in version 0.1-1:
NEW FEATURES AND FUNCTIONS
flatten
to create tabular representation of resultsChanges in version 0.0-2:
NEW FEATURES AND FUNCTIONS
The package is now fully documented
created helper functions: countChildren
, attrExtract
and
attrExtractNameValuePair
Added NEWS file
Added README.md file
The parser now succesfully imports all test files on the HUPO mzIdentML page
PERFORMANCE
countChildren
, attrExtract
and attrExtractNameValuePair
)Changes in version 0.0-1:
NEW FEATURES AND FUNCTIONS
NEW FEATURES AND FUNCTIONS
mzID
, mzIDdatabase
, mzIDevidence
,
mzIDparameters
, mzIDpeptides
and mzIDpsm
with related
constructorsChanges in version 1.7.4:
Changes in version 1.7.3:
Changes in version 1.7.2:
Changes in version 1.7.1:
Changes in version 2.2.0 (2013-10-14):
New function to generate a Quality Control Report in PDF format including all the exploratory plots.
Plot to evaluate RNA composition bias has been changed.
Some bugs have been fixed.
Changes in version 1.8.1:
BUG FIXES
NEW FUNCTION
Changes in version 1.1.7:
Graphviz view can automatic choose different types of legends, either on nodes, edges or both depending on the specific pathways.
Vigette has been reformatted: the “Quick start” section added
Changes in version 1.1.6:
Pathview can plot/integrate/compare multiple states/samples in the same graph. Several functions and data objects are revised: including pathview, keggview.native, keggview.graph, render.kegg.node etc. New section on multiple state data with working exampleshas been added.
Vigette has been reformatted: Data integration section splitted into multiple sub-sections.
Changes in version 1.1.5:
Changes in version 1.1.3:
Changes in version 1.2.0:
NEW FEATURES
Added argument ncpus to runGSA(). Enables parts of this function to run in parallel, thus decreasing runtime. Requires R package snowfall.
Added function runGSAhyper() to perform gene set analysis using Fisher’s exact test, as an alternative to runGSA.
Added information about genes in each area of the Venn diagram in the output of diffExp().
Added volcano plot as optional output of diffExp() and added argument volcanoFC.
Added argument ncharLabel to networkPlot() and consensusHeatmap() to control the length of the labels in the plots and add the option to not truncate them.
Added the yeast metabolic model iTO977 to be loaded with loadGSC(), for detecting reporter metabolites using gene set analysis. (See vignette.)
Added support for running networkPlot() on objects returned by runGSAhyper().
USER-VISIBLE CHANGES
Minor updates to the vignette.
Updated diffExp() man page.
Updated the main legend of the plot from consensusScores() to make it clearer.
Updated error-messages in networkPlot().
Fixed typo in PC variance plot produced by runQC().
Restructered this NEWS file.
BUG FIXES
Updated diffExp() to handle changes in lmFit() and topTable() from limma.
Removed suppressWarnings(), as temporarily introduced in version 1.0.1, in polarPlot() around the calls to radial.plot() since warnings are now fixed in package plotrix.
Changes in version 1.0.7:
USER-VISIBLE CHANGES
Changes in version 1.0.6:
USER-VISIBLE CHANGES
Changes in version 1.0.5:
BUG FIXES
USER-VISIBLE CHANGES
Changes in version 1.0.4:
BUG FIXES
Changes in version 1.0.3:
USER-VISIBLE CHANGES
Changes in version 1.0.2:
USER-VISIBLE CHANGES
Changes in version 1.0.1:
USER-VISIBLE CHANGES
Updated CITATION information.
Fixed typos in DESCRIPTION and piano-package.Rd.
Updated the man file for loadGSC().
Added URL in DESCRIPTION.
BUG FIXES
Fixed bug in loadGSC() so that gmt-files are now loaded correctly.
Temporarily added suppressWarnings() in polarPlot() around the calls to radial.plot() since warnings appeared for example(“radial.plot”) in plotrix v3.4-6.
Changes in version 0.99.4:
SIGNIFICANT USER-VISIBLE CHANGES
NEW FEATURES
Changes in version 1.33.1:
Changes in version 0.99.2:
Changes in version 0.99.1:
Major update … moved to S4 methods (getters, setters, setMethods, etc).
Smaller sample data set for quick example runs in the man pages.
Integration with the MSnbase package. See the vignette for an example of raw data processing in preparation for network building. The main buildProconaNetwork function now takes either matrices of peptide data, or MSnSet objects containing data.
Man pages relating to the main proconaNet object have been combined.
Changes in version 1.1.8:
Changes in version 1.1.7:
Changes in version 1.1.6:
new outliers arg to plot2D <2013-09-23 Mon>
cite addMarkers in vignette <2013-09-26 Thu>
add code chunk in poster vig <2013-09-26 Thu>
Changes in version 1.1.5:
added biocViews <2013-09-19 Thu>
added knitr vig engine in ml <2013-09-19 Thu>
import dependencies <2013-09-20 Fri>
Changes in version 1.1.4:
Changes in version 1.1.3:
new private anyUnknown function, used in phenoDisco, to check for the presence of unlabelled (‘unknown’) data <2013-08-27 Tue>
added a note in vignette about “unknown” convention to define protein with unknown localisation <2013-08-28 Wed>
Added HUPO 2011 poster <2013-09-09 Mon>
Changes in version 1.1.2:
fixed Author[s]@R <2013-05-16 Thu>
na.rm=TRUE in f1Count <2013-05-19 Sun>
added CITATION file <2013-06-07 Fri>
new testMarkers function <2013-06-29 Sat>
error message in getBestParams suggests to use testMarkers <2013-06-29 Sat>
nndist methods (see issue #23) <2013-07-01 Mon>
remove unnecessary as.matrix in plot2D’s cmdscale <2013-07-19 Fri>
added plot2D(…, method = “MDS”) example <2013-07-19 Fri>
changed ‘euclidian’ to ‘euclidean’ in nndist_matrix <2013-07-26 Fri>
fixed row ordering in phenoDisco, input and output rownames are now the same <2013-08-13 Tue>
Using filterNA in phenoDisco <2013-08-13 Tue>
Changes in version 1.1.1:
Update README.md to reflect availability in stable release and biocLite installation <2013-04-07 Sun>
new MSe pipeline <2013-04-07 Sun>
perTurbo using Rcpp <2013-04-16 Tue>
initial clustering infrastructure (not exported) <2013-04-17 Wed>
new markerSet function <2013-04-24 Wed>
plsaOptim’s ncomp is now 2:6 <2013-04-27 Sat>
added forword to vignette <2013-04-29 Mon>
default k is now seq(3, 15, 2) in knnOptim <2013-05-09 Thu>
Changes in version 1.1.0:
Changes in version 2.4.4:
Changes in version 2.4.2:
Changes in version 2.4.0:
Major update with more functions and small bugfixes
Added sequenceReport() and groupReport() for easier report generation
Visualise motif scores along a sequence with plotMotifScores()
Creation of empirical CDFs for motif scores
Almost complete rewrite of the vignette to emphasize the main use cases
Converted documenation to roxygen2
Changes in version 2.3.2:
Changes in version 2.3.1:
Fix a bug with plotTopMotifsSequence() with calling an unknown function
Implement group.only for all background, not only pval in motifEnrichment()
New default to plotMultipleMotifs() so the margins are better
Changes in version 0.99.3:
fixed template - toc after begin document <2013-10-01 Tue>
updates to vignette <2013-10-01 Tue>
re-reoxygenise rnadeg man <2013-10-01 Tue>
Changes in version 0.99.2:
Changes in version 0.99.1:
Updated github README file <2013-09-18 Wed>
Added Arnoud’s suggestions to vig <2013-09-21 Sat>
rnadeg wrapper function available in the package <2013-09-21 Sat>
new QcMetadata class <2013-09-21 Sat>
metadata and mdata synonym <2013-09-21 Sat>
added metadata section in knitr reports <2013-09-21 Sat>
selectively import pander::pander.table to fix warning uppon installation <2013-09-21 Sat>
added n15qc wrapper <2013-09-21 Sat>
Changes in version 0.99.0:
Changes in version 1.18:
USER VISIBLE CHANGES
Updated the formatting of the vignettes to adhere to the Bioconductor style
Functions qpRndHMGM() and qpSampleFromHMGM() which were deprecated in the previous release, are now defunct.
NEW FEATURES
qpCItest() takes now also R/qtl cross objects as input, i.e., the user can test for conditional independence directly on R/qtl cross objects
added functions addGenes(), addeQTL(), and addGeneAssociation() to incrementally build and simulate eQTL networks
BUG FIXES
Real or integer valued levels in discrete variables now prompt an error when they are not positive integers
qpFunctionalCoherence() handles regulatory modules with just one target without giving an error
reQTLcross() can now simulate an initial eQTL model with no genes
fixed plotting for HMgmm objects
Changes in version 1.2.0:
NEW FEATURES
NEW FEATURES
NEW FEATURES
Changes in version 1.1.1:
NEW FEATURES
2.0:
Changes in version 0.99.1:
MINOR CHANGES
dontrun
tags have been removed from plotting examples (Thanks to
Valerie Obenchain).Changes in version 0.99.0:
DOCUMENTATION
NEWS
file was added.Changes in version 1.5.3:
Changes in version 1.5.2:
implement gseAnalyzer for GSEA analysis <2013-07-10, Wed>
implement viewPathway for visualizing pathway <2013-07-10, Wed>
Changes in version 1.5.1:
extend enrichPathway to support rat, mouse, celegans, zebrafish, and fly. <2013-03-27, Wed>
modify enrichPathway according to the change of enrich.internal, remove qvalueCutoff parameter, add pAdjustMethod, add universe paramter for user to specify background. <2013-05-29, Wed>
Changes in version 2.0.0:
Changes in version 2013-4-1:
HTML reports are now represented by the HTMLReportRef referenceClass
HTML output now fully customizable via .toHTML, .toDF and .modifyDF arguments to publish (see vignette)
Publication mechanism is abstracted and customizable via ReportHandlers class
ReportingTools output can be used within knitr documents and shiny Web applications (see vignettes knitr.Rmd and shiny.Rnw)
Persistent representation of the HTML report being created is stored and accessible in the .reportDOM field of HTMLReportRef objects
[[ and [[<- methods created for HTMLReportRef objects which allow selection, replacement and insertion of objects directly into reports
Publish generic now accepts a ‘name’ argument.
Existing reports can be read in via readReport, modified (via publish, [[<-, or direct manipulation of .reportDOM), and rewritten to file
Path generic now returns a list/vector of the location slot values of the attached ReportHandlers object(s). These can be paths, connections, or other indications of report destination.
Link generic function provided to build tables/sets of HTML links
Added support for publishing ggbio and recordedplot objects
CSS changed to Twitter Bootstrap
Bugfixes to how NAs are handled when filtering and sorting columns
New methods to handle output from running a glmLRT test in edgeR or nbinomTest in DESeq
DEPRECATED: HTMLReport class is superseded by HTMLReportRef
DEPRECATED: publication of HTMLReportRefs directly to a report (in order to make an index page) is no longer supported. Use the Link function.
DEPRECATED: the page generic is not meaningful for HTMLReportRef objects (not all of which have a corresponding connection) and is deprecated. Use path instead.
Changes in version 2.5:
Expose mai argument in plot,Ragraph-method.
Changed the LICENSE to EPL.
Fixed some wrong text in the DESCRIPTION file.
Fixed pieGylph to adress the issue of warning messages about rep(NULL) (reported by Cristobal Fresno Rodríguez Cristobalfresno@gmail.com).
Updated Imports, Depends, NAMESPACE as per R CMD check requirements.
Fixing issue with the lt~obsolete.m4 file(s) in Graphviz; R CMD check was issueing a warning.
Moved vignettes from inst/doc to vignettes directory.
Changes in version 2.6.0:
NEW FEATURES
support for logical added
support for reading attributes added (use read.attributes=TRUE)
enabeled compression for data.frame in h5write
USER VISIBLE CHANGES
1.3.3: 1. Fixed definitions of assay.filenames.per.sample and factors. 2. Fixed regulession of investigation file (i_) to be considered at the beginning of the string. 3. Added CITATION file.
Changes in version 1.0.1:
Changes in version 1.3.2:
Changes in version 1.3.1:
Changes in version 1.3.0:
Changes in version 1.2.0:
add the ability to analyze gene sets (pathways with no interaction) using only over-representation
bug fixes: plot boundaries, etc.
Changes in version 1.8.1 (2011-08-02):
Changes in version 1.8.0 (2011-07-11):
Changes in version 1.14.0:
NEW FEATURES
seqinfo(FaFile) returns available information on sequences and lengths on Fa (indexed fasta) files.
filterBam accepts FilterRules call-backs for arbitrary filtering.
add isIncomplete,BamFile-method to test for end-of-file
add count.mapped.reads to summarizeOverlaps,*,BamFileList-method; set to TRUE to collect read and nucleotide counts via countBam.
add summarizeOverlaps,*,character-method to count simple file paths
add sequenceLayer() and stackStringsFromBam()
add ‘with.which_label’ arg to readGAlignmentsFromBam(), readGappedReadsFromBam(), readGAlignmentPairsFromBam(), and readGAlignmentsListFromBam()
SIGNIFICANT USER-VISIBLE CHANGES
rename: readBamGappedAlignments() -> readGAlignmentsFromBam() readBamGappedReads() -> readGappedReadsFromBam() readBamGappedAlignmentPairs() -> readGAlignmentPairsFromBam() readBamGAlignmentsList() -> readGAlignmentsListFromBam() makeGappedAlignmentPairs() -> makeGAlignmentPairs()
speedup findMateAlignment()
DEPRECATED AND DEFUNCT
BUG FIXES
scanVcfHeader tolerates records without ID fields, and with fields named similar to ID.
close razip files only once.
report tabix input errors
Changes in version 1.12.0:
NEW FEATURES
NEW FEATURES
NEW FEATURES
NEW FEATURES
NEW FEATURES
NEW FEATURES
NEW FEATURES
NEW FEATURES
NEW FEATURES
Changes in version 1.1.6:
NEW FEATURES
Changes in version 1.1.5:
BUG FIXES
NEW FEATURES
Changes in version 1.1.4:
NEW FEATURES
BUG FIXES
Corrected a bug that prevented the use of multi-threading
Corrected a bug that could affect results when multiple fasta files are assigned to a same taxon.
Changes in version 2009-07-13:
combineRTCA(list): Additional column is renamed into Plate. The vlues is evaluated from list item names. When the list has no name, an integer index beginning from 1 is used. Special attentions to list partially with names is noted in the documentation.
parseRTCA(file, dec=”.”,phenoData, skipWell,…): Example is added in the documentation how to import pre-configured phenoData. Details section in the documentation is re-written to describe the process of parsing.
RTCA-class: Experiment ID added to RTCA class
Makefile: add Makefile to simplify common tasks like check and install
plotGridEffect: takes ‘column’ instead of ‘col’ as mode parameter, and renders the mode as the title of the legend. Documentation updated.
plotRTCA: is removed from the package and is substituted by the plot function.
Changes in version 1.0.0:
Changes in version 1.22:
NEW FEATURES
import,BigWigFile gains an asRle parameter that returns the data as an RleList (assuming it tiles the sequence); much faster than importing a GRanges and calling coverage() on it.
add export,RleList,BigWigFile method for direct (and much more efficient) output of RleLists (like coverage) to BigWig files.
SIGNIFICANT USER-VISIBLE CHANGES
BUG FIXES
handle different Set-Cookie header field casing; often due to proxies (thanks to Altuna Akalin)
attempt to more gracefully handle UCSC truncation of large data downloads
handle re-directs due to UCSC mirroring (thanks Martin Morgan)
Changes in version 1.0:
First release in Bioconductor.
Integration with Bioconductor packages: MotifDb and PWMEnrich, graph (limited).
Human and mouse BioGRID datasets updated to version 3.2.105 (October 2013).
Changes in version 1.0:
First Bioconductor release.
Provides a shiny interface to rTRM.
All options available in rTRM can be accesses from rTRMui.
Several utilities to control network appearance (node, edge and label size, etc.)
Download results in PDF and text format.
Changes in version 1.57.1:
NEW FEATURES
Added new function S4toS3() for converting S4 SBML models of rsbml into S3 SBMLR models.
Includes code from Vishak Venkateswaran’s branch of SBMLR on github (July 2011). This is may allow it to read more models in http://www.ebi.ac.uk/biomodels-main/ I say may because I don’t fully understand all of his codes, but add it in anyway.
Problem of libsbml allowing multiple args to multiplication operator was solved by using prod(). Similarly for sum(). Note that “*”() is strictly a binary operator.
SIGNIFICANT USER-LEVEL CHANGES
Call my model object call SBMLR now to let SBML refer to rsbml’s SBML object. Similary my simulate() is now sim() to keep it clear of rsbml’s simulate().
SBMLR model files no longer need to have the reversible flag set. The default is FALSE, which is the opposite of Level 2: all of my reaction rate laws have always been positive, and a design objective I like is to keep SBMLR model files as lean as possible (subject to the constraint that they be valid R code).
Simulate handles lsoda() event dataframes, see simulate help.
curtoNatural.R (see Fig. 7 BMC Bioinformatics 2004, 5:190) is now in the models folder.
The SOD model of Kowald et al, JTB 238 (2006) 828–840 is now also in this folder.
Two pdfs of publications that are freely available were removed to make the package lighter.
Similarly, only manual.doc remains: its redundant pdf is now out.
Notes
Changes in version 2.2.8:
NEW FEATURES
Ability to download microarray data directly from Gene Expression Omnibus and normalize the files in a single command.
Alternate functions (SCANfast and UPCfast) for performing SCAN and UPC normalization that use fewer probes and thus execute in ~60% less time.
Ability to execute normalize multiple .CEL files in parallel either across multiple cores on a single computer or across multiple computers on a cluster.
Ability to generate RNA-Seq annotation files to be used with the UPC_RNASeq function from GTF/FASTA source files.
Ability to download and install BrainArray packages via an R function.
Improved support for Affymetrix exon arrays.
Improved support for Affymetrix HT_HG-U133A early access exon arrays.
OTHER
Changes in version 1.1.5:
minor bug fix in asVCF
update man page “SeqVarGDSClass-class.Rd” with new methods
in DESCRIPTION, BiocGenerics listed in “Suggests” instead of “Imports” as suggested by R CMD check
bug fix in seqDelete
revise the function ‘seqTranspose’ according to the update of gdsfmt (v1.0.0)
Changes in version 1.1.4:
add a new argument “action” to the function ‘seqSetFilter’
add a new function ‘seqInfoNewVar’ which allows adding new variables to the INFO fields
Changes in version 1.1.3:
minor bug fix to avoid ‘seqGetData’ crashing when no value returned from a variable-length variable
update documents
Changes in version 1.1.2:
added methods ‘qual’, ‘filt’, ‘asVCF’
‘granges’ method uses length of reference allele to set width
Changes in version 1.1.1:
revise the argument ‘var.index’ in the function ‘seqApply’
basic supports of ‘GRanges’ and ‘DNAStringSetList’
Changes in version 1.1.5 (2013-09-01):
Added an all-in function runSeqGSEA() for one step analysis
Modified genpermuteMat() with invoking set.seed() for reproducibility
Vignette updated
Changes in version 1.1.4 (2013-08-10):
Updated functions to allow DE-only GSEA analysis.
Fixed a few bugs.
Vignette updated.
Changes in version 1.1.3 (2013-06-13):
Changes in version 1.1.2 (2013-05-01):
Changes in version 1.1.1 (2013-04-23):
The methodology paper of the SeqGSEA package published at BMC Bioinformatics (2013, 14(Suppl 5):S16).
Added a function writeScores to generate DE/DS and gene scores output.
Changes in version 0.99.1:
NEW FEATURES
Changes in version 0.99.0:
Changes in version 1.19:
SIGNIFICANT USER-VISIBLE CHANGES
NEW FEATURES
encoding,FastqQuality and encoding,SFastqQuality provide a convenient map between letter encodings and their corresponding integer quality values.
filterFastq transforms one fastq file to another, removing reads or nucleotides via a user-specified function. trimEnds,character-method & friends use this for an easy way to remove low-quality base.
BUG FIXES
writeFastq successfully writes zero-length fastq files.
FastqStreamer / FastqSampler warn on incomplete (corrupt) files
Changes in version 0.99.0:
First release of the SpacePAC package.
Two 3D clustering methods: Using a Simulation approach and using a Poisson approach.
Allows a rudimentary plotting function to visualize the most significant cluster. Currently only one sphere can be plotted at a time.
Changes in version 1.0.0:
Changes in version 1.0.0:
NEW FEATURES
NEW FEATURES
NEW FEATURES
Changes in version 1.3.4:
estimateMasterFdr now support list of vector as pepfiles <2013-09-27 Fri>
import(MSnbase) <2013-09-27 Fri>
Changes in version 1.3.3:
Changes in version 1.3.2:
Changes in version 1.3.1:
Reporting total number of peptides in dbUniquePeptideSet. Fixes issue #41. <2013-05-13 Mon>
New mergedEMRTs arg in findEMRTs. Closes issue #38. <2013-05-13 Mon>
fixed synapterTiny$QuantPep3DData, which had the rownames as first column synapterTiny$QuantPep3DData$X. Detected thanks to new mergedEMRTs arg. <2013-05-13 Mon>
added mergedEMRTs arg to synergise <2013-05-22 Wed>
Synapter checks that one file per list element is passed <2013-05-28 Tue>
minor typo/fixes <2013-05-28 Tue>
new idSource column when matching EMRTs <2013-05-29 Wed>
new performance2 method that shows identification source and NA values contingency table <2013-05-29 Wed>
new filterPeptideLength method <2013-05-29 Wed>
added peplen argument to synergise to filter on peptide length <2013-05-29 Wed>
Changes in version 1.3.0:
Changes in version 1.18.0:
NEW FEATURES
NEW FEATURES
NEW FEATURES
Changes in version 1.2.0:
NEW FEATURES
This package was released as a Bioconductor package (previously CRAN).
WAD method for identifying DEGs was added.
ROKU method for identifying tissue-specific genes was added.
‘increment’ argument of ‘calcNormFactor’ function was added.
SIGNIFICANT USER-VISIBLE CHANGES
Changes in version 1.1.3:
SIGNIFICANT USER-VISIBLE CHANGES
SIGNIFICANT USER-VISIBLE CHANGES
SIGNIFICANT USER-VISIBLE CHANGES
SIGNIFICANT USER-VISIBLE CHANGES
Changes in version 1.0.0:
SIGNIFICANT USER-VISIBLE CHANGES
Changes in version 3.0.0:
Changes in version 2.9.2:
Changes in version 1.14.1:
BUG FIXES
Changes in version 1.5.9:
BUG FIXES
Changes in version 1.5.8:
BUG FIXES
Changes in version 1.5.7:
BUG FIXES
Changes in version 1.5.6:
BUG FIXES
Changes in version 1.5.5:
BUG FIXES
Changes in version 1.5.4:
NEW FEATURES
BUG FIXES
Changes in version 1.5.3:
NEW FEATURES
Changes in version 1.5.2:
BUG FIXES
Changes in version 1.5.1:
BUG FIXES
Changes in version 1.2.0:
NEW FEATURES
NEW FEATURES
NEW FEATURES
NEW FEATURES
Changes in version 1.8.0:
NEW FEATURES
Add ‘upstream’ and ‘downstream’ arguments to IntergenicVariants() constructor.
Add ‘samples’ argument to ScanVcfParam().
Add readGT(), readGeno() and readInfo().
Add VRanges, VRangesList, SimpleVRangesList, and CompressedVRangesList classes.
Add coercion VRanges -> VCF and VCF -> VRanges.
Add methods for VRanges family: altDepth(), refDepth(), totalDepth(), altFraction() called(), hardFilters(), sampleNames(), softFilterMatrix() isIndel(), resetFilter().
Add stackedSamples,VRangesList method.
MODIFICATIONS
VCF validity method now requires the number of rows in info() to match the length of rowData().
PRECEDEID and FOLLOWID from locateVariants() are now CharacterLists with all genes in ‘upstream’ and ‘downstream’ range.
Modify rownames on rowData() GRanges to CHRAM:POS_REF/ALT for variants with no ID.
readVcf() returns info() and geno() in the order specified in the ScanVcfParam.
Work on scanVcf(): - free parse memory at first opportunity - define it_next in .c rather than .h - parse ALT “.” in C - hash incoming strings - parse only param-requested ‘fixed’, ‘info’, ‘geno’ fields
Add dimnames<-,VCF method to prevent ‘fixed’ fields from being copied into ‘rowData’ when new rownames or colnames were assigned.
Support read/write for an emtpy VCF.
readVcf(file=character, …) method attempts coercion to TabixFile.
Support for read/write an emtpy VCF.
Add performance section to vignette; convert to BiocStyle.
DEPRECATED and DEFUNCT
Defunct dbSNPFilter(), regionFilter() and MatrixToSnpMatrix().
Deprecate readVcfLongForm().
BUG FIXES
Fix bug in compatibility of read/writeVcf() when no INFO are columns present.
Fix bug in locateVariants() when ‘features’ has no txid and cdsid.
Fix bug in asVCF() when writing header lines.
Fix bug in “expand” methods for VCF to handle multiple ‘A’ columns in info().
Changes in version 1.4:
NEW FEATURES
tallyVariants will now keep ref rows if variant_strand=0; this is useful for getting information when no alts are present (e.g., for making wildtype calls). Better have a big cluster to do this over the whole genome.
add a keep_extra_stats param to TallyVariantsParam; setting this to FALSE will speed things up when the extra stats are not needed.
idVerify now supports VCF input like that output by GATK.
callableFraction() now supports GRangesList and TranscriptDb.
USER-VISIBLE CHANGES
The API is now based on VRanges, a formal GRanges-derived class for representing variants; use of so-called “tally” or “variant” GRanges is deprecated.
Disable proximity filter by default; we recommend this now only for whole genome calling.
QA filtering is no longer a formal part of the calling pipeline; we recommend to apply QA filters “softly” via qaVariants() and use the results for diagnostics only.
Use BiocParallel (BPPARAM argument) for tallyVariants
VariantTallyParam deprecated; use TallyVariantsParam
BUG FIXES
idVerify now correctly computes cliques instead of connected components
use the total count, rather than the ref count when calculating the alt frequency
Changes in version 1.37.6:
NEW FEATURE
USER VISIBLE CHANGES
Add Brigham Young University to LICENSE file for copyright purposes.
Add copyright information display when running findPeaks.massifquant() within xcmsRaw.R
Clean and update documentation for findPeaks.massifquant-methods.Rd
BUG FIXES
Changes in version 1.37.5:
BUG FIXES
Changes in version 1.37.4:
BUG FIXES
Changes in version 1.37.3:
BUG FIXES
Changes in version 1.37.1:
BUG FIXES
NEW FEATURES
Changes in version 3.00:
VERSION xps-1.21.5
add QualTreeSet methods NUSE() and RLE() to get stats and values
update man export.Rd
VERSION xps-1.21.4
VERSION xps-1.21.3
VERSION xps-1.21.2
VERSION xps-1.21.1
update README
update Makefile to set include path (for ~/.R/Makevars)
update XPSUtils.cxx to eliminate warning with clang
VERSION xps-1.19.10
VERSION xps-1.19.9
VERSION xps-1.19.8
VERSION xps-1.19.7
VERSION xps-1.19.2 - 6
VERSION xps-1.19.1
update Import..Annotation() methods in XPSchemes.cxx to protect against tabs in Affymetrix annotation files
update script4schemes.R to include schemes with annotation na33
Changes in version 2.15:
VERSION xps-1.17.2
update script4schemes.R to include schemes for HuGene-2_x-st arrays
update script4xps.R with example 4a for HuGene-2_1-st arrays
update README
VERSION xps-1.17.1
remove warnings: partial argument match
zzz.R: use .onAttach()
VERSION xps-1.15.2
VERSION xps-1.15.1
Changes in version 2.14.0:
VERSION xps-1.13.10
VERSION xps-1.13.9
add quality report function xpsQAReport()
update vignette xps.Rnw
VERSION xps-1.13.8
add functions attachProbe(), removeProbe(), etc.
add functions contentGC(), probeSequence()
add functions inten2GCplot(), plotInten2GC()
update vignette xps.Rnw
VERSION xps-1.13.7
add function unitID2symbol()
add function plotProbeset()
update vignette xps.Rnw
VERSION xps-1.13.6
update function indexUnits() for exon probesets
add function symbol2unitID()
add function probesetplot()
VERSION xps-1.13.5
update script4schemes.R to include schemes with annotation na32
update script4xps.R and script4exon.R
VERSION xps-1.13.4
move to ROOT version 5.30/00, update README
update vignettes xps.Rnw and xpsClasses.Rnw
VERSION xps-1.13.3
VERSION xps-1.13.2
add functions plotXXX()
function hist() no longer requires to attachInten()
add functions indexUnits(), pmindex(), mmindex()
add functions probesetID2unitID(), unitID2probesetID(), etc
add functions attachUnitNames(), removeUnitNames()
add functions attachDataXY(), removeDataXY()
VERSION xps-1.13.1
Changes in version 2.13.0:
VERSION xps-1.11.12
VERSION xps-1.11.11
VERSION xps-1.11.10
add functions: plotImage(), plotBoxplot()
update methods image()
VERSION xps-1.11.9
add method: pcaplot()
update method plotAffyRNAdeg()
VERSION xps-1.11.8
VERSION xps-1.11.7
VERSION xps-1.11.6
add methods for RNA degradation plots: xpsRNAdeg(), plotAffyRNAdeg()
add man pages
VERSION xps-1.11.5
correct minor bug in XPSProcessing.cxx: ExportExprTreeInfo()
update method image()
add man pages
VERSION xps-1.11.4
add new class QualTreeSet to add quality control features
add functions qualify() and fitQC() and derived functions
add method image() for residual plots of IVT, Gene ST, Exon ST and plate arrays
add new plots coiplot() and borderplot()
update boxplot(), callplot(), image() to be independent of slot ‘data’
VERSION xps-1.11.3
VERSION xps-1.11.1
update DESCRIPTION to correct SystemRequirements to root_v5.27.04
update function READ_WSTRING() to handle big endian for PPC
Changes in version 2.12.0:
VERSION xps-1.9.9
VERSION xps-1.9.8
VERSION xps-1.9.7
update Makefile.win to clean xpsLinkDef.h
update script4schemes.R for annotation na31 (updated release)
VERSION xps-1.9.6
update information files for new ROOT Version 5.27/04 (root_v5.27/04)
update script4xps.R, script4schemes.R for annotation na31
VERSION xps-1.9.5
VERSION xps-1.9.4
update root.profile.R, macroDrawProfilePlot.C to allow selecting subset of trees
in read.table() set stringsAsFactors=FALSE
VERSION xps-1.9.3
VERSION xps-1.9.2
VERSION xps-1.9.1
Changes in version 2.11.0:
VERSION xps-1.7.9
update method validData() to handle slot data containing different column types
update methods seExprTreeSet(), rleplot(), mvaplot(), nuseplot()
VERSION xps-1.7.8
add method xpsFIRMA()
add functions firma(), firma.expr(), firma.score()
VERSION xps-1.7.7
update bgcorrect.R to warn from using tmpdir resulting in empty root file
update normalize.R to warn from using tmpdir resulting in empty root file
VERSION xps-1.7.6
VERSION xps-1.7.4
VERSION xps-1.7.3
add ExprTreeSet methods validSE(), nuseplot(), rleplot()
allow to export layout trees for incomplete *.CLF files
update examples/updateAnnotation.R
VERSION xps-1.7.2
add examples/updateAnnotation.R
update script4xps.R
VERSION xps-1.7.1
allow using mas5() and mas5.call() with plate arrays w/o MMs
update script4xps.R
Changes in version 2.10.0:
VERSION xps-1.5.19
VERSION xps-1.5.18
VERSION xps-1.5.17
VERSION xps-1.5.16
VERSION xps-1.5.15
validBgrd() implement ‘which’
add vignette xpsPreprocess.pdf
add example/macro4xpsPreprocess.R
VERSION xps-1.5.14
update export() to include read.table(..,comment.char=’’)
update methods.DataTreeSet.R to allow probe-level lowess and supsmu normalization
VERSION xps-1.5.13
VERSION xps-1.5.12
VERSION xps-1.5.9
VERSION xps-1.5.8
VERSION xps-1.5.7
update method validCall()
add methods validExpr() and validPVal()
update vignette APTvsXPS.pdf
update examples script4xps2apt.R and script4bestmatch.R
VERSION xps-1.5.4
update function exonLevel() to use affx=c(4,8,16,32)
update function dataDataTreeSet() to return correct ids for mask
add new internal function exonLevelIDs()
VERSION xps-1.5.3
VERSION xps-1.5.1
update validData() to check for duplicate rownames
allow reading of genetitan plate data
Changes in version 2.9.0:
VERSION xps-1.3.13
update DESCRIPTION to mention root version
update README
VERSION xps-1.3.12
VERSION xps-1.3.11
VERSION xps-1.3.8
update all initialize methods to prevent checkS3forClass warnings
update bgcorrect.rma, bgcorrect.mas5
update script4xps.R, script4exon.R
VERSION xps-1.3.6
VERSION xps-1.3.5
VERSION xps-1.3.4
correct bug in xpsPreprocess for add.data=FALSE
correct sub(.root, .txt, x) to sub(.root, .txt, x)
update root.image() to get setname from setName()
VERSION xps-1.3.3
VERSION xps-1.3.1
Changes in version 2.8.0:
VERSION xps-1.1.9
protect class XRMABackground against defect Affy chips, e.g. zero division
protect root.data() etc against duplicate celnames or treenames
VERSION xps-1.1.8
VERSION xps-1.1.7
VERSION xps-1.1.6
prevent import of CEL-files with zero max intensity
update functions returning ExprTreeSet to import results as option only
update functions returning CallTreeSet to import results as option only
update root.density etc to allow saving from R function
add root.profile to use root graphics for boxplots
add summarization method FARMS (Hochreiter et al)
add summarization method DFW (Chen et al)
update vignette xps.pdf
VERSION xps-1.1.5
VERSION xps-1.1.4
update vignette xps.pdf
add new vignette APTvsXPS.pdf
update examples script4exon.R
add examples script4xps2apt.R and script4bestmatch.R
update README
VERSION xps-1.1.3
to allow CEL-names starting with a number, update to read.table(…, check.names=FALSE)
update ExprTreeSet to set slot exprtype to correct type
add functions root.expr() and root.call()
need to change setname for dabg.call() from CallTreeSet to CallSet as for mas5.call()
VERSION xps-1.1.2
allow different exonlevels for bgrd, normalization, summarization
update replacement methods exprs, pvalData, presCall to allow subsetting
add function metaProbesets to compute metacoreList.mps for apt
VERSION xps-1.1.1
increase maximum root file size from 2GB to 2TB
decrease computation time
correct bug preventing export of exon probeset normalized data
Changes in version 2.7.0:
VERSION xps-0.99.11
VERSION xps-0.99.10
update source code to handle tmpdir correctly on WinXP
update examples script4xps.R and script4exon.R
VERSION xps-0.99.9
VERSION xps-0.99.8
VERSION xps-0.99.3
package can now be built for Windows XP
added possibility to add current date and/or time to root filename
added function existsROOTFile
updated vignette xps.Snw
VERSION xps-0.4.3
VERSION xps-0.4.2
add support to import generic (calvin) CEL-files
update method volcanoplot
VERSION xps-0.4.1
change DESCRIPTION
add method volcanoplot
correct update bug in xpsUniFilter
VERSION xps-0.4.0
import.data: import CEL-files from different directories
update DESCRIPTION, NAMESPACE
add possibility to apply non-sepcific filters and univariate filters
add S4 classes Filter, PreFilter, UniFilter
add S4 classes FilterTreeSet and AnalysisTreeSet
The following packages are no longer in the release:
dualKS, externalVector, GeneGroupAnalysis, iFlow, KEGGSOAP, xmapcore