GOTHiC Binomial test for Hi-C data analysis
This is a Hi-C analysis package using a cumulative binomial test to detect interactions between distal genomic loci that have significantly more reads than expected by chance in Hi-C experiments. It takes mapped paired NGS reads as input and gives back the list of significant interactions for a given bin size in the genome.
GenomicAlignments Representation and manipulation of short genomic alignments
Provides efficient containers for storing and manipulating short alignments against a reference genome.
CNVrd2 CNVrd2: a read depth-based method to detect and genotype complex common copy number variants from next generation sequencing data.
CNVrd2 uses next-generation sequencing data to measure human gene copy number for multiple samples, indentify SNPs tagging copy number variants and detect copy number polymorphic genomic regions.
PSICQUIC Protemics Standard Initiative Common QUery InterfaCe
PSICQUIC is a project within the HUPO Proteomics Standard Initiative (HUPO-PSI). It standardises programmatic access to molecular interaction databases.
h5vc Managing alignment tallies using a hdf5 backend
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.
metaSeq Meta-analysis of RNA-Seq count data in multiple studies
The probabilities by one-sided NOISeq are combined by Fisher's method or Stouffer's method
interactiveDisplay Package for enabling powerful shiny web displays of Bioconductor objects
The interactiveDisplay package contains the methods needed to generate interactive Shiny based display methods for Bioconductor objects.
ChAMP Chip Analysis Methylation Pipeline for Illumina HumanMethylation450
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.
flipflop Fast lasso-based isoform prediction as a flow problem
Flipflop discovers which isoforms of a gene are expressed in a given sample together with their abundances, based on RNA-Seq read data.
FGNet Functional gene networks derived from biological enrichment analyses
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.
TFBSTools Software package for TFBS
Software package for TFBS.
sRAP Simplified RNA-Seq Analysis Pipeline
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.
spliceSites Manages align gap positions from RNA-seq data
Align gap positions from RNA-seq data
shinyTANDEM Provides a GUI for rTANDEM
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.
qcmetrics A Framework for Quality Control
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.
openCyto Hierarchical Gating Pipeline for flow cytometry data
This package is designed to facilitate the automated gating methods in sequential way to mimic the manual gating strategy.
MSstats Protein Significance Analysis in LC-MS, SRM and DIA for Label-free or Label-based Proteomics Experiments
A set of tools for protein significance analysis in label-free or LC-MS, SRM and DIA experiments.
methylMnM detect different methylation level (DMR)
To give the exactly p-value and q-value of MeDIP-seq and MRE-seq data for different samples comparation.
flowMap A probabilistic algorithm for matching and comparing multiple flow cytometry samples
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.
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
if you have any questions.
epivizr R Interface to epiviz web app
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.
DNaseR DNase I footprinting analysis of DNase-seq data
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).
Visualize significant conserved amino acid sequence pattern in groups based on probability theory
CexoR An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates
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'.
bioassayR R library for Bioactivity analysis
bioassayR provides tools for statistical analysis of small molecule bioactivity data
ampliQueso Analysis of amplicon enrichment panels
The package provides tools and reports for the analysis of amplicon sequencing panels, such as AmpliSeq
AllelicImbalance Investigates allele specific expression
Provides a framework for allelic specific expression investigation using RNA-seq data
STRINGdb STRINGdb (Search Tool for the Retrieval of Interacting proteins database)
The STRINGdb package provides a user-friendly interface to the STRING protein-protein interactions database ( http://www.string-db.org ).
SimBindProfiles Similar Binding Profiles
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.
rTRMui A shiny user interface for rTRM
This package provides a web interface to compute transcriptional regulatory modules with rTRM.
ProCoNA Protein co-expression network analysis (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)
omicade4 Multiple co-inertia analysis of omics datasets
Multiple co-inertia analysis of omics datasets
neaGUI An R package to perform the network enrichment analysis (NEA).
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.
GOSim Computation of functional similarities between GO terms and gene products; GO enrichment analysis
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
BiRewire High-performing routines for the randomization of a bipartite graph (or a binary event matrix) preserving degree distribution (or marginal totals).
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.
ArrayTV Implementation of wave correction for arrays
Wave correction for genotyping and copy number arrays
mzID An mzIdentML parser for R
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.
BADER Bayesian Analysis of Differential Expression in RNA Sequencing Data
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.
Roleswitch Infer miRNA-mRNA interactions using paired expression data from a single sample
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.
chipenrich Gene set enrichment for ChIP-seq peak data
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.
BiGGR Creates an interface to the BiGG database, provides a framework for simulation and produces flux graphs
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.
TCC TCC: Differential expression analysis for tag count data with robust normalization strategies
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).
qusage qusage: Quantitative Set Analysis for Gene Expression
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 (firstname.lastname@example.org) or Steven Kleinstein (email@example.com)
ChemmineOB R interface to a subset of OpenBabel functionalities
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 more. 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.
ASSET An R package for subset-based association analysis of heterogeneous traits and subtypes
An R package for subset-based analysis of heterogeneous traits and subtypes
supraHex A supra-hexagonal map for analysing tabular omics data
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 input data. The supraHex is able to carray out gene clustering/meta-clustering and sample correlation, plus intuitive visualisations to facilitate exploratory analysis. More importantly, it allows for overlaying additional data onto the trained map to explore relations between input and additional data. So with supraHex, it is also possible to carry out multilayer omics data comparisons. Uniquely to this package, users can ultrafastly understand any tabular omics data, both scientifically and artistically, especially in a sample-specific fashion but without loss of information on large genes.
SwimR SwimR: A Suite of Analytical Tools for Quantification of C. elegans Swimming Behavior
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.
trio Testing of SNPs and SNP Interactions in Case-Parent Trio Studies
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.
SpacePAC Identification of Mutational Clusters in 3D Protein Space via Simulation.
Identifies clustering of somatic mutations in proteins via a simulation approach while considering the protein's tertiary structure.
SeqVarTools Tools for variant data
An interface to the fast-access storage format for VCF data provided in SeqArray, with tools for common operations and analysis.
RTN Reconstruction of transcriptional networks and analysis of master regulators
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.
rfPred Assign rfPred functional prediction scores to a missense variants list
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).
Rchemcpp Similarity measures for chemical compounds
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.
msmsTests LC-MS/MS Differential Expression Tests
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.
RRHO Inference on agreement between two lists
The package is aimed at inference on the amount of agreement in two sorted lists using the Rank-Rank Hypergeometric Overlap test.
msmsEDA Exploratory Data Analysis of LC-MS/MS data by spectral counts
Exploratory data analysis to assess the quality of a set of LC-MS/MS experiments, and visualize de influence of the involved factors.
intansv Integrative analysis of structural variations
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.
cobindR Finding Co-occuring motifs of transcription factor binding sites
Finding and analysing co-occuring motifs of transcription factor binding sites in groups of genes
CSSP ChIP-Seq Statistical Power
Power computation for ChIP-Seq data based on Bayesian estimation for local poisson counting process.
TargetScore TargetScore: Infer microRNA targets using microRNA-overexpression data and sequence information
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.
Algorithm for testing significance of clustering in RNA-seq data.
seqCNA Copy number analysis of high-throughput sequencing cancer data
Copy number analysis of high-throughput sequencing cancer data with fast summarization, extensive filtering and improved normalization
OmicCircos High-quality circular visualization of omic data
OmicCircos is an R application and package for generating high-quality circular maps for omic data
cleanUpdTSeq This package classifies putative polyadenylation sites as true or false/internally oligodT primed.
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.
BiocStyle Standard styles for vignettes and other Bioconductor documents
Provides standard formatting styles for Bioconductor documents. The vignette illustrates use and functionality.
maPredictDSC Phenotype prediction using microarray data: approach of the best overall team in the IMPROVER Diagnostic Signature Challenge
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.
rTRM Identification of transcriptional regulatory modules from PPI networks
rTRM identifies transcriptional regulatory modules (TRMs) from protein-protein interaction networks.
pathifier Quantify deregulation of pathways in cancer
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.
paircompviz Multiple comparison test visualization
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.
NetSAM Network Seriation And Modularization
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.
mitoODE Implementation of the differential equation model described in "Dynamical modelling of phenotypes in a genome-wide RNAi live-cell imaging assay" (submitted).
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).
customProDB Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics search.
Generate customized protein sequence database from RNA-Seq data for proteomics search
cleaver Cleavage of polypeptide sequences
In-silico cleavage of polypeptide sequences. The cleavage rules are taken from: http://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html
spliceR Classification of alternative splicing and prediction of coding potential from RNA-seq data.
An R package for classification of alternative splicing and prediction of coding potential from RNA-seq data.
flowBeads flowBeads: Analysis of flow bead data
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.
vtpnet variant-transcription factor-phenotype networks
variant-transcription factor-phenotype networks, inspired by Maurano et al., Science (2012), PMID 22955828
tRanslatome Comparison between multiple levels of gene expression.
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.
prot2D Statistical Tools for volume data from 2D Gel Electrophoresis
The purpose of this package is to analyze (i.e. Normalize and select significant spots) data issued from 2D GEl experiments
EBSeq An R package for gene and isoform differential expression analysis of RNA-seq data
Differential Expression analysis at both gene and isoform level using RNA-seq data
plethy R framework for exploration and analysis of respirometry data
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.
flowFit Estimate proliferation in cell-tracking dye studies
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.
clonotypeR High throughput analysis of T cell antigen receptor sequences
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.
XVector Representation and manpulation of external sequences
Memory efficient S4 classes for storing sequences "externally" (behind an R external pointer, or on disk).
sSeq Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size
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.
SplicingGraphs Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them
This package allows the user to create, manipulate, and visualize splicing graphs and their bubbles based on a gene model for a given organism. Additionally it allows the user to assign RNA-seq reads to the edges of a set of splicing graphs, and to summarize them in different ways.
BiSeq Processing and analyzing bisulfite sequencing data
The BiSeq package provides useful classes and functions to handle and analyze targeted bisulfite sequencing (BS) data such as reduced-representation bisulfite sequencing (RRBS) data. In particular, it implements an algorithm to detect differentially methylated regions (DMRs). The package takes already aligned BS data from one or multiple samples.
triplex Search and visualize intramolecular triplex-forming sequences in DNA
This package provides functions for identification and visualization of potential intramolecular triplex patterns in DNA sequence. The main functionality is to detect the positions of subsequences capable of folding into an intramolecular triplex (H-DNA) in a much larger sequence. The potential H-DNA (triplexes) should be made of as many cannonical nucleotide triplets as possible. The package includes visualization showing the exact base-pairing in 1D, 2D or 3D.
prebs Probe region expression estimation for RNA-seq data for improved microarray comparability
The prebs package aims at making RNA-sequencing (RNA-seq) data more comparable to microarray data. The comparability is achieved by summarizing sequencing-based expressions of probe regions using a modified version of RMA algorithm. The pipeline takes mapped reads in BAM format as an input and produces either gene expressions or original microarray probe set expressions as an output.
piano Platform for integrative analysis of omics data
Piano performs gene set analysis using various statistical methods, from different gene level statistics and a wide range of gene-set collections. Furthermore, the Piano package contains functions for combining the results of multiple runs of gene set analyses.
MMDiff Statistical Testing for ChIP-Seq data sets
This package detects statistically significant difference between read enrichment profiles in different ChIP-Seq samples. To take advantage of shape differences it uses Kernel methods (Maximum Mean Discrepancy, MMD).
GENE.E Interact with GENE-E from R
Interactive exploration of matrices in GENE-E.
PAPi Predict metabolic pathway activity based on metabolomics data
The Pathway Activity Profiling - PAPi - is an R package for predicting the activity of metabolic pathways based solely on a metabolomics data set containing a list of metabolites identified and their respective abundances in different biological samples. PAPi generates hypothesis that improves the final biological interpretation. See Aggio, R.B.M; Ruggiero, K. and Villas-Boas, S.G. (2010) - Pathway Activity Profiling (PAPi): from metabolite profile to metabolic pathway activity. Bioinformatics.
antiProfiles Implementation of gene expression anti-profiles
Implements gene expression anti-profiles as described in Corrada Bravo et al., BMC Bioinformatics 2012, 13:272 doi:10.1186/1471-2105-13-272.
copynumber Segmentation of single- and multi-track copy number data by penalized least squares regression.
Penalized least squares regression is applied to fit piecewise constant curves to copy number data to locate genomic regions of constant copy number. Procedures are available for individual segmentation of each sample, joint segmentation of several samples and joint segmentation of the two data tracks from SNP-arrays. Several plotting functions are available for visualization of the data and the segmentation results.
geNetClassifier classify diseases and build associated gene networks using gene expression profiles
Comprehensive package to automatically train a multi-class SVM classifier based on gene expression data. Provides transparent selection of gene markers, their coexpression networks, and an interface to query the classifier.
SeqGSEA Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing
The package generally provides methods for gene set enrichment analysis of high-throughput RNA-Seq data by integrating differential expression and splicing. It uses negative binomial distribution to model read count data, which accounts for sequencing biases and biological variation. Based on permutation tests, statistical significance can also be achieved regarding each gene's differential expression and splicing, respectively.
DASiR Distributed Annotation System in R
R package for programmatic retrieval of information from DAS servers
metagenomeSeq Statistical analysis for sparse high-throughput sequencing
metagenomeSeq is designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. metagenomeSeq is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations.
AnnotationHub A client for retrieving Bioconductor objects from AnnotationHub
A client for retrieving data from the Bioconductor AnnotationHub online services.
ROntoTools R Onto-Tools suite
Suite of tools for functional analysis
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