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https://www.bioconductor.org/packages/release/workflows/html/RnaSeqGeneEdgeRQL.html

Software to study analysis of an RNA-Seq experiment using the Rsubread and edgeR packages. The workflow starts from read alignment and continues on to data exploration, to differential expression and, finally, to pathway analysis. The analysis includes plots, GO and KEGG analyses, and the analysis of a expression signature as generated by a prior experiment.

Proper citation: RnaSeqGeneEdgeRQL (RRID:SCR_016699) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/release/bioc/html/clusterProfiler.html

Software R package for statistical analysis and visualization of functional profiles for genes and gene clusters.

Proper citation: clusterProfiler (RRID:SCR_016884) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/release/data/experiment/html/affydata.html

Software R package for analysis of Affymetrix Data. Contains samples data files of a large size.

Proper citation: affydata (RRID:SCR_016976) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/CATALYST/

Software R package to provide pipeline for preprocessing of cytometry data, including normalization using bead standards, single cell deconvolution, and bead based compensation.

Proper citation: CATALYST (RRID:SCR_017127) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/gage/

Software R package for gene set enrichment or pathway analysis. Applicable independent of microarray or RNAseq data attributes including sample sizes, experimental designs, assay platforms, and other types of heterogeneity. Pipeline routines of multiple GAGE analyses in batch, comparison between parallel analyses, and combined analysis of heterogeneous data from different sources and studies.

Proper citation: GAGE (RRID:SCR_017067) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/ggtree/

Software R package for visualization and annotation of phylogenetic trees with their covariates and other tree like structures with their annotation data. Can import evolutionary data from different tree file formats and analysis programs as well as other associated data from experiments so that various sources and types of data can be displayed on tree for comparison and further analyses.

Proper citation: ggtree (RRID:SCR_018560) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/minet/

Open source software R package for inferring large transcriptional networks using mutual information. Implements algorithms for inferring networks such as gene networks from microarray data.

Proper citation: minet (RRID:SCR_018661) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages//2.10/bioc/html/spade.html

An analysis and visualization software tool for high dimensional flow cytometry data that organizes cells into hierarchies of related phenotypes.

Proper citation: SPADE (RRID:SCR_001810) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/release/bioc/html/DESeq.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. Software for differential gene expression analysis based on the negative binomial distribution. It estimates variance-mean dependence in count data from high-throughput sequencing assays and tests for differential expression.

Proper citation: DESeq (RRID:SCR_000154) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.13/bioc/html/bsseq.html

R package with tools for analyzing and visualizing bisulfite sequencing data.

Proper citation: bsseq (RRID:SCR_001072) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/MmPalateMiRNA.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software R package written for analysis of murine palate miRNA two-color expression data.

Proper citation: MmPalateMiRNA (RRID:SCR_001070) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.10/bioc/html/R453Plus1Toolbox.html

R software toolbox of functions for the analysis of data generated by Roche's 454 sequencing platform. Additional functions are included for quality assurance, annotation and visualization of detected variants, complementing the software tools shipped by Roche with their product. A pipeline for the detection of structural variants is provided.

Proper citation: R453Plus1Toolbox (RRID:SCR_001105) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/RmiR.html

R package that contains functions to merge microRNA and respective targets using different databases.

Proper citation: RmiR (RRID:SCR_001069) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/CGEN.html

Software R package for analysis of case-control studies in genetic epidemiology.

Proper citation: CGEN (RRID:SCR_001251) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.12/bioc/html/jmosaics.html

R software that detects enriched regions of ChIP-seq data sets jointly.

Proper citation: Jmosaics (RRID:SCR_001094) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/genoset.html

Software package to load, manipulate, and plot copynumber and BAF data by providing classes similar to ExpressionSet for copy number analysis. The class extends ExpressionSet by adding a locData slot for a RangedData or GRanegs object. This object contains feature genome location data and provides for efficient subsetting on genome location. CNSet and BAFSet extend GenoSet and require assayData matrices for Copy Number (cn) or Log-R Ratio (lrr) and B-Allele Frequency (baf) data. Implements and provides convenience functions for processing of copy number and B-Allele Frequency data.

Proper citation: GenoSet (RRID:SCR_001275) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.14/bioc/html/CGHbase.html

Software package that contains functions and classes that are needed by arrayCGH packages.

Proper citation: CGHbase (RRID:SCR_001279) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.4/bioc/html/rMAT.html

Software package for normalizing and analyzing tiling arrays and ChIP-chip data. It is the R-version of a MAT program.

Proper citation: rMAT (RRID:SCR_001583) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.12/bioc/html/CGHcall.html

Software that calls aberrations for array CGH data using a six state mixture model and several biological concepts. It is written in R.

Proper citation: CGHcall (RRID:SCR_001578) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/simpleaffy.html

Software package that provides high level functions for reading Affy .CEL files, phenotypic data, and then computing simple things with it, such as t-tests, fold changes and the like. It makes heavy use of the affy library. It also has some basic scatter plot functions and mechanisms for generating high resolution journal figures.

Proper citation: Simpleaffy (RRID:SCR_001302) Copy   

•   Source: SciCrunch Registry