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

Software package that implements gene and gene-set level analysis methods for somatic mutation studies of cancer.

Proper citation: CancerMutationAnalysis (RRID:SCR_013181) Copy   

•   Source: SciCrunch Registry

http://bioinf.wehi.edu.au/limma/

Software package for the analysis of gene expression microarray data, especially the use of linear models for analyzing designed experiments and the assessment of differential expression.

Proper citation: LIMMA (RRID:SCR_010943) Copy   

•   Source: SciCrunch Registry

http://msstats.org/

A package for statistical relative quantification of proteins and peptides in global, targeted, and data-independent proteomics. It handles shotgun, label-free, and label-based Selected Reaction Monitoring, as well as SWATH/DIA (Data Independent Acquisition) experiments. MSStats provide functionality for data processing and visualization, model-based statistical analysis, and model-based sample size calculations.

Proper citation: MSstats (RRID:SCR_014353) Copy   

•   Source: SciCrunch Registry

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

Software that segments DNA copy number data using circular binary segmentation to detect regions with abnormal copy number.

Proper citation: DNAcopy (RRID:SCR_012560) Copy   

•   Source: SciCrunch Registry

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

R functions for the normalization of Exiqon miRNA array data.

Proper citation: ExiMiR (RRID:SCR_012753) Copy   

•   Source: SciCrunch Registry

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

Software tool for automated meta-analysis of mass and flow cytometry data. Provides functions for preprocessing, automated gating and meta-analysis of cytometry data and collection of cytometry data from the ImmPort database.

Proper citation: MetaCyto (RRID:SCR_016415) Copy   

•   Source: SciCrunch Registry

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://www.bioconductor.org/packages/release/bioc/html/ReQON.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Algorithm for recalibrating the base quality scores for aligned sequencing data in BAM format.

Proper citation: ReQON (RRID:SCR_000075) Copy   

•   Source: SciCrunch Registry

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

Software package that defines general purpose containers for storing genomic intervals as well as more specialized containers for storing alignments against a reference genome.

Proper citation: GenomicRanges (RRID:SCR_000025) Copy   

•   Source: SciCrunch Registry

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

Software that establishes a bridge between GEO and BioConductor.

Proper citation: GEOquery (RRID:SCR_000146) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software for semantic labelling of flow cytometric cell populations.

Proper citation: flowCL (RRID:SCR_000046) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/data/annotation/html/RmiR.Hs.miRNA.html

Software package for various databases of microRNA Targets.

Proper citation: RmiR.Hs.miRNA (RRID:SCR_000101) 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://bioconductor.org/packages/scTHI/

Software R package to identify active pairs of ligand receptors from single cells in order to study,among others, tumor host interactions. Contains set of signatures to classify cells from tumor microenvironment.

Proper citation: scTHI (RRID:SCR_018918) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/variancePartition/

Software R package to quantify and interpret divers of variation in multilevel gene expression experiments.Provides statistical and visualization framework for studying drivers of variation in RNA-seq datasets in many types of high throughput genomic assays including RNA-seq gene-, exon- and isoform-level quantification, splicing efficiency, protein quantification, metabolite quantification, metagenomic assays, methylation arrays and epigenomic sequencing assays.

Proper citation: variancePartition (RRID:SCR_019204) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/synergyfinder/

Software R package as efficient implementations for all popular synergy scoring models for drug combinations, including HSA, Loewe, Bliss and ZIP and visualization of synergy scores as either two dimensional or three dimensional interaction surface over dose matrix. Used to calculate and visualize synergy scores for drug combinations.

Proper citation: SynergyFinder (RRID:SCR_019318) Copy   

•   Source: SciCrunch Registry

https://sydneybiox.github.io/CiteFuse/

Software R package consisting of suite of tools for doublet detection, modality integration, clustering, differential RNA and protein expression analysis, antibody-derived tag evaluation, ligand-receptor interaction analysis and interactive web-based visualization of CITE-seq data.

Proper citation: CiteFuse (RRID:SCR_019321) 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/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