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https://bioconductor.org/packages/StructuralVariantAnnotation/

Software R package for structural variant analysis. Contains helper functions for dealing with structural variants in VCF format. Contains functions for parsing VCFs from number of popular callers as well as functions for dealing with breakpoints involving two separate genomic loci encoded as GRanges objects.

Proper citation: StructuralVariantAnnotation (RRID:SCR_018683) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/EnhancedVolcano/

Software R package to produce publication ready volcano plots with enhanced colouring and labeling. Used to visualise results of differential expression analyses.

Proper citation: EnhancedVolcano (RRID:SCR_018931) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/DEGreport/

Software R package for creation of HTML report of differential expression analyses of count data. Integrates some of code mentioned in DESeq2 and edgeR vignettes, and reports ranked list of genes according to fold changes mean and variability for each selected gene.

Proper citation: DEGreport (RRID:SCR_018941) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/ReactomePA/

Software R package provides functions for pathway analysis based on REACTOME pathway database. It implements enrichment analysis, gene set enrichment analysis and several functions for visualization.

Proper citation: ReactomePA (RRID:SCR_019316) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/MSnbase/

Software R package provides infrastructure for manipulation, processing and visualisation of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data. Used for isobaric tagged mass spectrometry data visualization, processing and quantitation.

Proper citation: MSnbase (RRID:SCR_019317) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/biomaRt/

Software package that integrates BioMart data resources with data analysis software in Bioconductor. Can annotate range of gene or gene product identifiers including Entrez Gene and Affymetrix probe identifiers with information such as gene symbol, chromosomal coordinates, Gene Ontology and OMIM annotation. Enables retrieval of genomic sequences and single nucleotide polymorphism information, which can be used in data analysis.

Proper citation: biomaRt (RRID:SCR_019214) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages/release/bioc/html/GSVA.html

Open source software R package for assaying variation of gene set enrichment over sample population.Used for microarray and RNA-seq data analysis. Gene set enrichment method that estimates variation of pathway activity over sample population in unsupervised manner.

Proper citation: GSVA (RRID:SCR_021058) Copy   

•   Source: SciCrunch Registry

https://scicrunch.org/resolver/SCR_002250

THIS RESOURCE IS NO LONGER IN SERVICE. Documented Jul 19, 2024. Metadatabase manually curated that provides web accessible tools related to genomics, transcriptomics, proteomics and metabolomics. Used as informative directory for multi-omic data analysis.

Proper citation: OMICtools (RRID:SCR_002250) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/cn.farms.html

Software R package for copy number variation analysis that allows analysis of the most common Affymetrix (250K-SNP6.0) array types and supports high-performance computing using snow and ff.

Proper citation: cn.FARMS (RRID:SCR_000289) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Software package for computing correlated mutations based on selection pressure. Three methods are provided for detecting correlated mutations, including conditional selection pressure, mutual information and Jaccard index. The computation consists of two steps: First, the positive selection sites are detected; second, the mutation correlations are computed among the positive selection sites. Note that the first step is optional. Meanwhile, CorMut facilitates the comparison of the correlated mutations between two conditions by the means of correlated mutation network.

Proper citation: CorMut (RRID:SCR_000053) Copy   

•   Source: SciCrunch Registry

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

Software package for 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.

Proper citation: metaSeq (RRID:SCR_000056) Copy   

•   Source: SciCrunch Registry

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

Software package that provides a set of tools for analyzing data from a factorial designed microarray experiment, or any microarray experiment for which a linear model is appropriate. The functions can be used to evaluate tests of contrast of biological interest and perform single outlier detection.

Proper citation: factDesign (RRID:SCR_001330) Copy   

•   Source: SciCrunch Registry

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

Software for adaptive Gene Picking for Microarray Expression Data Analysis.

Proper citation: pickgene (RRID:SCR_001331) Copy   

•   Source: SciCrunch Registry

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

Software package providing a collection of meta-analysis tools for analysing high throughput experimental data.

Proper citation: GeneMeta (RRID:SCR_001201) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Software R package for the analysis of ChIP-chip data and Affymetrix tiling arrays. It provides functions for data import, quality assessment, and data visualization. The software provides tools for the efficient mapping of genomic sequences.

Proper citation: Starr (RRID:SCR_001071) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Software tools for meta-analysis in the presence of hierarchical (and/or sampling) dependence, including with gene expression studies.

Proper citation: metahdep (RRID:SCR_001225) Copy   

•   Source: SciCrunch Registry

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

An easy to use software tool for dual color microarray data. Its GUI-Tk based environment lets any non-experienced user perform a basic, but not simple, data analysis just following a wizard. In addition it provides some tools for the developer.

Proper citation: genArise (RRID:SCR_001346) Copy   

•   Source: SciCrunch Registry

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

A software package for meta-analysis of high-throughput experiments using feature annotations. It calculates significant annotations (categories) in each of two (or more) feature (i.e. gene) lists, determines the overlap between the annotations, and returns graphical and tabular data about the significant annotations and which combinations of feature lists the annotations were found to be significant. Interactive exploration is facilitated through the use of RCytoscape (heavily suggested).

Proper citation: categoryCompare (RRID:SCR_001223) Copy   

•   Source: SciCrunch Registry

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

R software package that uses a Bayesian hierarchical model to detect enriched regions from ChIP-chip experiments.

Proper citation: BAC (RRID:SCR_001067) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/data/annotation/html/targetscan.Hs.eg.db.html

R software that predicts biological targets of miRNAs by searching for the presence of conserved 8mer and 7mer sites that match the seed region of each miRNA.

Proper citation: targetscan.Hs.eg.db (RRID:SCR_001068) Copy   

•   Source: SciCrunch Registry