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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
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
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
https://bioconductor.org/packages/AUCell/
Software R package to identify cells with active gene sets in single cell RNA-seq data. Used for analysis of gene set activity in single cell RNA-seq data.Used to calculate whether critical subset of input gene set is enriched within expressed genes for each cell.
Proper citation: AUCell (RRID:SCR_021327) Copy
http://www.bioconductor.org/packages/release/bioc/html/iontree.html
Software package that provides utility functions to manage and analyse MS2/MS3 fragmentation data from ion trap mass spectrometry. It was designed for high throughput metabolomics data with many biological samples and a large numer of ion trees collected. Tests have been done with data from low-resolution mass spectrometry but could be readily extended to precursor ion based fragmentation data from high resoultion mass spectrometry.
Proper citation: iontree (RRID:SCR_002813) Copy
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
https://www.ncbi.nlm.nih.gov/geo/info/geo2r.html
Software as an interactive web tool to compare two or more groups of samples in a Gene Expression Omnibus (GEO) series regardless of data type and quality. Used to identify genes that are differentially expressed across experimental conditions. Results are presented as a table of genes ordered by significance.
Proper citation: GEO2R (RRID:SCR_016569) Copy
https://bioconductor.org/packages/KEGGgraph/
Software R package interface between KEGG pathway and graph object as well as collection of tools to analyze, dissect and visualize these graphs.
Proper citation: KEGGgraph (RRID:SCR_023788) Copy
http://bioconductor.org/packages/release/bioc/html/topGO.html
Software package which provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied.
Proper citation: topGO (RRID:SCR_014798) Copy
http://www.bioconductor.org/packages/devel/bioc/html/GeneNetworkBuilder.html
Software application for discovering direct or indirect targets of transcription factors (TFs) using ChIP-chip or ChIP-seq, and microarray or RNA-seq gene expression data. Inputting a list of genes of potential targets of one TF from ChIP-chip or ChIP-seq, and the gene expression results, it generates a regulatory network of the TF.
Proper citation: GeneNetworkBuilder (RRID:SCR_006455) Copy
https://bioconductor.org/packages/Orthology.eg.db/
Software R package to provide orthology mappings between species, based on NCBI Gene IDs and NCBI orthology mappings.
Proper citation: Orthology.eg.db (RRID:SCR_024740) Copy
https://www.bioconductor.org/packages/release/bioc/html/ExperimentHub.html
Software R package provides central location where curated data from experiments, publications or training courses can be accessed.
Proper citation: ExperimentHub (RRID:SCR_024820) Copy
http://www.bioconductor.org/packages/release/bioc/html/ncdfFlow.html
Software package that provides netCDF storage based methods and functions for manipulation of flow cytometry data.
Proper citation: ncdfFlow (RRID:SCR_000009) Copy
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