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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   

•   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

http://r3cseq.genereg.net/Site/index.html

An R/Bioconductor package to identify chromosomal interaction regions generated by chromosome conformation capture (3C) coupled to next-generation sequencing (NGS), a technique termed 3C-seq. It performs data analysis for a number of different experimental designs, as it can analyze 3C-seq data with or without a control experiment and it can be used to facilitate data analysis for experiments with multiple replicates. The r3Cseq package provides functions to perform data normalization, statistical analysis for cis/trans interactions and visualization in order to help scientists identify genomic regions that physically interact with the given viewpoints of interest. This tool greatly facilitates hypothesis generation and the interpretation of experimental results.

Proper citation: r3Cseq (RRID:SCR_003198) Copy   

•   Source: SciCrunch Registry

http://bioinfo.cipf.es/noiseq/doku.php?id=start

Software used for the identification of differentially expressed genes from count data or previously normalized count data. It empirically models the noise distribution of count changes by contrasting fold-change differences (M) and absolute expression differences (D) for all the features in samples within the same condition. This reference distribution is then used to assess whether the M-D values computed between two conditions for a given gene is likely to be part of the noise or represent a true differential expression.

Proper citation: NOISeq (RRID:SCR_003002) Copy   

•   Source: SciCrunch Registry

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

Software package for low-throughput real-time quantitative PCR data analysis. The package allows you to import easily qPCR data files. Thereafter, you can calculate amplification efficiencies, relative quantities and their standard errors, normalization factors based on the best reference genes choosen (using the SLqPCR package), and then the normalized relative quantities, the NRQs scaled to your control and their standard errors.

Proper citation: EasyqpcR (RRID:SCR_003406) 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

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry