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http://www.bioconductor.org/packages/2.12/bioc/html/VariantAnnotation.html
Software package to annotate variants, compute amino acid coding changes, and predict coding outcomes.
Proper citation: VariantAnnotation (RRID:SCR_000074) Copy
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
https://github.com/cancerit/BRASS
Software tool for analysis of one or more related BAM files of paired end sequencing to determine potential rearrangement breakpoints. Identifies breaks and attempts to assemble rearrangements.
Proper citation: BRASS (RRID:SCR_017091) Copy
https://github.com/dgrun/RaceID
Algorithm for identification of rare and abundant cell types from single cell transcriptome data. Based on transcript counts obtained with unique molecular identifies. Used for discovering rare cell types and corresponding marker genes in healthy and diseased organs. Operating system Unix/Linux, Mac OS, Windows.
Proper citation: RaceID (RRID:SCR_017045) Copy
http://www.cbs.dtu.dk/biotools/sequenza/
Software package for copy number estimation from tumor genome sequencing data.Tools to analyze genomic sequencing data from paired normal-tumor samples, including cellularity and ploidy estimation; mutation and copy number (allele-specific and total copy number) detection, quantification and visualization.
Proper citation: Sequenza (RRID:SCR_016662) Copy
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