PureCN - Copy number calling and SNV classification using targeted short read sequencing
This package estimates tumor purity, copy number, and loss of heterozygosity (LOH), and classifies single nucleotide variants (SNVs) by somatic status and clonality. PureCN is designed for targeted short read sequencing data, integrates well with standard somatic variant detection and copy number pipelines, and has support for tumor samples without matching normal samples.
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copynumbervariationsoftwaresequencingvariantannotationvariantdetectioncoverageimmunooncologybioconductor-packagecell-free-dnacopy-numberlohtumor-heterogeneitytumor-mutational-burdentumor-purity
9.48 score 150 stars 77 scripts 931 downloadscuratedBladderData - Bladder Cancer Gene Expression Analysis
Manually curated bladder cancer ExpressionSet objects from 10 studies (12 objects, since two studies contributed data on two platforms each), with uniformly processed expression data and curated clinical metadata. Datasets are hosted on Zenodo and downloaded on first use, then cached locally with BiocFileCache. Includes a configurable script for rule-based creation of filtered dataset lists for meta-analysis.
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experimentdatacancerdatamicroarraydataexpressiondatageobioconductor-packagedatapkg
4.62 score 1 stars 12 scripts