Tools

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Current Tools

ABSOLUTE

ABSOLUTE source code that works with allelic copy ratio on both hg19 and hg38

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Last Updated 22 Mar 2023 by julianhess

AsymTools 2

AsymTools is a package for analyzing transcriptional and replicative mutational strand asymmetries in cancer sequencing datasets.

getzlab/AsymTools2

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Last Updated 17 Jul 2023 by njharlen

CLUMPS 2

Re-factored code for CLUMPS.

getzlab/CLUMPS2

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Last Updated 6 Mar 2023 by ajdunford

DeTiN

DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated matched control.

getzlab/deTiN

Topics: cancer-genomics , cancer-variants , cancer-genome-atlas , tumor , detection , tumor-in-normal , somatic-mutations , tin

Last Updated 20 May 2022 by briandiamondage-sema4

GISTIC 2

Genomic Identification of Significant Targets in Cancer (GISTIC), version 2

broadinstitute/gistic2

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Last Updated 8 Apr 2022 by stevenschumacher

MSMuTect 2

Accurate detection of somatic MS (microsatellite) indels.

getzlab/MSMuTect2

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Last Updated 30 Mar 2022 by cbirger

MSMutSig

Detects loci with a significantly higher-than-expected frequency of somatic MS (microsatellite) indels.

getzlab/MSMutSig

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Last Updated 28 Mar 2022 by dheiman

MuTect 1

MuTect -- Accurate and sensitive cancer mutation detection

getzlab/mutect

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Last Updated 13 Sep 2021 by julianhess

MutSig2CV

MutSig2CV from Lawrence et al. 2014

getzlab/MutSig2CV

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Last Updated 18 Aug 2020 by julianhess

PHIAL

Precision Heuristics for Interpreting the Alteration Landscape

vanallenlab/phial

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Last Updated 12 Feb 2021 by brendanreardon

PhylogicNDT

broadinstitute/PhylogicNDT

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Last Updated 12 Jun 2020 by iglc

RNA-SeQC 2

Fast, efficient RNA-Seq metrics for quality control and process optimization

getzlab/rnaseqc

Topics: rnaseq , rna-seq , bioinformatics

Last Updated 12 Mar 2023 by francois-a

SignatureAnalyzer

Updated SignatureAnalyzer-GPU with mutational spectra & RNA expression compatibility.

getzlab/SignatureAnalyzer

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Last Updated 17 May 2023 by yoakiyama

tensorQTL

Ultrafast GPU-enabled QTL mapper

broadinstitute/tensorqtl

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Last Updated 17 Jul 2023 by francois-a

Historic Tools

CLUMPS

getzlab/CLUMPS

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Last Updated 19 Jul 2022 by ajdunford

MSMuTect1

getzlab/MSMuTect1

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Last Updated 15 Mar 2021 by AvrahamKahan123