There are no reviews yet. Be the first to send feedback to the community and the maintainers!
rnaseqc
Fast, efficient RNA-Seq metrics for quality control and process optimizationdeTiN
DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated matched control.MutSig2CV
MutSig2CV from Lawrence et al. 2014dalmatian
dalmatian is a collection of high-level companion functions for Firecloud and FISS.CPTAC_PanCan_PTM_2023
scrinvex
Single Cell RNA Intron-Exon countingHaradhvala_et_al_2022
10x-cd45-isoform-quantification
CLUMPS-PTM
CLUMPS adapted to post-translational modifications.ABSOLUTE
ABSOLUTE source code that works with allelic copy ratio on both hg19 and hg38canine
A modular, high-performance computing solution to run jobs using SLURMAnnoMate
Review anything (purities, mutations, etc) within a jupyter notebook with plotly dash and jupyter widgetsBoiarsky-etal-2022
Code to reproduce methods & results from Boiarsky et. al., Nature Communications 2022igv_remote
A Python interface for interacting with IGV desktop over a port using IGV batch commandsSMM_clustering_2020
Repo for analysis of SMM DNA + RNA data.LUAD_subtypes
CApy
Cancer Analysis tools in PythonCLUMPS
rnaseqc2-paper
RNA-SeQC 2 manuscript materialspathway_based_biomarker
CLUMPS2
Re-factored code for CLUMPS.mudi
A collection of downstream python single-cell utilities.mutect-benchmark
Code repo for master thesisMSMuTect2
Accurate detection of somatic MS (microsatellite) indels.CLLmap
PurityReviewer
Suite of purity reviewers and review componentsigv_gdc_buddy
stream & update gdc signed url to IGVgbm_icb_manuscript
Code for reproducing the figures in the Ghannam et al. GBM ICB manuscriptGISTIC2_postprocessing
The repo contains codes (in matlab) to force call GISTIC2 driver events at sample levellapdog
A python module, CLI, and browser-based UI to run jobs outside of FirecloudMSMuTect1
MSMuTect
Calling indels in microsatellite lociREBC_tools
Repo for code & tasks used for REBC analysisAsymTools2
AsymTools is a package for analyzing transcriptional and replicative mutational strand asymmetries in cancer sequencing datasets.MSMutSig
Detects loci with a significantly higher-than-expected frequency of somatic MS (microsatellite) indels.PhylogicNDTReviewer
Interactive app to review Phylogic solutions and data.bladder_cancer_classifier
DLBclass-tool
Love Open Source and this site? Check out how you can help us