rpensch

rpensch's Stars

• ucsd-ccbb/NetColoc

  development of network co-localization tool

  Language:Jupyter Notebook136

• AlexandrovLab/SigProfilerMatrixGenerator

  SigProfilerMatrixGenerator creates mutational matrices for all types of somatic mutations. It allows downsizing the generated mutations only to parts for the genome (e.g., exome or a custom BED file). The tool seamlessly integrates with other SigProfiler tools.

  Language:Python10137

• etal/cnvkit

  Copy number variant detection from targeted DNA sequencing

  Language:Python563166

• nf-core/rnaseq

  RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

  Language:Nextflow938712

• hdng/clonevol

  Inferring and visualizing clonal evolution in multi-sample cancer sequencing

  Language:R14445

• im3sanger/dndscv

  dN/dS methods to quantify selection in cancer and somatic evolution

  Language:HTML21348

• tgen/tCoNuT

  TGen Copy Number Tool

  Language:MATLAB44

• AlexandrovLab/SigProfilerExtractor

  SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.

  Language:Python15452

• snakemake-workflows/rna-seq-star-deseq2

  RNA-seq workflow using STAR and DESeq2

  Language:Python331205

• Chao912/Mischka

  6

• amcpherson/citup

  Clonality inference in multiple tumor samples using phylogeny

  Language:C++134

• erdogant/kaplanmeier

  kaplanmeier is an python library to create survival curves using kaplan-meier, and compute the log-rank test.

  Language:Python3211

• nf-core/sarek

  Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

  Language:Nextflow411417

• broadinstitute/PhylogicNDT

  Language:HTML7139

• Roth-Lab/pyclone-vi

  Fast method for inferring cancer clonal population structure from SNV data.

  Language:Python5111