cancer-genomics

Unix, R and python tools for genomics and data science

cBioPortal for Cancer Genomics

DELLY2: Structural variant discovery by integrated paired-end and split-read analysis

Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

#Awesome#A community-maintained repository of cancer clinical knowledge bases and databases focused on cancer variants.

Chromosome visualization for the web

fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"

Personal Cancer Genome Reporter (PCGR)

An ensemble approach to accurately detect somatic mutations using SomaticSeq

Lollipop-style mutation diagrams for annotating genetic variations.

Haplotype-aware CNV analysis from single-cell RNA-seq

A visualization grammar and GPU-accelerated toolkit for genomic data

#计算机科学#Training and evaluating a variational autoencoder for pan-cancer gene expression data

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 e...

Microassembly based somatic variant caller for NGS data

microsatellite instability detection using tumor only or paired tumor-normal data

React Frontend of cBioPortal 🎉

What you need to process the Quarterly DepMap-Omics releases from Terra

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)....