somatic-mutations

ShixiangWang/sigminer

🌲 An easy-to-use and scalable toolkit for genomic alteration signature (a.k.a. mutational signature) analysis and visualization in R https://shixiangwang.github.io/sigminer/reference/index.html

crazyhottommy/DNA-seq-analysis

DNA sequencing analysis notes from Ming Tang

google/deepsomatic

DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal and tumor-only sequencing data.

FunGeST/Palimpsest

An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.

HKU-BAL/ClairS

ClairS - a deep-learning method for long-read somatic small variant calling

single-cell-genetics/cardelino

Clone identification from single-cell data

getzlab/deTiN

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

IARCbioinfo/needlestack

Multi-sample somatic variant caller

Clinical-Genomics/BALSAMIC

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer

HKU-BAL/ClairS-TO

ClairS-TO - a deep-learning method for tumor-only somatic variant calling

akiomiyao/tif

Transposon Insertion Finder - Detection of new TE insertions in NGS data

PoisonAlien/somaticfreq

knowledge-based genotyping of cancer hotspots from the tumor BAM files

tobiasrausch/nRex

nRex: Germline and somatic single-nucleotide, short indel and structural variant calling

mdelcorvo/TOSCA

Snakemake workflow for somatic mutation detection without matched normal samples

akiomiyao/tef

Transposable Element Finder - Detection of active transposable elements from NGS data

nriddiford/svParser

Explore and filter structural variant calls from Lumpy and Delly VCF files

pllittle/UNMASC

Tumor-only variant calling

likelet/CaMutQC

An R package for mutation quality control of cancer genomic sequening dataset

caravagn/evoverse.datasets

Datasets and analysis results released with the REVOLVER package for Cancer Evolution.

daormar/geno-debasher

Geno-DeBasher package for detection of germline and somatic variants

akiomiyao/ped

Polymorphic Edge Detection - An efficient polymorphism detector for NGS data

haoziyeung/somatic_pipeline

肿瘤体细胞突变检测流程（组织、cfDNA均可，需要有对照）

cbrueffer/MutationExplorer

R Shiny based lightweight mutation exploration tool

morinlab/tools-morinlab

Galaxy Tool Shed repositories maintained and developed by the Morin Lab.

nickveltmaat/SNVcaller

Pipeline to call SNV's with 4 tools (VarDict, LoFreq, Mutect2 & SiNVICT)

USCbiostats/HiLDA

:package: An R package for inferring the mutational exposures difference between groups.

KarchinLab/HotMAPS_2016

Detects hotspot regions for somatic mutations in 3D protein structures

caravagnalab/lineaGT

Lineage inference from Gene Therapy assays with insertional mutagenesis and somatic mutations

ghga-de/nf-aceseq

a Nextflow ACE-Seq calling and annotation pipeline based on DKFZ-ODCF/ACEseqWorkflow

ghga-de/nf-platypusindelcalling

This page is reserved for NextFlow based Indell Calling Workflow (with Platypus) from DKFZ

ghga-de/nf-snvcalling

a Nextflow SNV calling and annotation pipeline based on DKFZ-ODCF/SNVCallingWorkflow

gvisona/COSMIC_Embedding

TheOrangeBraincell/variants_in_AS_Pipeline

Depository for Bioinformatics Master Project HT2022-VT2023

sebastian-gregoricchio/SPACCa

Snakemake Pipeline for the Analyses of ChIP-seq data in Cancer samples

pllittle/ROKETworkflow

This repo contains an R package to execute ROKET's real data analysis workflow on TCGA cancer types