somatic-mutations
There are 45 repositories under somatic-mutations topic.
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.
nygenome/lancet
Microassembly based somatic variant caller for NGS data
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
HKU-BAL/ClairS
ClairS - a deep-learning method for long-read somatic small variant calling
FunGeST/Palimpsest
An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.
single-cell-genetics/cardelino
Clone identification from single-cell data
HKU-BAL/ClairS-TO
ClairS-TO - a deep-learning method for tumor-only somatic variant calling
IARCbioinfo/needlestack
Multi-sample somatic variant caller
getzlab/deTiN
DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated matched control.
Clinical-Genomics/BALSAMIC
Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
PoisonAlien/somaticfreq
knowledge-based genotyping of cancer hotspots from the tumor BAM files
akiomiyao/tif
Transposon Insertion Finder - Detection of new TE insertions in NGS data
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
pllittle/UNMASC
Tumor-only variant calling
nriddiford/svParser
Explore and filter structural variant calls from Lumpy and Delly VCF files
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
mirjamcmmueller/variants_in_AS_Pipeline
Depository for Bioinformatics Master Project HT2022-VT2023
Vedbar/DNA-seq_Somatic_Variants
Somatic Variants
Ddafnoudis/Somatic-Mutations
Analysis of somatic mutations in patients with Leukemia. Optimizing Machine and Deep Learning models for multi-classification tasks.