somatic-mutations

There are 0 repository under somatic-mutations topic.

nygenome / lancet
Microassembly based somatic variant caller for NGS data
somatic-mutations cancer-genomics variant-callers debruijn-graph snvs indels local-assembly
Language:C 153
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
mutational-signatures copynumber-signatures somatic-variants somatic-mutations cosmic-signatures signature-extraction nmf nmf-extraction bayesian-nmf bioinformatics r cancer-research visualization sbs dbs indel cnv easy-to-use
Language:R 142
crazyhottommy / DNA-seq-analysis
DNA sequencing analysis notes from Ming Tang
cancer-genomes genome-sequencing somatic-mutations
Language:Shell 139
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.
bioinformatics deep-learning deepsomatic dna genome genomics machine science sequencing somatic-mutations somatic-variants
131
FunGeST / Palimpsest
An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.
cancer-genomics genomics visualization r somatic-mutations mutational-signatures structural-variation clonality tumor-heterogeneity tumor-evolution signature-extraction nmf nmf-extraction structural-variant-signatures bioinformatics bioinformatics-analysis cancer-research driver-events
Language:R 69
HKU-BAL / ClairS
ClairS - a deep-learning method for long-read somatic small variant calling
deep-learning long-reads nanopore ont somatic-mutations somatic-variants bioinformatics genomics haplotypes phasing snvs indels illumina long-read-sequencing short-reads pacbio
Language:Python 68
single-cell-genetics / cardelino
Clone identification from single-cell data
clonal-clustering gibbs-sampling scrna-seq single-cell somatic-mutations
Language:R 57
getzlab / deTiN
DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated matched control.
cancer-genomics cancer-variants cancer-genome-atlas tumor detection tumor-in-normal somatic-mutations tin
Language:Jupyter Notebook 49
IARCbioinfo / needlestack
Multi-sample somatic variant caller
bam-files docker negative-binomial-regression nextflow ngs pipeline regression samtools somatic-mutations variants
Language:R 48
HKU-BAL / ClairS-TO
ClairS-TO - a deep-learning method for tumor-only somatic variant calling
bioinformatics deep-learning genomics illumina long-read-sequencing long-reads nanopore ont pacbio snvs somatic-mutations somatic-variants tumor-only tumors variant-calling variants
Language:Python 45
Clinical-Genomics / BALSAMIC
Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
genomics somatic-mutations snakemake-workflows variant-calling bioinformatics
Language:Python 44
akiomiyao / tif
Transposon Insertion Finder - Detection of new TE insertions in NGS data
ngs somatic-indels somatic-mutations somatic-variants transposable-elements transposons
Language:Perl 19
PoisonAlien / somaticfreq
knowledge-based genotyping of cancer hotspots from the tumor BAM files
bam-files cancer-genomics somatic-mutations html-report
Language:C 19
tobiasrausch / nRex
nRex: Germline and somatic single-nucleotide, short indel and structural variant calling
variant-calling sequencing alignment germline somatic-variants somatic-mutations mutations structural-variation
Language:Shell 12
mdelcorvo / TOSCA
Snakemake workflow for somatic mutation detection without matched normal samples
workflow snakemake somatic-mutations
Language:Python 11
akiomiyao / tef
Transposable Element Finder - Detection of active transposable elements from NGS data
somatic-indels somatic-mutations somatic-variants transposable-elements transposons
Language:Perl 8
nriddiford / svParser
Explore and filter structural variant calls from Lumpy and Delly VCF files
structural-variation vcf wgs-data somatic-mutations cancer-genomics filter-structural-variants filter-lumpy-express variants filtering-variants
Language:Perl 8
pllittle / UNMASC
Tumor-only variant calling
somatic-mutations tumor-only ngs bioinformatics genomics vcf
Language:R 8
likelet / CaMutQC
An R package for mutation quality control of cancer genomic sequening dataset
cancer-genomics somatic-mutations
Language:R 7
caravagn / evoverse.datasets
Datasets and analysis results released with the REVOLVER package for Cancer Evolution.
revolver dataset genomic sequencing somatic-mutations cancer-evolution
Language:R 5
daormar / geno-debasher
Geno-DeBasher package for detection of germline and somatic variants
bioinformatics bioinformatics-pipeline cancer genomics germline-variants next-generation-sequencing somatic-mutations somatic-variants workflow
Language:Shell 5
akiomiyao / ped
Polymorphic Edge Detection - An efficient polymorphism detector for NGS data
polymorphism inversion insertion ngs deletion snp k-mer ngstools somatic-mutations genotype sequence-alignments variant cnv copy-number-variation crispr-cas9
Language:Perl 4
haoziyeung / somatic_pipeline
肿瘤体细胞突变检测流程（组织、cfDNA均可，需要有对照）
cnv fusion-genes sentieon somatic-mutations
Language:Perl 4
cbrueffer / MutationExplorer
R Shiny based lightweight mutation exploration tool
cancer cancer-genomics mutations shinyapp bioinformatics somatic-mutations rna-seq scanb r shiny
Language:R 3
morinlab / tools-morinlab
Galaxy Tool Shed repositories maintained and developed by the Morin Lab.
cancer genomics mutation somatic-variants somatic-mutations copy-number-variation visualization circos
Language:Python 3
nickveltmaat / SNVcaller
Pipeline to call SNV's with 4 tools (VarDict, LoFreq, Mutect2 & SiNVICT)
somatic-variants somatic-mutations snvs snv snv-annotation cell-free-dna ctdna cfdna lofreq mutect2 vardict sinvict indel
Language:Python 3
USCbiostats / HiLDA
:package: An R package for inferring the mutational exposures difference between groups.
mutational-signatures r-package rjags somatic-mutations
Language:R 3
KarchinLab / HotMAPS_2016
Detects hotspot regions for somatic mutations in 3D protein structures
cancer exome-scale hotspot hotspot-regions missense-mutations protein-structure somatic-mutations
Language:Python 2
caravagnalab / lineaGT
Lineage inference from Gene Therapy assays with insertional mutagenesis and somatic mutations
clonal-evolution gene-therapy lineage-tracing somatic-mutations
Language:R 1
ghga-de / nf-aceseq
a Nextflow ACE-Seq calling and annotation pipeline based on DKFZ-ODCF/ACEseqWorkflow
ace dkfz ghga odcf somatic-mutations somatic-variants sv ace-seq
Language:R 1
ghga-de / nf-platypusindelcalling
This page is reserved for NextFlow based Indell Calling Workflow (with Platypus) from DKFZ
annotation annotations nextflow nextflow-pipeline pipeline platypus variant-calling workflow indel-calling dkfz ghga odcf somatic-mutations somatic-variants
Language:Python 1
ghga-de / nf-snvcalling
a Nextflow SNV calling and annotation pipeline based on DKFZ-ODCF/SNVCallingWorkflow
snv snv-call snv-annotation dkfz ghga somatic-mutations somatic-variants odcf
Language:Python 1
gvisona / COSMIC_Embedding
embeddings infovae pytorch representation-learning somatic-mutations vae
Language:Python 1
TheOrangeBraincell / variants_in_AS_Pipeline
Depository for Bioinformatics Master Project HT2022-VT2023
alternative-splicing bioinformatics germline-variants somatic-mutations
Language:Python 1
sebastian-gregoricchio / SPACCa
Snakemake Pipeline for the Analyses of ChIP-seq data in Cancer samples
chip-seq chip-seq-analysis chip-seq-callers chip-seq-data chip-seq-peaks chipseq copynumber gatk gatk4 macs macs2 mutation mutation-analysis mutations normalization somatic-indels somatic-mutations somatic-variant somatic-variants
Language:Python 0
pllittle / ROKETworkflow
This repo contains an R package to execute ROKET's real data analysis workflow on TCGA cancer types
somatic-mutations optimal-transport kernel-regression
Language:R