akiomiyao/ped

Polymorphic Edge Detection - An efficient polymorphism detector for NGS data

Language: Perl - Size: 12.8 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 4 - Forks: 2

ghga-de/nf-platypusindelcalling

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

Language: Python - Size: 119 MB - Last synced at: 3 days ago - Pushed at: 10 months ago - Stars: 2 - Forks: 0

ghga-de/nf-snvcalling

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

Language: Python - Size: 16.7 MB - Last synced at: 3 days ago - Pushed at: 10 months ago - Stars: 3 - Forks: 0

ghga-de/nf-aceseq

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

Language: R - Size: 49.6 MB - Last synced at: 3 days ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 0

caravagnalab/INCOMMON

Bayesian inference of gene mutant dosage from targeted panels without matched normal

Language: R - Size: 102 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 2 - Forks: 1

HKU-BAL/ClairS-TO

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

Language: Python - Size: 12.1 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 68 - Forks: 4

caravagnalab/tickTack

Pseudo-timing copy number alterations in cancer

Language: R - Size: 8.96 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 0 - Forks: 0

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.

Size: 66.4 KB - Last synced at: 5 days ago - Pushed at: 4 months ago - Stars: 180 - Forks: 22

akiomiyao/tef

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

Language: Perl - Size: 816 KB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 9 - Forks: 0

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

Language: R - Size: 59.7 MB - Last synced at: 17 days ago - Pushed at: 17 days ago - Stars: 154 - Forks: 19

crazyhottommy/DNA-seq-analysis

DNA sequencing analysis notes from Ming Tang

Language: Shell - Size: 247 KB - Last synced at: 7 days ago - Pushed at: over 2 years ago - Stars: 146 - Forks: 61

Clinical-Genomics/BALSAMIC

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer

Language: Python - Size: 229 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 49 - Forks: 15

sebastian-gregoricchio/SPACCa

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

Language: Python - Size: 4.74 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

single-cell-genetics/cardelino

Clone identification from single-cell data

Language: R - Size: 9.8 MB - Last synced at: 26 days ago - Pushed at: almost 3 years ago - Stars: 61 - Forks: 13

likelet/CaMutQC

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

Language: R - Size: 70.6 MB - Last synced at: 16 days ago - Pushed at: about 2 months ago - Stars: 7 - Forks: 0

HKU-BAL/ClairS

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

Language: Python - Size: 12.7 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 85 - Forks: 8

KarchinLab/HotMAPS_2016

Detects hotspot regions for somatic mutations in 3D protein structures

Language: Python - Size: 113 KB - Last synced at: about 2 months ago - Pushed at: over 1 year ago - Stars: 3 - Forks: 0

uab-cgds-worthey/somatic-mutation-signal-identification

Mutational signal profiling from somatic variation to detect disrupted mechanisms in somatic cells (typically cancers) using https://github.com/AlexandrovLab/SigProfilerExtractor

Language: Python - Size: 35.2 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

Ddafnoudis/Somatic-Mutations

Analysis of somatic mutations in patients with Leukemia. Optimizing Machine and Deep Learning models for multi-classification tasks.

Language: Python - Size: 3.99 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

tobiasrausch/nRex

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

Language: Shell - Size: 1.87 MB - Last synced at: 3 days ago - Pushed at: 5 months ago - Stars: 12 - Forks: 2

pllittle/UNMASC

Tumor-only variant calling

Language: HTML - Size: 712 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 9 - Forks: 1

caravagnalab/lineaGT

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

Language: R - Size: 20 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 1 - Forks: 0

PoisonAlien/somaticfreq

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

Language: C - Size: 4.7 MB - Last synced at: 4 months ago - Pushed at: over 3 years ago - Stars: 21 - Forks: 4

Vedbar/DNA-seq_Somatic_Variants

Somatic Variants

Size: 128 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

pllittle/ROKET

This R package repository performs optimal transport and kernel regression hypothesis testing. Functions to perform large scale simulations are also provided.

Language: HTML - Size: 2.91 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

akiomiyao/tif

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

Language: Perl - Size: 229 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 20 - Forks: 4

gvisona/COSMIC_Embedding

Language: Python - Size: 54.6 MB - Last synced at: 1 day ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 1

TheOrangeBraincell/variants_in_AS_Pipeline

Depository for Bioinformatics Master Project HT2022-VT2023

Language: Python - Size: 943 KB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 0

nygenome/lancet

Microassembly based somatic variant caller for NGS data

Language: C - Size: 8.67 MB - Last synced at: about 1 year ago - Pushed at: about 3 years ago - Stars: 153 - Forks: 33

daormar/geno-debasher

Geno-DeBasher package for detection of germline and somatic variants

Language: Shell - Size: 3.36 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 5 - Forks: 1

jtwrt/VARIANT_VISUALIZER

Language: Jupyter Notebook - Size: 16.7 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

IARCbioinfo/needlestack

Multi-sample somatic variant caller

Language: R - Size: 49.8 MB - Last synced at: almost 2 years ago - Pushed at: over 3 years ago - Stars: 46 - Forks: 14

nriddiford/svParser

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

Language: Perl - Size: 4.07 MB - Last synced at: almost 2 years ago - Pushed at: almost 5 years ago - Stars: 8 - Forks: 1

haoziyeung/somatic_pipeline

肿瘤体细胞突变检测流程（组织、cfDNA均可，需要有对照）

Language: Perl - Size: 6.12 MB - Last synced at: about 2 years ago - Pushed at: over 7 years ago - Stars: 4 - Forks: 9

FunGeST/Palimpsest

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

Language: R - Size: 58.2 MB - Last synced at: almost 2 years ago - Pushed at: about 4 years ago - Stars: 67 - Forks: 19

getzlab/deTiN

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

Language: Jupyter Notebook - Size: 17.6 MB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 47 - Forks: 20

cbrueffer/MutationExplorer

R Shiny based lightweight mutation exploration tool

Language: R - Size: 354 KB - Last synced at: 5 months ago - Pushed at: over 4 years ago - Stars: 3 - Forks: 0

nickveltmaat/SNVcaller

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

Language: Python - Size: 193 KB - Last synced at: 6 months ago - Pushed at: almost 3 years ago - Stars: 3 - Forks: 1

mdelcorvo/TOSCA

Snakemake workflow for somatic mutation detection without matched normal samples

Language: Python - Size: 137 MB - Last synced at: over 2 years ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 1

pllittle/ROKETworkflow

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

Language: R - Size: 257 KB - Last synced at: over 2 years ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0

caravagn/evoverse.datasets

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

Language: R - Size: 4.15 MB - Last synced at: over 2 years ago - Pushed at: over 5 years ago - Stars: 4 - Forks: 0

morinlab/tools-morinlab

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

Language: Python - Size: 54.3 MB - Last synced at: over 2 years ago - Pushed at: almost 8 years ago - Stars: 3 - Forks: 6

Ala-Eddine-BOUDEMIA/TRC-related-mutational-signatures

Analysis of mutational signatures associated with replication stress in cancer

Language: HTML - Size: 1.87 GB - Last synced at: over 2 years ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 0

QBRC/QBRC-Somatic-Pipeline Fork of tianshilu/QBRC-Somatic-Pipeline

QBRC Somatic Mutation Calling Pipeline

Language: C - Size: 87.9 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 1

USCbiostats/HiLDA

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

Language: R - Size: 21.1 MB - Last synced at: 13 days ago - Pushed at: almost 4 years ago - Stars: 3 - Forks: 2

maofengbiao/AI-Driver Fork of hatchetProject/AI-Driver

AI-based prediction of driver mutations

Language: Python - Size: 10.2 MB - Last synced at: almost 2 years ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0

theLongLab/PRESM

Personalized reference editor for somatic mutation discovery

Language: Java - Size: 506 KB - Last synced at: over 2 years ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0