nf-core/raredisease

Call and score variants from WGS/WES of rare disease patients.

Language: Nextflow - Size: 187 MB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 100 - Forks: 44

XWangLabTHU/cfDNApipe

cfDNApipe: A comprehensive quality control and analysis pipeline for cell-free DNA high-throughput sequencing data

Language: Python - Size: 158 MB - Last synced at: 17 days ago - Pushed at: almost 3 years ago - Stars: 65 - Forks: 33

zhengxwen/SeqArray

Data management of large-scale whole-genome sequence variant calls using GDS files (Development version only)

Language: C++ - Size: 9.82 MB - Last synced at: 7 days ago - Pushed at: about 1 month ago - Stars: 45 - Forks: 12

sigven/gvanno

Generic human DNA variant annotation pipeline

Language: Python - Size: 13.7 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 44 - Forks: 11

cancerit/dockstore-cgpwgs

Dockstore implementation of CGP core WGS analysis

Language: Shell - Size: 3.74 MB - Last synced at: over 1 year ago - Pushed at: almost 5 years ago - Stars: 25 - Forks: 14

Adigorla/xgap

xGAP is an efficient, modular, extensible and fault-tolerant pipeline for massively parallelized genomic analysis/variant discovery from next-generation DNA sequencing data.

Language: Python - Size: 113 KB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 10 - Forks: 2

shewa12/svn-guide-to-upload-wp-plugin

This guide outlines a step-by-step process for managing your WordPress plugin to add/update in the WordPress repository using SVN (Subversion). SVN is a version control system that helps you track changes, collaborate with others, and maintain a history of your project.

Size: 5.86 KB - Last synced at: about 5 hours ago - Pushed at: 9 months ago - Stars: 9 - Forks: 0

waqasuddinkhan/MACARON-GenMed-LabEx

Multi-bAse Codon-Associated variant Re-annotatiON (MACARON)

Language: Python - Size: 121 KB - Last synced at: over 1 year ago - Pushed at: about 5 years ago - Stars: 7 - Forks: 3

bcgsc/ntRoot

🌳 Human ancestry inference from genomic data

Language: Python - Size: 84.2 MB - Last synced at: 25 days ago - Pushed at: 2 months ago - Stars: 6 - Forks: 0

PathoGenOmics-Lab/get_MNV

Identifies multiple SNVs within the same codon, reclassifies them as MNVs, and accurately computes resulting amino acid changes from genomic reads

Language: Rust - Size: 3.36 MB - Last synced at: about 2 months ago - Pushed at: 3 months ago - Stars: 6 - Forks: 1

dbmi-bgm/granite Fork of bgm-cwg/novoCaller

A collection of software to work with genomic variants

Language: Python - Size: 46 MB - Last synced at: 12 days ago - Pushed at: 9 months ago - Stars: 6 - Forks: 0

jingxinfu/TCGAdnloader

TCGA hg19 and hg38 data downloader.

Language: Python - Size: 52.1 MB - Last synced at: 11 months ago - Pushed at: over 4 years ago - Stars: 4 - Forks: 1

chadlaing/feht

Predictive marker discovery for groups; binary data, genomic data (single nucleotide variants), arbitrary character data.

Language: Haskell - Size: 129 KB - Last synced at: about 1 year ago - Pushed at: almost 7 years ago - Stars: 4 - Forks: 2

Computational-Genomics-BSC/plink-bed-reader

Lightweight and memory efficient reader for PLINK BED files. It supports both SNP-major and individual-major formats. Written in Python.

Language: Python - Size: 3.96 MB - Last synced at: 3 days ago - Pushed at: 3 months ago - Stars: 3 - Forks: 0

xjtu-omics/ChineseQuartetGenome

Genome assembly and variant benchmarks for Chinese Quartet

Language: Python - Size: 60.8 MB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 3 - Forks: 0

TNTurnerLab/acorn

acorn is an R package that examines various features of de novo variants including subsetting DNVs by individual, variant type, or genomic region; calculating features including variant change counts, lengths, and presence/absence at CpG sites; and characteristics of parental age and number of DNVs.

Language: R - Size: 17 MB - Last synced at: almost 2 years ago - Pushed at: about 2 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: 3 months ago - Pushed at: over 2 years ago - Stars: 3 - Forks: 1

nriddiford/mutationProfiles

Extract and explore snv data

Language: R - Size: 65.2 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 3 - Forks: 3

cancerit/dockstore-cgpwxs

Dockstore implementation of CGP core WXS analysis

Language: Shell - Size: 758 KB - Last synced at: over 1 year ago - Pushed at: almost 5 years ago - Stars: 3 - Forks: 2

TomMakesThings/Cancer-Evolution

Estimates the clonal population structure in a tumour sample given a cell mutation matrix

Language: Jupyter Notebook - Size: 1.45 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 0

TC-Hewitt/MuTrigo

pipeline for mutant gene candidate discovery

Language: Python - Size: 81.1 KB - Last synced at: over 1 year ago - Pushed at: almost 3 years ago - Stars: 2 - Forks: 0

quinlan-lab/constraint-tools

Tools to discover natural selection given multiple evolved DNA sequences (e.g., gnomad cohort, or multiple tumor samples)

Language: Jupyter Notebook - Size: 601 MB - Last synced at: 2 months ago - Pushed at: 4 months ago - Stars: 1 - 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: about 2 months ago - Pushed at: 7 months ago - Stars: 1 - Forks: 0

Mahsa-Ehsanifard/maftools

maftools for SNV mutation analysis, summarizes, and visualization

Language: R - Size: 3.2 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 1 - Forks: 0

auroramaurizio/my_DNA_seq_pipelines

In this repository I backup the pipelines I write for the project I am involved

Language: Python - Size: 2.85 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

EUCANCan/prepy-wrapper

Wrapper for pre.py from Illumina's hap.py package. It is used to preprocess VCF files in order to normalize SNVs and indels for downstream analysis.

Language: Python - Size: 25.4 KB - Last synced at: 11 days ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

laura-budurlean/GATK-WGS-Pipeline

GATK WGS workflow

Language: Shell - Size: 10.7 KB - Last synced at: 2 months ago - Pushed at: almost 2 years ago - Stars: 1 - Forks: 0

ashudva/SNV-Business

Front-End for SNV Business firm

Language: CSS - Size: 10.1 MB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 0

oicr-gsi/varscan

varscan repo contains code for Varscan workflow

Language: WDL - Size: 124 KB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 0 - Forks: 0

samueltonao/Lauth

Enterprise-grade unified authentication platform with multi-application support, built with Go for high performance and security.

Size: 1.95 KB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0

swvanderlaan/MonopogenLite

Germline SNV calling and phasing from single cell sequencing (for macOS Sequoia and Rocky8).

Language: Python - Size: 5.19 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 0 - Forks: 0

tsar123/neutral-single-nucleotide-polymorphisms-analysis

analysis of data on neutral single nucleotide polymorphisms

Language: Jupyter Notebook - Size: 2.46 MB - Last synced at: about 2 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 0

NCI-CGR/HPV_low_VAF_SNV_prediction

Predicting true low-VAF SNVs in HPV using triplicate NGS samples and machine learning

Language: Jupyter Notebook - Size: 17.3 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

anbianchi/IntegratedSNVINDELSandCNV

An adaptable method for analyzing SNVs, INDELs, and CNVs from Whole Exome Sequencing (WES) data, emphasizing germline variants.

Language: Python - Size: 22.9 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

auroramaurizio/WES_ESOCA

WES Analysis scripts for "Immune determinants of response to neoadjuvant chemo-radiation in esophageal adenocarcinoma" publication

Language: Python - Size: 69.3 KB - Last synced at: 10 months ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

petermchale/genomics-web-app

vue app with flask REST api to process genomic data

Language: Jupyter Notebook - Size: 49.5 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

wennj/pileupReformater

Convert output from Samtools pileup into a matrix.

Language: Java - Size: 25.4 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

deropi/BathyBrooksiSymbionts

Language: Python - Size: 16.7 MB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

bdolmo/CeLAuth

Cell Line Authentication from ChIP-seq data

Language: Perl - Size: 53.9 MB - Last synced at: about 2 years ago - Pushed at: about 4 years ago - Stars: 0 - Forks: 0

ToolsVanBox/SNVFI Fork of UMCUGenetics/SNVFI

Single Nucleotide Variant Filtering

Language: Shell - Size: 31.3 KB - Last synced at: 12 months ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0

qbicsoftware/mtb-parser-lib

A simple module for diagnostic variant information parsing

Language: Python - Size: 86.9 KB - Last synced at: 21 days ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0

maxim-k/PyVep

Python wrapper and web-server for Ensembl VEP

Language: Python - Size: 84 KB - Last synced at: almost 2 years ago - Pushed at: about 8 years ago - Stars: 0 - Forks: 0