snv

There are 0 repository under snv topic.

nf-core / raredisease
Call and score variants from WGS/WES of rare disease patients.
nf-core nextflow workflow pipeline wgs wes variant-calling snv structural-variants variant-annotation diagnostics rare-disease
Language:Nextflow 75
XWangLabTHU / cfDNApipe
cfDNApipe: A comprehensive quality control and analysis pipeline for cell-free DNA high-throughput sequencing data
cell-free-dna cfdna wgs-data wgbs-data snv virus-detection cnv
Language:Python 57
sigven / gvanno
Generic human DNA variant annotation pipeline
docker gene vep vcfanno germline variant-annotations vcf snv indels annotation-framework annotation-tool workflow singularity snvs variants disease-gene-association
Language:Python 53
zhengxwen / SeqArray
Data management of large-scale whole-genome sequence variant calls (Development version only)
bioinformatics gds-format r snp snv wes wgs
Language:C++ 43
cancerit / dockstore-cgpwgs
Dockstore implementation of CGP core WGS analysis
dockstore ngs somatic somatic-variants snv indels
Language:Shell 29
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.
ngs snv indels bioinformatics-pipeline bioinformatics genomics hpc slurm sge pipeline-framework
Language:Python 10
waqasuddinkhan / MACARON-GenMed-LabEx
Multi-bAse Codon-Associated variant Re-annotatiON (MACARON)
macaron snpcluster pcsnv snv-annotation snp codon annotator annotation-framework vcf snpeff gatk snv variants python github
Language:Python 7
dbmi-bgm / granite
A collection of software to work with genomic variants
vcf variants variant-analysis trio de-novo-mutation compound-heterozygous de-novo-mutations variant-filtration snv snvs single-nucleotide-variation
Language:Python 6
acorn
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.
denovo genome genomics indel mnv r snv variants
Language:R 6
chadlaing / feht
Predictive marker discovery for groups; binary data, genomic data (single nucleotide variants), arbitrary character data.
binay snp snv comparison fet haskell groups predictive markers genome
Language:Haskell 4
jingxinfu / TCGAdnloader
TCGA hg19 and hg38 data downloader.
tcga-data hg38 hg19 rna-seq cnv snv
Language:Python 4
bcgsc / ntRoot
🌳 Human ancestry inference from genomic data
ancestry ancestry-inference ancestrydna genome genome-assembly genomic-data genomic-data-analysis sequencing-data snv snv-call
Language:Python 3
cancerit / dockstore-cgpwxs
Dockstore implementation of CGP core WXS analysis
dockstore ngs snv indels
Language:Shell 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
nriddiford / mutationProfiles
Extract and explore snv data
snv plot-mutations mutational-signatures plot-mutect plot-varscan filter-mutect filter-varscan
Language:R 3
TC-Hewitt / MuTrigo
Pipeline for gene candidate discovery based on mutagenesis. Featured in gene cloning research published in Nature (DOIs: 10.1038/s41467-020-14937-2, 10.1038/s41467-021-23738-0, 10.1038/s41477-021-00971-5), Molecular Plant (DOI: 10.1016/j.molp.2021.05.010) and New Phytologist (DOI: 10.1111/nph.17075).
ngs-analysis ngs-pipeline ngs snp snv python samtools mpileup fasta pileup snps mutant python3
Language:Python 3
TomMakesThings / Cancer-Evolution
Estimates the clonal population structure in a tumour sample given a cell mutation matrix
cancer-genomic cancer-evolution snv bioinformatics
Language:Jupyter Notebook 3
xjtu-omics / ChineseQuartetGenome
Genome assembly and variant benchmarks for Chinese Quartet
chinese-quartet genome-assembly haplotype-resolved-assembly indel snv structural-variants variant-benchmark
Language:Python 3
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 pure Python.
bed bioinformatics genetics genotype indel plink snv variant
Language:Python 2
SNV-Business
ashudva / SNV-Business
Front-End for SNV Business firm
html-css-javascript fornt-end snv
Language:CSS 1
auroramaurizio / my_DNA_seq_pipelines
In this repository I backup the pipelines I write for the project I am involved
cnv contamination-detection dna-sequencing snv tas wes wgs plots vaf variant-calling purity structural-variants
Language:Python 1
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.
genomics indel snv variants vcf
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
Mahsa-Ehsanifard / maftools
maftools for SNV mutation analysis, summarizes, and visualization
maftools mutation snv
Language:R 1
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.
snv wordpress wordpress-plugin
1
anbianchi / IntegratedSNVINDELSandCNV
An adaptable method for analyzing SNVs, INDELs, and CNVs from Whole Exome Sequencing (WES) data, emphasizing germline variants.
breast-cancer cnv indels snv whole-exome-sequencing
Language:Python 0
bdolmo / CeLAuth
Cell Line Authentication from ChIP-seq data
chip-seq authentication snv cell-lines rna-seq
Language:Perl 0
deropi / BathyBrooksiSymbionts
population-structure symbiont snv
Language:Python 0
jiatuya / SNV_prediction_model
Note: This is a detailed Intro to this project. A brief users guide can be found at users_guide.md
exome-sequencing machine-learning snv
Language:Jupyter Notebook 0
laura-budurlean / GATK-WGS-Pipeline
GATK WGS workflow
bioinformatics gatk gatk-bestpractices illumina ngs wgs wholegenomesequencing snv
Language:Shell 0
wennj / pileupReformater
Convert output from Samtools pileup into a matrix.
linkage matrix nanopore-sequencing nucleotides pileup samtools snp snv
Language:Java 0
auroramaurizio / WES_ESOCA
WES Analysis scripts for "Immune determinants of response to neoadjuvant chemo-radiation in esophageal adenocarcinoma" publication
copy-number-variation maf purity quality-control somatic-variants variant-annotations variant-calling cnv snv
Language:Python
NCI-CGR / HPV_low_VAF_SNV_prediction
Predicting true low-VAF SNVs in HPV using triplicate NGS samples and machine learning
hpv machine-learning ngs-analysis single-nucleotide-variation ion-torrent extreme-gradient-boosting intrahost cancer-genomics intrahost-genetic-diversity snv variant-call-format variant-calling vcf vcf-files human-papillomavirus isnv vcfgenie
Language:Jupyter Notebook
oicr-gsi / varscan
varscan repo contains code for Varscan workflow
varscan cromwell workflow cnv snv variant-calling
Language:WDL
petermchale / genomics-web-app
vue app with flask REST api to process genomic data
axios flask-api kmer-counting plotlyjs pysam snv spa vue-material vuejs vuex
Language:Jupyter Notebook
ToolsVanBox / SNVFI
Single Nucleotide Variant Filtering
dna filtering snv wgs
Language:Shell

snv

nf-core / raredisease

XWangLabTHU / cfDNApipe

sigven / gvanno

zhengxwen / SeqArray

cancerit / dockstore-cgpwgs

adigorla / xgap

waqasuddinkhan / MACARON-GenMed-LabEx

dbmi-bgm / granite

TNTurnerLab / acorn

chadlaing / feht

jingxinfu / TCGAdnloader

bcgsc / ntRoot

cancerit / dockstore-cgpwxs

nickveltmaat / SNVcaller

nriddiford / mutationProfiles

TC-Hewitt / MuTrigo

TomMakesThings / Cancer-Evolution

xjtu-omics / ChineseQuartetGenome

Computational-Genomics-BSC / plink-bed-reader

ashudva / SNV-Business

auroramaurizio / my_DNA_seq_pipelines

EUCANCan / prepy-wrapper

ghga-de / nf-snvcalling

Mahsa-Ehsanifard / maftools

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

anbianchi / IntegratedSNVINDELSandCNV

bdolmo / CeLAuth

deropi / BathyBrooksiSymbionts

jiatuya / SNV_prediction_model

laura-budurlean / GATK-WGS-Pipeline

wennj / pileupReformater

auroramaurizio / WES_ESOCA

NCI-CGR / HPV_low_VAF_SNV_prediction

oicr-gsi / varscan

petermchale / genomics-web-app

ToolsVanBox / SNVFI