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snvs

Here are 10 public repositories matching this topic...

edawson / assisi

A somatic mutation signature simulator

simulation autoencoders snvs mutational-signatures

Updated Feb 13, 2020
Python

nalomran / PyReQTL

A collection of Python modules equivalent to R ReQTL Toolkit aims to identify the association between expressed SNVs with their gene expression using RNA-sequencing data.

python data-science bioinformatics rna-seq r numpy gene-expression pandas python3 scipy rna-seq-analysis bioinformatics-analysis snvs rpy2 bioinformatics-tool matrixeqtl

Updated Jan 20, 2022
Python

j3551ca / SNPerr

Determine read depth and variant frequency thresholds to distinguish NGS sequencing errors from true SNPs. Simulates effect of changing per-site read depth and variant frequency on accuracy of genetic diversity measures (pi, alterante allele frequency, shannon diversity).

diversity ngs error snvs

Updated Jun 16, 2022
Python

myonaung / sm-SNIPER

A snakemake pipeline that performs variant calling of Nanopore reads from FastQ files for non-model organisms

genomics bioinformatics-pipeline variant-calling variant snvs snakemake-workflows

Updated Oct 13, 2022
Python

nickveltmaat / SNVcaller

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

somatic-variants somatic-mutations snv ctdna snvs cfdna vardict mutect2 cell-free-dna snv-annotation indel lofreq sinvict

Updated Nov 8, 2022
Python

sigven / gvanno

Generic human DNA variant annotation pipeline

docker workflow gene singularity vcf variants snv vep disease-gene-association indels annotation-tool vcfanno germline variant-annotations annotation-framework snvs

Updated Feb 13, 2024
Python

dbmi-bgm / granite

A collection of software to work with genomic variants

vcf variants snv variant-filtration variant-analysis snvs trio de-novo-mutation single-nucleotide-variation de-novo-mutations compound-heterozygous

Updated Sep 11, 2024
Python

HKU-BAL / ClairS-TO

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

bioinformatics deep-learning nanopore genomics somatic-variants variants pacbio variant-calling somatic-mutations illumina snvs long-reads ont long-read-sequencing tumors tumor-only

Updated Oct 11, 2024
Python

cpwardell / FiNGS

Filters for Next Generation Sequencing

genomics cancer ngs sequencing variants cancer-genomics filtering snvs

Updated Oct 31, 2024
Python

HKU-BAL / ClairS

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

bioinformatics deep-learning nanopore genomics somatic-variants haplotypes pacbio somatic-mutations illumina indels phasing snvs long-reads ont long-read-sequencing short-reads

Updated Nov 14, 2024
Python

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