Alternatives and similar repositories for bioinfotools

Users that are interested in bioinfotools are comparing it to the libraries listed below

• gatk-workflows / gatk4-exome-analysis-pipeline
  This WDL pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and In…
  ☆54Updated 4 years ago
• gatk-workflows / gatk4-somatic-snvs-indels
  This repo has been archived, these workflows are still available in the GATK repository under the scripts directory. The workflows are al…
  ☆77Updated 5 years ago
• Illumina / Pisces
  Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
  ☆98Updated 3 years ago
• geocarvalho / sv-cnv-studies
  Relevant papers for CNV and SV approaches
  ☆94Updated 9 months ago
• chrisamiller / readDepth
  R package for inferring copy number from read depth
  ☆32Updated 2 years ago
• broadinstitute / oncotator
  ☆69Updated 3 years ago
• ding-lab / MuSiC2
  identifying mutational significance in cancer genomes
  ☆61Updated 2 years ago
• secastel / phaser
  phasing and Allele Specific Expression from RNA-seq
  ☆116Updated last year
• cancerit / ascatNgs
  Somatic copy number analysis using WGS paired end wholegenome sequencing
  ☆72Updated 4 years ago
• getzlab / deTiN
  DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated ma…
  ☆51Updated 3 years ago
• gatk-workflows / broad-prod-wgs-germline-snps-indels
  Workflows for germline short variant discovery in WGS data. PairedEndSingleSampleWf has been superseded in Broad production by https://gi…
  ☆56Updated 5 years ago
• Jeltje / varscan2
  Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2
  ☆29Updated 7 years ago
• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆97Updated 4 years ago
• FoundationMedicineInc / SGZ
  ☆41Updated last year
• ccagc / QDNAseq
  QDNAseq package for Bioconductor
  ☆50Updated last year
• patidarr / ngs_pipeline
  Exome/Capture/RNASeq Pipeline Implementation using snakemake
  ☆47Updated 7 years ago
• rhshah / IMPACT-Pipeline
  Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay
  ☆57Updated 4 years ago
• tderrien / FEELnc
  FEELnc : FlExible Extraction of LncRNA
  ☆90Updated 2 weeks ago
• bioinfo-pf-curie / TMB
  Tumor Mutational Burden
  ☆62Updated last week
• arq5x / bedtools-protocols
  ☆78Updated 11 years ago
• griffithlab / regtools
  Integrate DNA-seq and RNA-seq data to identify mutations that are associated with regulatory effects on gene expression.
  ☆131Updated 11 months ago
• mskcc / mutation-signatures
  Create mutation signatures from MAF's, and decompose them into Stratton signatures
  ☆60Updated 6 years ago
• AstraZeneca-NGS / reference_data
  Reference data: BED files, genes, transcripts, variations.
  ☆83Updated 7 years ago
• smithlabcode / preseq
  Software for predicting library complexity and genome coverage in high-throughput sequencing.
  ☆87Updated 9 months ago
• humanlongevity / HLA
  xHLA: Fast and accurate HLA typing from short read sequence data
  ☆113Updated last year
• PapenfussLab / StructuralVariantAnnotation
  R package designed to simplify structural variant analysis
  ☆73Updated 3 years ago
• bioinform / rnacocktail
  ☆89Updated 4 years ago
• GooglingTheCancerGenome / sv-callers
  Snakemake-based workflow for detecting structural variants in genomic data
  ☆80Updated 5 months ago
• IARCbioinfo / BAM-tricks
  Tip and tricks for BAM files
  ☆86Updated 7 years ago
• OpenGene / ctdna-pipeline
  A simplified pipeline for ctDNA sequencing data analysis
  ☆37Updated 7 years ago