Alternatives and similar repositories for vcf2maf

Users that are interested in vcf2maf are comparing it to the libraries listed below

• shenlab-sinai / ngsplot
  Quick mining and visualization of NGS data by integrating genomic databases
  ☆266Updated 2 years ago
• dpryan79 / ChromosomeMappings
  This repository contains chromosome/contig name mappings between UCSC <-> Ensembl <-> Gencode for a variety of genomes.
  ☆243Updated 2 years ago
• broadinstitute / gtex-pipeline
  GTEx & TOPMed data production and analysis pipelines
  ☆376Updated 2 months ago
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆256Updated 2 years ago
• STAR-Fusion / STAR-Fusion
  STAR-Fusion codebase
  ☆244Updated last month
• FelixKrueger / Bismark
  A tool to map bisulfite converted sequence reads and determine cytosine methylation states
  ☆429Updated this week
• rvalieris / parallel-fastq-dump
  parallel fastq-dump wrapper
  ☆299Updated 2 years ago
• Boyle-Lab / Blacklist
  Application for making ENCODE Blacklists
  ☆314Updated 4 years ago
• snakemake-workflows / rna-seq-star-deseq2
  RNA-seq workflow using STAR and DESeq2
  ☆344Updated last year
• deweylab / RSEM
  RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
  ☆448Updated last year
• WGLab / doc-ANNOVAR
  Documentation for the ANNOVAR software
  ☆243Updated last week
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆245Updated 2 weeks ago
• nservant / HiC-Pro
  HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
  ☆415Updated last year
• CGATOxford / UMI-tools
  Tools for handling Unique Molecular Identifiers in NGS data sets
  ☆515Updated last month
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆544Updated last year
• comprna / SUPPA
  SUPPA: Fast quantification of splicing and differential splicing
  ☆278Updated last year
• hbctraining / Intro-to-ChIPseq
  Intro to ChIPseq using HPC
  ☆309Updated 2 years ago
• nf-core / atacseq
  ATAC-seq peak-calling and QC analysis pipeline
  ☆207Updated last month
• ENCODE-DCC / chip-seq-pipeline2
  ENCODE ChIP-seq pipeline
  ☆271Updated last year
• sdparekh / zUMIs
  zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
  ☆281Updated last year
• Xinglab / rmats-turbo
  ☆269Updated 8 months ago
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆319Updated 3 years ago
• Illumina / strelka
  Strelka2 germline and somatic small variant caller
  ☆375Updated 3 years ago
• igordot / genomics
  A collection of scripts and notes related to genomics and bioinformatics
  ☆214Updated 2 weeks ago
• mhammell-laboratory / TEtranscripts
  A package for including transposable elements in differential enrichment analysis of sequencing datasets.
  ☆255Updated 6 months ago
• nf-core / chipseq
  ChIP-seq peak-calling, QC and differential analysis pipeline.
  ☆218Updated last month
• davidaknowles / leafcutter
  Annotation-free quantification of RNA splicing. Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae …
  ☆222Updated last year
• jsh58 / Genrich
  Detecting sites of genomic enrichment
  ☆192Updated 2 years ago
• maxplanck-ie / snakepipes
  Customizable workflows based on snakemake and python for the analysis of NGS data
  ☆398Updated this week
• igvteam / igv-reports
  Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.
  ☆369Updated last month