Alternatives and similar repositories for vcf2maf:

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

• broadinstitute / gtex-pipeline
  GTEx & TOPMed data production and analysis pipelines
  ☆363Updated 3 months ago
• shenlab-sinai / ngsplot
  Quick mining and visualization of NGS data by integrating genomic databases
  ☆264Updated 2 years ago
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆253Updated last year
• deweylab / RSEM
  RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
  ☆438Updated last year
• nf-core / chipseq
  ChIP-seq peak-calling, QC and differential analysis pipeline.
  ☆212Updated this week
• Boyle-Lab / Blacklist
  Application for making ENCODE Blacklists
  ☆303Updated 4 years ago
• igordot / genomics
  A collection of scripts and notes related to genomics and bioinformatics
  ☆210Updated 3 weeks ago
• bli25 / RSEM_tutorial
  A short tutorial on how to use RSEM
  ☆136Updated 5 years ago
• snakemake-workflows / rna-seq-star-deseq2
  RNA-seq workflow using STAR and DESeq2
  ☆339Updated 9 months ago
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆238Updated last month
• rvalieris / parallel-fastq-dump
  parallel fastq-dump wrapper
  ☆292Updated 2 years ago
• dpryan79 / ChromosomeMappings
  This repository contains chromosome/contig name mappings between UCSC <-> Ensembl <-> Gencode for a variety of genomes.
  ☆241Updated 2 years ago
• nf-core / atacseq
  ATAC-seq peak-calling and QC analysis pipeline
  ☆200Updated this week
• mhammell-laboratory / TEtranscripts
  A package for including transposable elements in differential enrichment analysis of sequencing datasets.
  ☆248Updated 3 months ago
• davidaknowles / leafcutter
  Annotation-free quantification of RNA splicing. Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae …
  ☆213Updated 11 months ago
• FelixKrueger / Bismark
  A tool to map bisulfite converted sequence reads and determine cytosine methylation states
  ☆417Updated last week
• STAR-Fusion / STAR-Fusion
  STAR-Fusion codebase
  ☆240Updated last week
• ENCODE-DCC / rna-seq-pipeline
  ☆150Updated 2 years ago
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆265Updated last year
• hbctraining / Intro-to-ChIPseq
  Intro to ChIPseq using HPC
  ☆302Updated 2 years ago
• saketkc / pysradb
  Package for fetching metadata and downloading data from SRA/ENA/GEO
  ☆326Updated 2 months ago
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆541Updated 9 months ago
• nservant / HiC-Pro
  HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
  ☆402Updated last year
• VanLoo-lab / ascat
  ASCAT R package
  ☆180Updated last month
• nf-core / methylseq
  Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
  ☆165Updated this week
• WGLab / doc-ANNOVAR
  Documentation for the ANNOVAR software
  ☆244Updated last month
• kundajelab / atac_dnase_pipelines
  ATAC-seq and DNase-seq processing pipeline
  ☆165Updated 2 years ago
• sdparekh / zUMIs
  zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
  ☆279Updated 9 months ago
• maxplanck-ie / snakepipes
  Customizable workflows based on snakemake and python for the analysis of NGS data
  ☆396Updated last week
• loosolab / TOBIAS
  Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal
  ☆210Updated 3 months ago