Alternatives and similar repositories for cgat:

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

• arq5x / bedtools-protocols
  ☆78Updated 10 years ago
• slowkow / snakefiles
  Snakefiles for common RNA-seq data analysis workflows (STAR and Kallisto).
  ☆92Updated 7 years ago
• hartleys / QoRTs
  Quality of RNA-Seq Toolset
  ☆52Updated 5 years ago
• SciLifeLab / NGI-RNAseq
  Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.
  ☆51Updated 6 years ago
• ncbi / TPMCalculator
  TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files
  ☆127Updated 7 months ago
• cancerit / cgpBattenberg
  Battenberg algorithm and associated implementation script
  ☆52Updated 4 years ago
• geocarvalho / sv-cnv-studies
  Relevant papers for CNV and SV approaches
  ☆94Updated 2 months ago
• secastel / phaser
  phasing and Allele Specific Expression from RNA-seq
  ☆111Updated 6 months ago
• Ensembl / WiggleTools
  Basic operations on the space of numerical functions defined on the genome using lazy evaluators for flexibility and efficiency
  ☆146Updated 2 months ago
• vastgroup / vast-tools
  A toolset for profiling alternative splicing events in RNA-Seq data.
  ☆80Updated this week
• Zhong-Lab-UCSD / Genomic-Interactive-Visualization-Engine
  Genomic Interactive Visualization Engine
  ☆145Updated 2 years ago
• CGATOxford / CGATPipelines
  Collection of CGAT NGS Pipelines
  ☆43Updated 6 years ago
• cc2qe / vawk
  An awk-like VCF parser
  ☆55Updated last year
• thelovelab / tximport
  Transcript quantification import for modular pipelines
  ☆137Updated 10 months ago
• dariober / bioinformatics-cafe
  Unsorted scripts for bioinformatics
  ☆60Updated 3 years ago
• TrinityCTAT / Trinity_CTAT
  ☆116Updated last year
• nygenome / lancet
  Microassembly based somatic variant caller for NGS data
  ☆154Updated 2 years ago
• LiuLabUB / HMMRATAC
  HMMRATAC peak caller for ATAC-seq data
  ☆100Updated 2 months ago
• GreenleafLab / NucleoATAC
  nucleosome calling using ATAC-seq
  ☆106Updated 4 years ago
• hbc / bcbioRNASeq
  R package for bcbio RNA-seq analysis.
  ☆59Updated 4 months ago
• genome / sciclone
  An R package for inferring the subclonal architecture of tumors
  ☆117Updated last year
• 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  This repo has been archived, these workflows are still available in the GATK repository under the scripts directory.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…
  ☆76Updated 4 years ago
• IARCbioinfo / BAM-tricks
  Tip and tricks for BAM files
  ☆84Updated 6 years ago
• CRG-Barcelona / bwtool
  A tool for bigWig files.
  ☆118Updated 6 years ago
• ding-lab / MuSiC2
  identifying mutational significance in cancer genomes
  ☆60Updated 2 years ago
• nunofonseca / irap
  integrated RNA-seq Analysis Pipeline
  ☆85Updated 5 years ago
• ParkerLab / ataqv
  A toolkit for QC and visualization of ATAC-seq results.
  ☆67Updated 3 weeks ago
• macarthur-lab / igv_utils
  utilities for working with IGV: opening files remotely in either desktop IGV or a web viewer (igv.js), creating screenshots, etc.
  ☆48Updated 5 years ago
• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆96Updated 3 years ago
• cancerit / ascatNgs
  Somatic copy number analysis using WGS paired end wholegenome sequencing
  ☆69Updated 4 years ago