Alternatives and similar repositories for cgat:

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

• arq5x / bedtools-protocols
  ☆78Updated 11 years ago
• relipmoc / skewer
  ☆94Updated 2 years ago
• hartleys / QoRTs
  Quality of RNA-Seq Toolset
  ☆53Updated 6 years ago
• CGATOxford / CGATPipelines
  Collection of CGAT NGS Pipelines
  ☆43Updated 6 years ago
• cancerit / ascatNgs
  Somatic copy number analysis using WGS paired end wholegenome sequencing
  ☆71Updated 4 years ago
• geocarvalho / sv-cnv-studies
  Relevant papers for CNV and SV approaches
  ☆94Updated 6 months ago
• nygenome / lancet
  Microassembly based somatic variant caller for NGS data
  ☆154Updated 2 years ago
• slowkow / snakefiles
  Snakefiles for common RNA-seq data analysis workflows (STAR and Kallisto).
  ☆92Updated 7 years ago
• Ensembl / WiggleTools
  Basic operations on the space of numerical functions defined on the genome using lazy evaluators for flexibility and efficiency
  ☆148Updated 6 months ago
• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆97Updated 4 years ago
• SciLifeLab / NGI-RNAseq
  Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.
  ☆51Updated 6 years ago
• JohnLonginotto / pybam
  Very simple, pure python, BAM file reader
  ☆79Updated 6 years ago
• GreenleafLab / NucleoATAC
  nucleosome calling using ATAC-seq
  ☆106Updated 4 years ago
• Czh3 / NGSTools
  Next-Generation Sequencing(NGS) toolkits.
  ☆45Updated 9 years ago
• secastel / phaser
  phasing and Allele Specific Expression from RNA-seq
  ☆114Updated 9 months ago
• bowhan / piPipes
  piRNA pipeline collection developed in the Zamore Lab and ZLab in UMass Med School
  ☆59Updated 10 months 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
• cc2qe / vawk
  An awk-like VCF parser
  ☆56Updated last year
• cancerit / BRASS
  Breakpoints via assembly - Identifies breaks and attempts to assemble rearrangements in whole genome sequencing data.
  ☆57Updated 9 months ago
• parklab / ShatterSeek
  ☆68Updated last year
• ExpressionAnalysis / ea-utils
  Automatically exported from code.google.com/p/ea-utils
  ☆96Updated last year
• hbc / bcbioRNASeq
  R package for bcbio RNA-seq analysis.
  ☆62Updated 7 months ago
• slowkow / picardmetrics
  Run Picard on BAM files and collate 90 metrics into one file.
  ☆41Updated 7 years ago
• vastgroup / vast-tools
  A toolset for profiling alternative splicing events in RNA-Seq data.
  ☆81Updated 3 months ago
• cancerit / cgpBattenberg
  Battenberg algorithm and associated implementation script
  ☆52Updated 4 years ago
• kvittingseerup / IsoformSwitchAnalyzeR
  An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)
  ☆112Updated 3 months ago
• Zhong-Lab-UCSD / Genomic-Interactive-Visualization-Engine
  Genomic Interactive Visualization Engine
  ☆145Updated 2 years ago
• CRG-Barcelona / bwtool
  A tool for bigWig files.
  ☆119Updated 6 years ago
• jdidion / atropos
  An NGS read trimming tool that is specific, sensitive, and speedy. (production)
  ☆121Updated last week
• bahlolab / bioinfotools
  Documenting usage and experience with bioinformatic tools
  ☆41Updated 9 years ago