Alternatives and similar repositories for cgat

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

• nunofonseca / irap
  integrated RNA-seq Analysis Pipeline
  ☆84Updated 6 years ago
• hartleys / QoRTs
  Quality of RNA-Seq Toolset
  ☆53Updated 6 years ago
• vastgroup / vast-tools
  A toolset for profiling alternative splicing events in RNA-Seq data.
  ☆81Updated 4 months ago
• slowkow / snakefiles
  Snakefiles for common RNA-seq data analysis workflows (STAR and Kallisto).
  ☆93Updated 7 years ago
• ncbi / TPMCalculator
  TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files
  ☆130Updated 11 months ago
• SciLifeLab / NGI-RNAseq
  Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.
  ☆51Updated 6 years ago
• GreenleafLab / NucleoATAC
  nucleosome calling using ATAC-seq
  ☆106Updated 4 years ago
• slowkow / picardmetrics
  Run Picard on BAM files and collate 90 metrics into one file.
  ☆41Updated 7 years ago
• arq5x / bedtools-protocols
  ☆78Updated 11 years ago
• bowhan / piPipes
  piRNA pipeline collection developed in the Zamore Lab and ZLab in UMass Med School
  ☆60Updated 11 months ago
• secastel / phaser
  phasing and Allele Specific Expression from RNA-seq
  ☆115Updated 10 months ago
• IARCbioinfo / BAM-tricks
  Tip and tricks for BAM files
  ☆85Updated 6 years ago
• cancerit / ascatNgs
  Somatic copy number analysis using WGS paired end wholegenome sequencing
  ☆71Updated 4 years ago
• LiuLabUB / HMMRATAC
  HMMRATAC peak caller for ATAC-seq data
  ☆100Updated 6 months ago
• dariober / bioinformatics-cafe
  Unsorted scripts for bioinformatics
  ☆61Updated 3 years ago
• ExpressionAnalysis / ea-utils
  Automatically exported from code.google.com/p/ea-utils
  ☆96Updated last year
• geocarvalho / sv-cnv-studies
  Relevant papers for CNV and SV approaches
  ☆94Updated 7 months ago
• CRG-Barcelona / bwtool
  A tool for bigWig files.
  ☆119Updated 7 years ago
• cbg-ethz / NGS-pipe
  NGS-pipe: next-generation sequencing pipelines for precision oncology
  ☆111Updated 6 years ago
• Ensembl / WiggleTools
  Basic operations on the space of numerical functions defined on the genome using lazy evaluators for flexibility and efficiency
  ☆148Updated 7 months ago
• thelovelab / tximport
  Transcript quantification import for modular pipelines
  ☆138Updated last year
• CGATOxford / CGATPipelines
  Collection of CGAT NGS Pipelines
  ☆43Updated 6 years ago
• likelet / LncPipe
  A Nextflow-based pipeline for comprehensive analyses of long non-coding RNAs from RNA-seq datasets
  ☆82Updated 2 years ago
• parklab / ShatterSeek
  ☆69Updated last year
• genome / sciclone
  An R package for inferring the subclonal architecture of tumors
  ☆119Updated last year
• csf-ngs / fastqc
  csf fork of fastqc for usage on selected reads of unaligned bam file
  ☆49Updated 12 years ago
• Zhong-Lab-UCSD / Genomic-Interactive-Visualization-Engine
  Genomic Interactive Visualization Engine
  ☆145Updated 2 years 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)
  ☆113Updated 4 months ago
• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆97Updated 4 years ago