Alternatives and similar repositories for pipelines

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

• SciLifeLab / NGI-RNAseq
  Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.
  ☆51Updated 7 years ago
• nghiavtr / FuSeq
  ☆33Updated 3 years ago
• arq5x / bedtools-protocols
  ☆78Updated 11 years ago
• bahlolab / bioinfotools
  Documenting usage and experience with bioinformatic tools
  ☆40Updated 10 years ago
• slowkow / picardmetrics
  Run Picard on BAM files and collate 90 metrics into one file.
  ☆40Updated 8 years ago
• saketkc / rna-seq-snakemake
  Snakemake based pipeline for RNA-Seq analysis
  ☆31Updated 6 years ago
• hms-dbmi / spp
  SPP - R package for analysis of ChIP-seq and other functional sequencing data
  ☆43Updated 4 years ago
• GuangchuangYu / enrichment4GTEx_clusterProfiler
  reproduce the functional enrichment analysis presented in GTEx paper using clusterProfiler/DOSE
  ☆33Updated 4 years ago
• Zhong-Lab-UCSD / Genomic-Interactive-Visualization-Engine
  Genomic Interactive Visualization Engine
  ☆146Updated 3 years ago
• cc2qe / vawk
  An awk-like VCF parser
  ☆56Updated 2 years ago
• statgen / gotcloud
  Genomes on the Cloud, Mapping & Variant Calling Pipelines
  ☆33Updated 8 years 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.
  ☆49Updated 6 years ago
• mskcc / mutation-signatures
  Create mutation signatures from MAF's, and decompose them into Stratton signatures
  ☆60Updated 6 years ago
• kundajelab / phantompeakqualtools
  This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to…
  ☆62Updated 5 years ago
• CGATOxford / cgat
  Do not use - please refer to our newest code: https://github.com/cgat-developers/cgat-apps
  ☆124Updated 7 years ago
• brwnj / umitools
  Tools to handle reads sequenced with unique molecular identifiers (UMIs).
  ☆30Updated 8 years ago
• s-andrews / SeqMonk
  SeqMonk NGS visualisation and analysis tool
  ☆51Updated 2 months ago
• chrisamiller / readDepth
  R package for inferring copy number from read depth
  ☆32Updated 3 years ago
• broadinstitute / oncotator
  ☆69Updated 3 years ago
• dieterich-lab / DCC
  DCC uses output from the STAR read mapper to systematically detect back-splice junctions in next-generation sequencing data. DCC applies …
  ☆38Updated 3 years ago
• mskcc / ngs-filters
  Filters for false-positive mutation calls in NGS
  ☆34Updated 6 years ago
• ratschlab / RiboDiff
  RiboDiff: Tool to detect changes in translational efficiency based on ribosome footprinting data
  ☆24Updated 9 years ago
• csf-ngs / fastqc
  csf fork of fastqc for usage on selected reads of unaligned bam file
  ☆48Updated 12 years ago
• hbctraining / Intro-to-rnaseq-hpc-salmon
  ☆50Updated 4 years ago
• ajmazurie / kegg-animate-pathway
  Command-line utility to color objects of a KEGG pathway with arbitrary colors
  ☆34Updated 10 years ago
• CRG-Barcelona / bwtool
  A tool for bigWig files.
  ☆118Updated 7 years ago
• stephenfloor / extract-transcript-regions
  For biological deep sequencing data. Decompose a UCSC knownGenes/Ensembl GTF file into transcript regions (i.e. exons, introns, UTRs and…
  ☆36Updated 2 years ago
• yuchaojiang / CODEX2
  Full-spectrum copy number variation detection by high-throughput DNA sequencing
  ☆40Updated 4 years ago
• parklab / ShatterSeek
  ☆75Updated 2 years ago
• IARCbioinfo / IARC-nf
  List of IARC bioinformatics pipelines and resources
  ☆56Updated 2 months ago