Alternatives and similar repositories for pipelines

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

• arq5x / bedtools-protocols
  ☆78Updated 11 years ago
• brwnj / umitools
  Tools to handle reads sequenced with unique molecular identifiers (UMIs).
  ☆30Updated 8 years ago
• nghiavtr / FuSeq
  ☆33Updated 3 years ago
• dariober / bioinformatics-cafe
  Unsorted scripts for bioinformatics
  ☆61Updated 4 years ago
• hms-dbmi / spp
  SPP - R package for analysis of ChIP-seq and other functional sequencing data
  ☆43Updated 4 years ago
• crazyhottommy / pyflow-RNAseq
  RNAseq pipeline based on snakemake
  ☆26Updated 2 years ago
• SciLifeLab / NGI-RNAseq
  Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.
  ☆51Updated 7 years ago
• hartleys / QoRTs
  Quality of RNA-Seq Toolset
  ☆53Updated 6 years ago
• bahlolab / bioinfotools
  Documenting usage and experience with bioinformatic tools
  ☆40Updated 10 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 …
  ☆37Updated 3 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
• saketkc / rna-seq-snakemake
  Snakemake based pipeline for RNA-Seq analysis
  ☆31Updated 6 years ago
• slowkow / picardmetrics
  Run Picard on BAM files and collate 90 metrics into one file.
  ☆40Updated 8 years ago
• DaehwanKimLab / hisat-genotype
  ☆30Updated 4 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…
  ☆60Updated 5 years ago
• slowkow / snakefiles
  Snakefiles for common RNA-seq data analysis workflows (STAR and Kallisto).
  ☆93Updated 8 years ago
• broadinstitute / oncotator
  ☆69Updated 3 years ago
• csf-ngs / fastqc
  csf fork of fastqc for usage on selected reads of unaligned bam file
  ☆48Updated 12 years ago
• s-andrews / SeqMonk
  SeqMonk NGS visualisation and analysis tool
  ☆50Updated last month
• Zhong-Lab-UCSD / Genomic-Interactive-Visualization-Engine
  Genomic Interactive Visualization Engine
  ☆146Updated 2 years ago
• yuchaojiang / CODEX2
  Full-spectrum copy number variation detection by high-throughput DNA sequencing
  ☆40Updated 4 years ago
• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆98Updated 4 years ago
• geocarvalho / sv-cnv-studies
  Relevant papers for CNV and SV approaches
  ☆94Updated last year
• ajmazurie / kegg-animate-pathway
  Command-line utility to color objects of a KEGG pathway with arbitrary colors
  ☆34Updated 10 years ago
• cc2qe / vawk
  An awk-like VCF parser
  ☆56Updated last year
• patidarr / ngs_pipeline
  Exome/Capture/RNASeq Pipeline Implementation using snakemake
  ☆47Updated 7 years ago
• hbctraining / Intro-to-rnaseq-hpc-salmon
  ☆50Updated 4 years ago
• pachterlab / kallisto_paper_analysis
  Analysis from kallisto paper
  ☆32Updated 9 years ago
• daler / trackhub
  create, manage, and upload track hubs for use in the UCSC genome browser
  ☆54Updated last year
• YangLab / CIRCexplorer
  A combined strategy to identify circular RNAs (circRNAs and ciRNAs) (Zhang et al., Complementary Sequence-Mediated Exon Circularization, …
  ☆62Updated 6 years ago