gis-rpd / pipelines

Related projects ⓘ

Alternatives and complementary repositories for pipelines

• arq5x / bedtools-protocols
  ☆78Updated 10 years ago
• brwnj / umitools
  Tools to handle reads sequenced with unique molecular identifiers (UMIs).
  ☆30Updated 7 years ago
• Kingsford-Group / squid
  SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data
  ☆41Updated 2 years ago
• cc2qe / vawk
  An awk-like VCF parser
  ☆54Updated 10 months ago
• chrisamiller / readDepth
  R package for inferring copy number from read depth
  ☆31Updated 2 years ago
• aryeelab / umi
  Preprocessing tools for unique molecular index (UMI) sequencing reads
  ☆31Updated last year
• EI-CoreBioinformatics / portcullis
  Splice junction analysis and filtering from BAM files
  ☆38Updated 2 years ago
• CshlSiepelLab / LINSIGHT
  ☆24Updated 5 months ago
• nghiavtr / FuSeq
  ☆32Updated 2 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…
  ☆33Updated last year
• bahlolab / bioinfotools
  Documenting usage and experience with bioinformatic tools
  ☆40Updated 9 years ago
• pachterlab / kallisto_paper_analysis
  Analysis from kallisto paper
  ☆32Updated 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.
  ☆48Updated 5 years ago
• hms-dbmi / spp
  SPP - R package for analysis of ChIP-seq and other functional sequencing data
  ☆39Updated 3 years ago
• hartleys / QoRTs
  Quality of RNA-Seq Toolset
  ☆52Updated 5 years ago
• AndreasHeger / gat
  Genomic Association Tester
  ☆29Updated last year
• grenaud / deML
  Maximum likelihood demultiplexing
  ☆46Updated last year
• hidelab / diffcoexp
  Differential coexpression analysis
  ☆15Updated last year
• getzlab / deTiN
  DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated ma…
  ☆49Updated 2 years ago
• yuchaojiang / CODEX2
  Full-spectrum copy number variation detection by high-throughput DNA sequencing
  ☆37Updated 3 years ago
• smithlabcode / preseq
  Software for predicting library complexity and genome coverage in high-throughput sequencing.
  ☆78Updated last month
• statgen / gotcloud
  Genomes on the Cloud, Mapping & Variant Calling Pipelines
  ☆32Updated 7 years ago
• stevekm / Bioinformatics
  Bioinformatics analysis scripts, workflows, general code examples
  ☆53Updated 3 years ago
• Jeltje / varscan2
  Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2
  ☆28Updated 6 years ago
• pmelsted / pizzly
  Fast fusion detection using kallisto
  ☆80Updated 3 weeks ago
• heathsc / gemBS
  gemBS is a bioinformatics pipeline designed for high throughput analysis of DNA methylation from Whole Genome Bisulfite Sequencing data (…
  ☆32Updated 2 years ago
• molgenis / capice
  ☆23Updated 3 months ago
• pachterlab / kma
  Keep Me Around: Intron Retention Detection
  ☆29Updated 5 years ago
• pachterlab / metakallisto
  Using kallisto for metagenomic analysis
  ☆50Updated 7 years ago
• ChristopherWilks / megadepth
  BigWig and BAM utilities
  ☆92Updated 7 months ago