Alternatives and similar repositories for bcbioRNASeq

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

• 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…
  ☆59Updated 5 years ago
• saketkc / rna-seq-snakemake
  Snakemake based pipeline for RNA-Seq analysis
  ☆31Updated 6 years ago
• thelovelab / tximport
  Transcript quantification import for modular pipelines
  ☆141Updated last week
• slowkow / snakefiles
  Snakefiles for common RNA-seq data analysis workflows (STAR and Kallisto).
  ☆93Updated 8 years ago
• BIMSBbioinfo / genomation
  R package for genomic feature analysis and visualization
  ☆79Updated 4 months ago
• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆97Updated 4 years ago
• cancerit / cgpBattenberg
  Battenberg algorithm and associated implementation script
  ☆53Updated 4 years ago
• crazyhottommy / DNA-methylation-analysis
  DNA methylation analysis notes from Ming Tang
  ☆87Updated 5 years ago
• genome / sciclone
  An R package for inferring the subclonal architecture of tumors
  ☆122Updated last year
• GreenleafLab / NucleoATAC
  nucleosome calling using ATAC-seq
  ☆106Updated 4 years ago
• patidarr / ngs_pipeline
  Exome/Capture/RNASeq Pipeline Implementation using snakemake
  ☆47Updated 7 years ago
• olgabot / rna-seq-diff-exprn
  RNA-Sequencing data differential expression analysis pipeline. Performs: genome coverage (via bedtools and HTSeq), generates Circos code …
  ☆55Updated 12 years ago
• GenomiqueENS / eoulsan
  A pipeline and a framework for NGS analysis (RNA-seq and scRNA-seq)
  ☆54Updated 2 months ago
• ParkerLab / ataqv
  A toolkit for QC and visualization of ATAC-seq results.
  ☆71Updated 7 months ago
• kdkorthauer / dmrseq
  R package for Inference of differentially methylated regions (DMRs) from bisulfite sequencing
  ☆61Updated 3 months ago
• morrislab / qapa
  RNA-seq Quantification of Alternative Polyadenylation
  ☆47Updated last month
• LiuLabUB / HMMRATAC
  HMMRATAC peak caller for ATAC-seq data
  ☆99Updated 9 months ago
• snystrom / memes
  An R interface to the MEME Suite
  ☆52Updated 2 months ago
• YeoLab / outrigger
  Create a *de novo* alternative splicing database, validate splicing events, and quantify percent spliced-in (Psi) from RNA seq data
  ☆67Updated 5 years ago
• mskcc / mutation-signatures
  Create mutation signatures from MAF's, and decompose them into Stratton signatures
  ☆60Updated 6 years ago
• Nik-Zainal-Group / signature.tools.lib
  R package containing useful functions for mutational signature analysis
  ☆83Updated this week
• hms-dbmi / spp
  SPP - R package for analysis of ChIP-seq and other functional sequencing data
  ☆43Updated 4 years ago
• hbctraining / Intro-to-rnaseq-hpc-salmon
  ☆50Updated 4 years ago
• csoneson / ARMOR
  Light-weight Snakemake workflow for preprocessing and statistical analysis of RNA-seq data
  ☆165Updated 8 months ago
• vastgroup / vast-tools
  A toolset for profiling alternative splicing events in RNA-Seq data.
  ☆82Updated 7 months ago
• parklab / ShatterSeek
  ☆71Updated 2 years ago
• stevekm / Bioinformatics
  Bioinformatics analysis scripts, workflows, general code examples
  ☆53Updated 4 years ago
• vivekbhr / Subread_to_DEXSeq
  Scripts to import your FeatureCounts output into DEXSeq
  ☆34Updated 6 years ago
• ChristofferFlensburg / superFreq
  Analysis pipeline for cancer sequencing data
  ☆110Updated 4 months ago
• CGATOxford / CGATPipelines
  Collection of CGAT NGS Pipelines
  ☆43Updated 6 years ago