Alternatives and similar repositories for rna-seq-pipeline:

Users that are interested in rna-seq-pipeline are comparing it to the libraries listed below

• mhammell-laboratory / TEtranscripts
  A package for including transposable elements in differential enrichment analysis of sequencing datasets.
  ☆244Updated last month
• ENCODE-DCC / chip-seq-pipeline
  ENCODE Uniform processing pipeline for ChIP-seq
  ☆123Updated 4 years ago
• bli25 / RSEM_tutorial
  A short tutorial on how to use RSEM
  ☆136Updated 4 years ago
• jsh58 / Genrich
  Detecting sites of genomic enrichment
  ☆190Updated last year
• nf-core / atacseq
  ATAC-seq peak-calling and QC analysis pipeline
  ☆196Updated last week
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆249Updated last year
• VanLoo-lab / ascat
  ASCAT R package
  ☆176Updated 3 months ago
• Boyle-Lab / Blacklist
  Application for making ENCODE Blacklists
  ☆294Updated 3 years ago
• yupenghe / methylpy
  WGBS/NOMe-seq Data Processing & Differential Methylation Analysis
  ☆140Updated last year
• FredHutch / SEACR
  SEACR: Sparse Enrichment Analysis for CUT&RUN
  ☆108Updated 2 years ago
• davidaknowles / leafcutter
  Annotation-free quantification of RNA splicing. Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae …
  ☆212Updated 9 months ago
• nloyfer / wgbs_tools
  tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies
  ☆142Updated last week
• igordot / genomics
  A collection of scripts and notes related to genomics and bioinformatics
  ☆206Updated last month
• zhxiaokang / RASflow
  RNA-Seq analysis workflow
  ☆104Updated 3 years ago
• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆210Updated last week
• comprna / SUPPA
  SUPPA: Fast quantification of splicing and differential splicing
  ☆271Updated 9 months ago
• rajewsky-lab / mirdeep2
  Discovering known and novel miRNAs from small RNA sequencing data
  ☆144Updated 6 months ago
• loosolab / TOBIAS
  Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal
  ☆208Updated last month
• ENCODE-DCC / long-rna-seq-pipeline
  STAR based ENCODE Long RNA-Seq processing pipeline
  ☆94Updated 3 years ago
• shenlab-sinai / ngsplot
  Quick mining and visualization of NGS data by integrating genomic databases
  ☆264Updated last year
• ndaniel / fusioncatcher
  Finder of Somatic Fusion Genes in RNA-seq data
  ☆145Updated last year
• kundajelab / atac_dnase_pipelines
  ATAC-seq and DNase-seq processing pipeline
  ☆165Updated 2 years ago
• deeptools / HiCExplorer
  HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
  ☆239Updated 3 months ago
• harvardinformatics / ATAC-seq
  ☆127Updated 6 years ago
• Xinglab / rmats2sashimiplot
  ☆142Updated last month
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆234Updated this week
• virajbdeshpande / AmpliconArchitect
  AmpliconArchitect (AA) is a tool to identify one or more connected genomic regions which have simultaneous copy number amplification and …
  ☆144Updated 9 months ago
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆264Updated last year
• signalbash / how_are_we_stranded_here
  Check strandedness of RNA-Seq fastq files
  ☆119Updated 2 years ago
• kundajelab / chipseq_pipeline
  AQUAS TF and histone ChIP-seq pipeline
  ☆107Updated 2 years ago