Alternatives and similar repositories for RNA-seq:

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

• hbctraining / Investigating-chromatin-biology-ChIPseq
  ☆88Updated last month
• loosolab / TOBIAS
  Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal
  ☆209Updated last month
• hbctraining / Intro-to-rnaseq-hpc-salmon-flipped
  Introduction to bulk RNA-seq
  ☆104Updated last month
• nf-core / atacseq
  ATAC-seq peak-calling and QC analysis pipeline
  ☆197Updated last week
• BioOmics / iSeq
  Download sequencing data and metadata from GSA, SRA, ENA, and DDBJ databases.
  ☆174Updated last week
• harvardinformatics / ATAC-seq
  ☆127Updated 6 years ago
• rajewsky-lab / mirdeep2
  Discovering known and novel miRNAs from small RNA sequencing data
  ☆145Updated 6 months ago
• erilu / bulk-rnaseq-analysis
  A complete guide for analyzing bulk RNA-seq data. Go from raw FASTQ files to mapping reads using STAR and differential gene expression an…
  ☆77Updated 4 years ago
• CompEpigen / figeno
  Tool for plotting sequencing data along genomic coordinates.
  ☆259Updated last month
• CebolaLab / ATAC-seq
  Analysis pipeline for ATAC-seq data
  ☆48Updated last year
• FredHutch / SEACR
  SEACR: Sparse Enrichment Analysis for CUT&RUN
  ☆108Updated 2 years ago
• hbctraining / Intro-to-rnaseq-hpc-O2
  This repository has teaching materials for a 2 and 3-day Introduction to RNA-sequencing data analysis workshop using the O2 Cluster
  ☆166Updated 3 years ago
• hbctraining / Intro-to-DGE
  ☆192Updated this week
• Xinglab / rmats-turbo
  ☆244Updated 4 months ago
• ENCODE-DCC / rna-seq-pipeline
  ☆147Updated 2 years ago
• nf-core / cutandrun
  Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes QC, support for spike-ins, IgG controls, peak calling and downstream …
  ☆89Updated last month
• PoisonAlien / trackplot
  Generate IGV style locus tracks from bigWig files in R
  ☆155Updated 4 months ago
• sib-swiss / single-cell-training
  SIB course on single cell transcriptomics by mostly using the Seurat pipeline
  ☆81Updated last week
• zhxiaokang / RASflow
  RNA-Seq analysis workflow
  ☆104Updated 3 years ago
• signalbash / how_are_we_stranded_here
  Check strandedness of RNA-Seq fastq files
  ☆119Updated 2 years ago
• cortes-ciriano-lab / SComatic
  A tool for detecting somatic variants in single cell data
  ☆193Updated 6 months ago
• mhammell-laboratory / TEtranscripts
  A package for including transposable elements in differential enrichment analysis of sequencing datasets.
  ☆244Updated last month
• bli25 / RSEM_tutorial
  A short tutorial on how to use RSEM
  ☆136Updated 4 years ago
• rpetit3 / fastq-dl
  Download FASTQ files from SRA or ENA repositories.
  ☆309Updated 5 months ago
• Boyle-Lab / Blacklist
  Application for making ENCODE Blacklists
  ☆294Updated 3 years ago
• crazyhottommy / scATACseq-analysis-notes
  my notes for scATACseq analysis
  ☆122Updated 10 months ago
• cellgeni / scRNA.seq.course
  Analysis of single cell RNA-seq data course
  ☆131Updated 2 years ago
• ENCODE-DCC / chip-seq-pipeline
  ENCODE Uniform processing pipeline for ChIP-seq
  ☆123Updated 4 years ago
• rvalieris / parallel-fastq-dump
  parallel fastq-dump wrapper
  ☆288Updated last year
• jsh58 / Genrich
  Detecting sites of genomic enrichment
  ☆190Updated last year