Alternatives and similar repositories for single-cell-rna-seq:

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

• tobiasrausch / ATACseq
  Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)
  ☆75Updated last year
• tallulandrews / scRNASeqPipeline
  ☆118Updated 6 years ago
• CebolaLab / ATAC-seq
  Analysis pipeline for ATAC-seq data
  ☆58Updated last year
• reskejak / ATAC-seq
  Basic workflow for ATAC-seq analysis
  ☆77Updated last year
• GreenleafLab / chromVAR
  chromatin Variability Across Regions (of the genome!)
  ☆172Updated 9 months ago
• harvardinformatics / ATAC-seq
  ☆131Updated 6 years ago
• JiekaiLab / scTE
  ☆105Updated last year
• FredHutch / SEACR
  SEACR: Sparse Enrichment Analysis for CUT&RUN
  ☆109Updated 2 years ago
• crazyhottommy / pyflow-ATACseq
  ATAC-seq snakemake pipeline
  ☆87Updated 5 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 …
  ☆91Updated last month
• BaderLab / CellAnnotationTutorial
  Accompanying code for the tutorial: Annotating single cell transcriptomic maps using automated and manual methods
  ☆92Updated 2 years ago
• TrinityCTAT / Trinity_CTAT
  ☆116Updated last year
• bli25 / RSEM_tutorial
  A short tutorial on how to use RSEM
  ☆136Updated 5 years ago
• rpolicastro / scProportionTest
  ☆61Updated last year
• tavareshugo / tutorial_DESeq2_contrasts
  ☆59Updated 11 months ago
• timoast / sinto
  Tools for single-cell data processing
  ☆123Updated 10 months ago
• QuKunLab / ATAC-pipe
  Analysis pipeline for ATAC-seq Data
  ☆60Updated 3 years ago
• ENCODE-DCC / chip-seq-pipeline
  ENCODE Uniform processing pipeline for ChIP-seq
  ☆123Updated 5 years ago
• crazyhottommy / pyflow-ChIPseq
  a snakemake pipeline to process ChIP-seq files from GEO or in-house
  ☆107Updated 5 years ago
• databio / awesome-atac-analysis
  Links to ATAC-seq analysis tools
  ☆65Updated 3 years ago
• loosolab / TOBIAS
  Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal
  ☆210Updated 3 months ago
• vib-singlecell-nf / vsn-pipelines
  A repository of pipelines for single-cell data in Nextflow DSL2
  ☆75Updated 2 years ago
• indrops / indrops
  Pipeline for processing inDrops sequencing data
  ☆76Updated 6 years ago
• GreenleafLab / NucleoATAC
  nucleosome calling using ATAC-seq
  ☆106Updated 4 years ago
• ENCODE-DCC / long-rna-seq-pipeline
  STAR based ENCODE Long RNA-Seq processing pipeline
  ☆94Updated 4 years ago
• yupenghe / methylpy
  WGBS/NOMe-seq Data Processing & Differential Methylation Analysis
  ☆140Updated last year
• PoisonAlien / trackplot
  Generate IGV style locus tracks from bigWig files in R
  ☆158Updated 5 months ago
• sansomlab / tenx
  Pipelines for the analysis of 10x single-cell RNA-sequencing data
  ☆57Updated last year
• LiuLabUB / HMMRATAC
  HMMRATAC peak caller for ATAC-seq data
  ☆100Updated 5 months ago
• AllonMKlein / scrublet
  Detect doublets in single-cell RNA-seq data
  ☆85Updated 5 years ago