Alternatives and similar repositories for pipelines:

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

• NBISweden / single-cell_sib_scilifelab
  SIB/Scilifelab autumn school in single cell omics 2019.
  ☆22Updated 5 years ago
• caleblareau / gchromVAR
  Cell type specific enrichments using finemapped variants and quantitative epigenetic data
  ☆43Updated last year
• UPSUTER / GEMLI
  ☆30Updated 2 months ago
• omicsCore / scTyper
  scTyper: a comprehensive pipeline for the cell typing analysis of single-cell RNA-seq data
  ☆29Updated 2 years ago
• Mayrlab / scUTRquant
  Bioinformatics pipeline for single-cell 3' UTR isoform quantification
  ☆21Updated 4 months ago
• nghiavtr / SCmut
  ☆31Updated 5 years ago
• wanglabtongji / SCRIP
  SCRIP(Single Cell Regulatory network Inference using ChIP-seq) is a tool for evaluating the binding enrichment of specific TR at single-c…
  ☆19Updated 8 months ago
• quadbio / RNAseq_tutorial
  ☆24Updated 5 months ago
• wenweixiong / MARVEL
  ☆45Updated 7 months ago
• broadinstitute / gtex-single-nucleus-reference
  Code repository for the snRNA-seq cross-tissue atlas project
  ☆20Updated 3 years ago
• wzthu / esATAC
  Bioconductor package esATAC: an Easy-to-use Systematic pipeline for ATAC-seq data analysis
  ☆23Updated 2 years ago
• gxiaolab / scAllele
  ☆33Updated 11 months ago
• karthikj89 / scgenetics
  identifying disease critical cell types and programs from single cell RNAseq
  ☆52Updated 2 years ago
• dbrg77 / scATAC_snakemake
  Snakemake pipeline for plate scATAC-seq processing
  ☆26Updated last year
• lkmklsmn / MitoTrace
  ☆15Updated 9 months ago
• shendurelab / single-cell-ko-screens
  Repository containing all code for secondary analysis in the manuscript "On the design of CRISPR-based single cell molecular screens", Hi…
  ☆26Updated 3 years ago
• PCAWG-11 / Heterogeneity
  Code accompanying Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes
  ☆43Updated 3 years ago
• tushiqi / MAnorm2
  MAnorm2 for Normalizing and Comparing ChIP-seq Samples
  ☆32Updated 2 years ago
• McGranahanLab / TcellExTRECT
  ☆47Updated 2 months ago
• seasoncloud / Alleloscope
  Alleloscope is a method for allele-specific copy number estimation that can be applied to single cell DNA and ATAC sequencing data (separ…
  ☆29Updated 2 years ago
• gambalab / gficf
  An R implementation of the Gene Frequency - Inverse Cell Frequency method for single cell data normalization
  ☆18Updated last year
• lhe17 / nebula
  ☆37Updated last year
• ManchesterBioinference / IntegratingATAC-RNA-HiC
  scripts for the integrating ATAC-seq, RNA-seq and CHi-C paper
  ☆23Updated 2 years ago
• CFeregrino / scWGCNA
  scWGCNA
  ☆58Updated 2 years ago
• wmacnair / psupertime
  psupertime is pseudotime ordering for single cell RNA-seq data with sequential labels
  ☆38Updated 2 years ago
• neurorestore / DE-analysis
  ☆37Updated 3 years ago
• haniffalab / scRNA-seq_analysis
  Single cell RNA-seq analysis bundle
  ☆34Updated 5 years ago
• veltenlab / CloneTracer
  This repository contains scripts to identify healthy and malignant cells from scRNAseq with CloneTracer and process data from Optimized 1…
  ☆25Updated 5 months ago
• netbiolab / scHumanNet
  Analysis cell-type-specific functional gene network, with SCINET and HumanNetv3
  ☆39Updated last year
• broadinstitute / single_cell_classification
  Methods to use SNPs or gene expression to classify single cell RNAseq to reference profiles
  ☆29Updated 4 years ago