Alternatives and similar repositories for pipelines:

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

• wenweixiong / MARVEL
  ☆49Updated 9 months ago
• UPSUTER / GEMLI
  ☆30Updated 3 months ago
• broadinstitute / gtex-single-nucleus-reference
  Code repository for the snRNA-seq cross-tissue atlas project
  ☆20Updated 3 years ago
• omicsCore / scTyper
  scTyper: a comprehensive pipeline for the cell typing analysis of single-cell RNA-seq data
  ☆29Updated 2 years ago
• ManchesterBioinference / IntegratingATAC-RNA-HiC
  scripts for the integrating ATAC-seq, RNA-seq and CHi-C paper
  ☆24Updated 2 years ago
• liulab-dfci / lisa2
  ☆30Updated 2 years ago
• Morriseylab / scExtras
  ☆12Updated 9 months ago
• caleblareau / maegatk
  Mitochondrial Alteration Enrichment and Genome Analysis Toolkit
  ☆19Updated last year
• gxiaolab / scAllele
  ☆33Updated last year
• dbrg77 / scATAC_snakemake
  Snakemake pipeline for plate scATAC-seq processing
  ☆26Updated last year
• veltenlab / CloneTracer
  This repository contains scripts to identify healthy and malignant cells from scRNAseq with CloneTracer and process data from Optimized 1…
  ☆25Updated 6 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
• wzthu / esATAC
  Bioconductor package esATAC: an Easy-to-use Systematic pipeline for ATAC-seq data analysis
  ☆23Updated 2 years ago
• CFeregrino / scWGCNA
  scWGCNA
  ☆59Updated 2 years ago
• caleblareau / gchromVAR
  Cell type specific enrichments using finemapped variants and quantitative epigenetic data
  ☆45Updated last year
• broadinstitute / single_cell_classification
  Methods to use SNPs or gene expression to classify single cell RNAseq to reference profiles
  ☆29Updated 5 years ago
• netbiolab / scHumanNet
  Analysis cell-type-specific functional gene network, with SCINET and HumanNetv3
  ☆42Updated last year
• WRui / Post_Implantation
  ☆27Updated 3 years ago
• quadbio / RNAseq_tutorial
  ☆27Updated 6 months ago
• nghiavtr / SCmut
  ☆32Updated 5 years ago
• Henikoff / scCUT-Tag
  ☆16Updated last year
• YiPeng-Gao / scDaPars
  Dynamic Analysis of Alternative Polyadenylation from single-cell RNA-seq (scDaPars)
  ☆15Updated 3 years ago
• TianLab-Bioinfo / scMAGIC
  A robust and accurate cell type classifier for single cell RNA-seq data
  ☆16Updated 2 years ago
• GreenleafLab / ChrAccR
  Analyzing chromatin accessibility data in R
  ☆18Updated last year
• NBISweden / single-cell_sib_scilifelab
  SIB/Scilifelab autumn school in single cell omics 2019.
  ☆22Updated 5 years ago
• PCAWG-11 / Heterogeneity
  Code accompanying Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes
  ☆43Updated 4 years ago
• lkmklsmn / MitoTrace
  ☆17Updated 10 months ago
• dbrg77 / plate_scATAC-seq
  A rapid and robust plate-based single cell ATAC-seq (scATAC-seq) method
  ☆43Updated 4 years ago
• PoolLab / ReferenceEnhancer
  ☆20Updated last year
• HectorRDB / condiments
  Trajectory inference across multiple conditions with condiments: differential topology, progression, differentiation, and expression
  ☆28Updated 5 months ago