Alternatives and similar repositories for cellranger

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

• Teichlab / scg_lib_structs
  Collections of library structure and sequence of popular single cell genomic methods
  ☆489Updated 8 months ago
• ENCODE-DCC / atac-seq-pipeline
  ENCODE ATAC-seq pipeline
  ☆444Updated last year
• hbctraining / Intro-to-ChIPseq
  Intro to ChIPseq using HPC
  ☆321Updated 2 years ago
• scRNA-tools / scRNA-tools
  Table of software for the analysis of single-cell RNA-seq data.
  ☆337Updated this week
• Boyle-Lab / Blacklist
  Application for making ENCODE Blacklists
  ☆331Updated 4 years ago
• liulab-dfci / TRUST4
  TCR and BCR assembly from RNA-seq data
  ☆338Updated this week
• r3fang / SnapATAC
  Analysis Pipeline for Single Cell ATAC-seq
  ☆320Updated 2 years ago
• GreenleafLab / ArchR
  ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
  ☆442Updated 11 months ago
• sdparekh / zUMIs
  zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
  ☆288Updated last year
• broadinstitute / ssGSEA2.0
  Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)
  ☆308Updated 3 months ago
• broadinstitute / gtex-pipeline
  GTEx & TOPMed data production and analysis pipelines
  ☆392Updated 4 months ago
• broadinstitute / CellBender
  CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
  ☆373Updated 5 months ago
• milaboratory / mixcr
  MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.
  ☆380Updated this week
• maxplanck-ie / snakepipes
  Customizable workflows based on snakemake and python for the analysis of NGS data
  ☆396Updated last week
• CGATOxford / UMI-tools
  Tools for handling Unique Molecular Identifiers in NGS data sets
  ☆535Updated 6 months ago
• ENCODE-DCC / chip-seq-pipeline2
  ENCODE ChIP-seq pipeline
  ☆278Updated last year
• cellgeni / scRNA.seq.course
  Analysis of single cell RNA-seq data course
  ☆161Updated 3 years ago
• cellgeni / sceasy
  A package to help convert different single-cell data formats to each other
  ☆452Updated last year
• aertslab / pySCENIC
  pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…
  ☆572Updated 6 months ago
• chris-mcginnis-ucsf / DoubletFinder
  R package for detecting doublets in single-cell RNA sequencing data
  ☆517Updated 10 months ago
• pachterlab / ffq
  A tool to find sequencing data and metadata from public databases.
  ☆592Updated last year
• dviraran / SingleR
  SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
  ☆317Updated 5 years ago
• Teichlab / cellphonedb
  ☆358Updated 4 years ago
• IanevskiAleksandr / sc-type
  ☆285Updated last year
• liulab-dfci / MAESTRO
  Single-cell Transcriptome and Regulome Analysis Pipeline
  ☆299Updated 2 years ago
• crazyhottommy / TCR-BCR-seq-analysis
  T/B cell receptor sequencing analysis notes
  ☆271Updated last year
• saeyslab / nichenetr
  NicheNet: predict active ligand-target links between interacting cells
  ☆609Updated 2 months ago
• omnideconv / immunedeconv
  A unified interface to immune deconvolution methods (CIBERSORT, EPIC, quanTIseq, TIMER, xCell, MCPcounter) and mouse deconvolution method…
  ☆513Updated 2 weeks ago
• theislab / scvelo
  RNA Velocity generalized through dynamical modeling
  ☆484Updated last month
• thelovelab / DESeq2
  Differential expression of RNA-seq data using the Negative Binomial
  ☆439Updated last month