Alternatives and similar repositories for singleCellSeq:

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

• hms-dbmi / scde
  R package for analyzing single-cell RNA-seq data
  ☆175Updated last year
• davismcc / archive-scater
  An archived version of the scater repository, see https://github.com/davismcc/scater for the active version.
  ☆64Updated 7 years ago
• bvieth / powsimR
  Power analysis is essential to optimize the design of RNA-seq experiments and to assess and compare the power to detect differentially ex…
  ☆106Updated last year
• tallulandrews / scRNASeqPipeline
  ☆118Updated 6 years ago
• drisso / bioc2016singlecell
  Bioconductor workshop: Analysis of single-cell RNA-seq data with R and Bioconductor
  ☆78Updated 8 years ago
• csoneson / conquer_comparison
  Code for evaluation of differential expression methods in single-cell RNA-seq data
  ☆112Updated 4 years ago
• PMBio / peer
  A factor analysis package
  ☆100Updated 12 years ago
• GreenleafLab / chromVAR
  chromatin Variability Across Regions (of the genome!)
  ☆173Updated 9 months ago
• Hoohm / dropSeqPipe
  A SingleCell RNASeq pre-processing snakemake workflow
  ☆149Updated 2 years ago
• velocyto-team / velocyto.R
  RNA velocity estimation in R
  ☆185Updated last year
• ENCODE-DCC / chip-seq-pipeline
  ENCODE Uniform processing pipeline for ChIP-seq
  ☆123Updated 5 years ago
• YeoLab / single-cell-bioinformatics
  Course material in notebook format for learning about single cell bioinformatics methods
  ☆102Updated 8 years ago
• snakemake-workflows / single-cell-rna-seq
  A single cell RNA-seq workflow, including highly variable gene analysis, cell type assignment and differential expression analysis.
  ☆101Updated 2 years ago
• alanocallaghan / scater
  Clone of the Bioconductor repository for the scater package.
  ☆96Updated last month
• iaconogi / bigSCale2
  Framework for clustering, phenotyping, pseudotiming and inferring gene regulatory networks from single cell data
  ☆103Updated last year
• stephenturner / annotables
  R data package for annotating/converting Gene IDs
  ☆163Updated 2 years ago
• compbiomed / singleCellTK
  Interactively analyze single cell genomic data
  ☆182Updated 2 weeks ago
• SingleR-inc / SingleR
  Clone of the Bioconductor repository for the SingleR package.
  ☆187Updated 2 months ago
• chrisamiller / fishplot
  Create timecourse "fish plots" that show changes in the clonal architecture of tumors
  ☆167Updated last year
• wjawaid / enrichR
  An R interface to enrichR
  ☆92Updated 3 months ago
• PMBio / scLVM
  scLVM is a modelling framework for single-cell RNA-seq data that can be used to dissect the observed heterogeneity into different sources…
  ☆106Updated 2 years ago
• ENCODE-DCC / long-rna-seq-pipeline
  STAR based ENCODE Long RNA-Seq processing pipeline
  ☆94Updated 4 years ago
• hdng / clonevol
  Inferring and visualizing clonal evolution in multi-sample cancer sequencing
  ☆147Updated 4 years ago
• kharchenkolab / dropEst
  Pipeline for initial analysis of droplet-based single-cell RNA-seq data
  ☆91Updated 2 years ago
• PoisonAlien / TCGAmutations
  R data package for pre-compiled somatic mutations from TCGA cohorts and CCLE
  ☆93Updated 7 months ago
• kevinblighe / E-MTAB-6141
  Data from Lewis, Barnes, Blighe et al., Cell Rep. 2019 Aug 27; 28(9): 2455–2470.e5.
  ☆119Updated 4 years ago
• crazyhottommy / pyflow-ATACseq
  ATAC-seq snakemake pipeline
  ☆87Updated 5 years ago
• czbiohub-sf / tabula-muris
  Code and annotations for the Tabula Muris single-cell transcriptomic dataset.
  ☆191Updated 2 years ago
• livnatje / ImmuneResistance
  This resource provides the code developed in the study of Jerby-Arnon _et al. "Single-cell RNA-seq of melanoma ecosystems reveals sources…
  ☆72Updated 6 years ago
• dviraran / xCell
  Cell types enrichment analysis
  ☆195Updated 11 months ago