Alternatives and similar repositories for batchbench:

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

• hemberg-lab / scmap
  A tool for unsupervised projection of single cell RNA-seq data
  ☆93Updated 4 years ago
• Single-Cell-Genomics-Group-CNAG-CRG / Tumor-Immune-Cell-Atlas
  Code repository for the Tumor Immune Cell Atlas (TICA) project
  ☆62Updated 2 years ago
• vib-singlecell-nf / vsn-pipelines
  A repository of pipelines for single-cell data in Nextflow DSL2
  ☆75Updated last year
• elimereu / matchSCore2
  ☆53Updated 4 years ago
• Coolgenome / iTALK
  ☆59Updated 5 years ago
• Hoohm / CITE-seq-Count
  A tool that allows to get UMI counts from a single cell protein assay
  ☆79Updated 6 months ago
• MarioniLab / EmbryoTimecourse2018
  Data and analysis scripts for our Embryo Timecourse paper.
  ☆67Updated 5 years ago
• immunogenomics / LISI
  Methods to compute Local Inverse Simpson's Index (LISI)
  ☆60Updated 3 years ago
• BlishLab / scriabin
  Analysis of cell-cell communication at single-cell resolution
  ☆100Updated 5 months ago
• rpolicastro / scProportionTest
  ☆60Updated last year
• crazyhottommy / scclusteval
  Single Cell Cluster Evaluation
  ☆87Updated 3 years ago
• theislab / scib-pipeline
  Snakemake pipeline that works with the scIB package to benchmark data integration methods.
  ☆68Updated 3 weeks ago
• chris-mcginnis-ucsf / MULTI-seq
  R implementation of MULTI-seq sample classification workflow
  ☆61Updated last year
• GreenleafLab / 10x-scATAC-2019
  Publication Page for Satpathy*, Granja* et al 2019
  ☆92Updated 4 years ago
• carmonalab / STACAS
  R package for semi-supervised single-cell data integration
  ☆79Updated last year
• EDePasquale / DoubletDecon
  A tool for removing doublets from single-cell RNA-seq data
  ☆71Updated 4 years ago
• RausellLab / CelliD
  Gene signature extraction and cell-identity recognition at individual cell level from single-cell RNA-seq.
  ☆93Updated last year
• carmonalab / scGate
  marker-based purification of cell types from single-cell RNA-seq datasets
  ☆102Updated last week
• aertslab / pycisTopic
  pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.
  ☆59Updated last month
• immunogenomics / symphony
  Efficient and precise single-cell reference atlas mapping with Symphony
  ☆102Updated 2 years ago
• MarioniLab / miloDE
  Framework for sensitive DE testing (using neighbourhoods)
  ☆64Updated 6 months ago
• MarioniLab / MNN2017
  Code for the MNN manuscript figures
  ☆51Updated 6 years ago
• ncborcherding / utility
  Collection of Tumor-Infiltrating Lymphocyte Single-Cell Experiments with TCR
  ☆83Updated 7 months ago
• AllonMKlein / scrublet
  Detect doublets in single-cell RNA-seq data
  ☆85Updated 5 years ago
• sridnona / cb_sniffer
  mutation(barcode) caller for 10x single cell data
  ☆44Updated 4 years ago
• single-cell-genetics / cellSNP
  Pileup biallelic SNPs from single-cell and bulk RNA-seq data
  ☆76Updated 2 years ago
• wbaopaul / scATAC-pro
  A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data
  ☆73Updated 2 months ago
• ggjlab / scMCA
  Mouse cell atlas
  ☆60Updated 4 years ago
• bvieth / scRNA-seq-pipelines
  Compendium to "A Systematic Evaluation of Single Cell RNA-Seq Analysis Pipelines"
  ☆53Updated 4 years ago
• Japrin / STARTRAC
  STARTRAC(Single T-cell Analysis by Rna-seq and Tcr TRACking)
  ☆93Updated last year