Alternatives and similar repositories for cisTopic

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

• theislab / kBET
  An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
  ☆169Updated 2 years ago
• mohuangx / SAVER
  Single-cell RNA-seq Gene Expression Recovery
  ☆114Updated last year
• saezlab / dorothea
  R package to access DoRothEA's regulons
  ☆154Updated last year
• CahanLab / singleCellNet
  SingleCellNet: classify single cells across species and platforms
  ☆140Updated 2 years ago
• asncd / MIMOSCA
  A repository for the design and analysis of pooled single cell RNA-seq perturbation experiments.
  ☆98Updated 6 years ago
• timoast / sinto
  Tools for single-cell data processing
  ☆131Updated last year
• GreenleafLab / chromVAR
  chromatin Variability Across Regions (of the genome!)
  ☆185Updated last year
• phbradley / conga
  Clonotype Neighbor Graph Analysis
  ☆94Updated 5 months ago
• SCCAF / sccaf
  Single-Cell Clustering Assessment Framework
  ☆107Updated 2 years ago
• tabdelaal / scRNAseq_Benchmark
  Bench-marking classification tools for scRNA-seq data
  ☆191Updated 3 years ago
• pinellolab / scATAC-benchmarking
  Benchmarking computational single cell ATAC-seq methods
  ☆184Updated 5 years ago
• aertslab / AUCell
  AUCell: score single cells with gene regulatory networks
  ☆182Updated last year
• hemberg-lab / scmap
  A tool for unsupervised projection of single cell RNA-seq data
  ☆96Updated 5 years ago
• AllonMKlein / scrublet
  Detect doublets in single-cell RNA-seq data
  ☆86Updated 6 years ago
• zhangzlab / covid_balf
  R script for the covid balf data analysis
  ☆65Updated 5 years ago
• Hoohm / CITE-seq-Count
  A tool that allows to get UMI counts from a single cell protein assay
  ☆87Updated 9 months ago
• velocyto-team / velocyto.py
  RNA velocity estimation in Python
  ☆175Updated 3 months ago
• GregorySchwartz / too-many-cells
  Cluster single cells and analyze cell clade relationships with colorful visualizations.
  ☆114Updated last year
• czbiohub-sf / tabula-muris
  Code and annotations for the Tabula Muris single-cell transcriptomic dataset.
  ☆196Updated 2 years ago
• kharchenkolab / dropEst
  Pipeline for initial analysis of droplet-based single-cell RNA-seq data
  ☆95Updated 3 years ago
• cellgeni / batchbench
  ☆46Updated 3 years ago
• rajewsky-lab / novosparc
  ☆131Updated 2 years ago
• bioinfo-ibms-pumc / SCSA
  SCSA: cell type annotation for single-cell RNA-seq data
  ☆94Updated 2 years ago
• GreenleafLab / 10x-scATAC-2019
  Publication Page for Satpathy*, Granja* et al 2019
  ☆94Updated 5 years ago
• theislab / scCODA
  A Bayesian model for compositional single-cell data analysis
  ☆187Updated 3 weeks ago
• pachterlab / kallistobustools
  kallisto | bustools workflow for pre-processing single-cell RNA-seq data
  ☆119Updated 3 years ago
• BlishLab / scriabin
  Analysis of cell-cell communication at single-cell resolution
  ☆106Updated last year
• Irrationone / cellassign
  Automated, probabilistic assignment of cell types in scRNA-seq data
  ☆210Updated 3 years ago
• calico / solo
  software to detect doublets
  ☆96Updated last year
• tanaylab / metacell
  Metacell - Single-cell mRNA Analysis
  ☆118Updated last year