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.
  ☆162Updated last year
• timoast / sinto
  Tools for single-cell data processing
  ☆125Updated last year
• GreenleafLab / chromVAR
  chromatin Variability Across Regions (of the genome!)
  ☆178Updated last year
• CahanLab / singleCellNet
  SingleCellNet: classify single cells across species and platforms
  ☆137Updated last year
• saezlab / dorothea
  R package to access DoRothEA's regulons
  ☆149Updated last year
• AllonMKlein / scrublet
  Detect doublets in single-cell RNA-seq data
  ☆85Updated 6 years ago
• czbiohub-sf / tabula-muris
  Code and annotations for the Tabula Muris single-cell transcriptomic dataset.
  ☆192Updated 2 years ago
• hemberg-lab / scmap
  A tool for unsupervised projection of single cell RNA-seq data
  ☆96Updated 4 years ago
• Hoohm / CITE-seq-Count
  A tool that allows to get UMI counts from a single cell protein assay
  ☆82Updated 2 months ago
• mohuangx / SAVER
  Single-cell RNA-seq Gene Expression Recovery
  ☆109Updated 7 months ago
• SCCAF / sccaf
  Single-Cell Clustering Assessment Framework
  ☆103Updated last year
• pinellolab / scATAC-benchmarking
  Benchmarking computational single cell ATAC-seq methods
  ☆184Updated 4 years ago
• GreenleafLab / 10x-scATAC-2019
  Publication Page for Satpathy*, Granja* et al 2019
  ☆94Updated 5 years ago
• asncd / MIMOSCA
  A repository for the design and analysis of pooled single cell RNA-seq perturbation experiments.
  ☆91Updated 5 years ago
• phbradley / conga
  Clonotype Neighbor Graph Analysis
  ☆89Updated 3 weeks ago
• crazyhottommy / scclusteval
  Single Cell Cluster Evaluation
  ☆94Updated 3 years ago
• tabdelaal / scRNAseq_Benchmark
  Bench-marking classification tools for scRNA-seq data
  ☆186Updated 3 years ago
• theislab / scCODA
  A Bayesian model for compositional single-cell data analysis
  ☆169Updated 2 years ago
• GregorySchwartz / too-many-cells
  Cluster single cells and analyze cell clade relationships with colorful visualizations.
  ☆114Updated 8 months ago
• 10XGenomics / single-cell-3prime-paper
  ☆85Updated 5 years ago
• Irrationone / cellassign
  Automated, probabilistic assignment of cell types in scRNA-seq data
  ☆202Updated 2 years ago
• farrellja / URD
  URD - Reconstruction of Branching Developmental Trajectories
  ☆124Updated 4 years ago
• rajewsky-lab / novosparc
  ☆130Updated last year
• bioinfo-ibms-pumc / SCSA
  SCSA: cell type annotation for single-cell RNA-seq data
  ☆90Updated 2 years ago
• theislab / anndata2ri
  Convert between AnnData and SingleCellExperiment
  ☆137Updated last week
• favilaco / deconv_benchmark
  ☆58Updated 4 years ago
• ncborcherding / utility
  Collection of Tumor-Infiltrating Lymphocyte Single-Cell Experiments with TCR
  ☆89Updated last year
• zhangzlab / covid_balf
  R script for the covid balf data analysis
  ☆65Updated 4 years ago
• cellgeni / batchbench
  ☆47Updated 3 years ago
• kharchenkolab / numbat
  Haplotype-aware CNV analysis from single-cell RNA-seq
  ☆186Updated 2 weeks ago