Alternatives and similar repositories for singleCellNet

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

• saezlab / dorothea
  R package to access DoRothEA's regulons
  ☆149Updated last year
• theislab / kBET
  An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
  ☆162Updated last year
• aertslab / AUCell
  AUCell: score single cells with gene regulatory networks
  ☆158Updated last year
• cole-trapnell-lab / garnett
  Automated cell type classification
  ☆111Updated 6 months ago
• quadbio / Pando
  Multiome GRN inference.
  ☆124Updated last year
• YosefLab / VISION
  Signature Analysis and Visualization for Single-Cell RNA-seq
  ☆168Updated last year
• Irrationone / cellassign
  Automated, probabilistic assignment of cell types in scRNA-seq data
  ☆202Updated 2 years ago
• theislab / scCODA
  A Bayesian model for compositional single-cell data analysis
  ☆169Updated 2 years ago
• campbio / celda
  Bayesian Hierarchical Modeling for Clustering Single Cell Genomic Data
  ☆148Updated 5 months ago
• JEFworks-Lab / STdeconvolve
  Reference-free cell-type deconvolution of multi-cellular spatially resolved transcriptomics data
  ☆134Updated last month
• immunogenomics / symphony
  Efficient and precise single-cell reference atlas mapping with Symphony
  ☆105Updated 2 years ago
• saezlab / liana
  LIANA: a LIgand-receptor ANalysis frAmework
  ☆211Updated 11 months ago
• crazyhottommy / scclusteval
  Single Cell Cluster Evaluation
  ☆94Updated 3 years ago
• enblacar / SCpubr
  Generate high quality, publication ready visualizations for single cell transcriptomics data.
  ☆199Updated last month
• theislab / scib-pipeline
  Snakemake pipeline that works with the scIB package to benchmark data integration methods.
  ☆74Updated 5 months ago
• timoast / sinto
  Tools for single-cell data processing
  ☆125Updated last year
• aertslab / cisTopic
  cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data
  ☆140Updated last year
• GreenleafLab / chromVAR
  chromatin Variability Across Regions (of the genome!)
  ☆178Updated last year
• rnabioco / clustifyr
  Infer cell types in scRNA-seq data using bulk RNA-seq or gene sets
  ☆123Updated 2 months ago
• theislab / zellkonverter
  Conversion between scRNA-seq objects
  ☆178Updated 3 weeks ago
• SCCAF / sccaf
  Single-Cell Clustering Assessment Framework
  ☆103Updated last year
• hemberg-lab / scmap
  A tool for unsupervised projection of single cell RNA-seq data
  ☆96Updated 4 years ago
• compbiomed / singleCellTK
  Interactively analyze single cell genomic data
  ☆182Updated last week
• ncborcherding / utility
  Collection of Tumor-Infiltrating Lymphocyte Single-Cell Experiments with TCR
  ☆89Updated last year
• satijalab / azimuth
  A Shiny web app for mapping datasets using Seurat v4
  ☆132Updated 8 months ago
• interactivereport / cellxgene_VIP
  Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey a…
  ☆150Updated last month
• carmonalab / scGate
  marker-based purification of cell types from single-cell RNA-seq datasets
  ☆115Updated 2 months ago
• colomemaria / epiScanpy
  Episcanpy: Epigenomics Single Cell Analysis in Python
  ☆144Updated 7 months ago
• Hoohm / CITE-seq-Count
  A tool that allows to get UMI counts from a single cell protein assay
  ☆82Updated 2 months ago
• carmonalab / UCell
  Gene set scoring for single-cell data
  ☆154Updated 2 months ago