Alternatives and similar repositories for singleCellNet

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

• cole-trapnell-lab / garnett
  Automated cell type classification
  ☆112Updated 8 months ago
• saezlab / dorothea
  R package to access DoRothEA's regulons
  ☆150Updated last year
• satijalab / azimuth
  A Shiny web app for mapping datasets using Seurat v4
  ☆132Updated 10 months ago
• aertslab / AUCell
  AUCell: score single cells with gene regulatory networks
  ☆166Updated last year
• immunogenomics / symphony
  Efficient and precise single-cell reference atlas mapping with Symphony
  ☆108Updated 2 years ago
• Irrationone / cellassign
  Automated, probabilistic assignment of cell types in scRNA-seq data
  ☆205Updated 2 years ago
• theislab / kBET
  An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
  ☆167Updated last year
• quadbio / Pando
  Multiome GRN inference.
  ☆127Updated last year
• crazyhottommy / scclusteval
  Single Cell Cluster Evaluation
  ☆97Updated 4 years ago
• saezlab / progeny
  R package for Pathway RespOnsive GENe activity inference
  ☆108Updated 2 years ago
• phbradley / conga
  Clonotype Neighbor Graph Analysis
  ☆90Updated 3 weeks ago
• interactivereport / cellxgene_VIP
  Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey a…
  ☆157Updated last week
• saezlab / liana
  LIANA: a LIgand-receptor ANalysis frAmework
  ☆214Updated last year
• ncborcherding / utility
  Collection of Tumor-Infiltrating Lymphocyte Single-Cell Experiments with TCR
  ☆92Updated last week
• cellgeni / batchbench
  ☆47Updated 3 years ago
• dpeerlab / SEACells
  SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data
  ☆167Updated 5 months ago
• hemberg-lab / scmap
  A tool for unsupervised projection of single cell RNA-seq data
  ☆95Updated 4 years ago
• theislab / scib-pipeline
  Snakemake pipeline that works with the scIB package to benchmark data integration methods.
  ☆76Updated 7 months ago
• GregorySchwartz / too-many-cells
  Cluster single cells and analyze cell clade relationships with colorful visualizations.
  ☆113Updated 10 months ago
• theislab / scCODA
  A Bayesian model for compositional single-cell data analysis
  ☆173Updated 2 years ago
• farrellja / URD
  URD - Reconstruction of Branching Developmental Trajectories
  ☆124Updated 4 years ago
• SCCAF / sccaf
  Single-Cell Clustering Assessment Framework
  ☆105Updated last year
• aertslab / cisTopic
  cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data
  ☆141Updated last year
• immunogenomics / LISI
  Methods to compute Local Inverse Simpson's Index (LISI)
  ☆68Updated 4 years ago
• GreenleafLab / MPAL-Single-Cell-2019
  Publication Page for MPAL Paper 2019
  ☆83Updated 5 years ago
• Dragonmasterx87 / Interactive-3D-Plotting-in-Seurat-3.0.0
  This repository contains R code, with which you can create 3D UMAP and tSNE plots of Seurat analyzed scRNAseq data
  ☆121Updated 2 years ago
• carmonalab / UCell
  Gene set scoring for single-cell data
  ☆160Updated 4 months ago
• calico / solo
  software to detect doublets
  ☆94Updated 8 months ago
• BaderLab / CellAnnotationTutorial
  Accompanying code for the tutorial: Annotating single cell transcriptomic maps using automated and manual methods
  ☆97Updated 2 years ago
• LocasaleLab / Single-Cell-Metabolic-Landscape
  Pipeline for exploring metebolic heterogeneity at single-cell resolution
  ☆74Updated 5 years ago