Alternatives and similar repositories for SEACells

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

• theislab / scCODA
  A Bayesian model for compositional single-cell data analysis
  ☆187Updated 3 weeks ago
• tanaylab / metacells
  Metacells - Single-cell RNA Sequencing Analysis
  ☆117Updated last year
• quadbio / Pando
  Multiome GRN inference.
  ☆133Updated last year
• dpeerlab / spectra
  Supervised Pathway DEConvolution of InTerpretable Gene ProgRAms
  ☆186Updated this week
• digitalcytometry / cytospace
  CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data
  ☆138Updated 11 months ago
• saeyslab / multinichenetr
  MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell trans…
  ☆179Updated 5 months ago
• changwn / scFEA
  single cell Flux Estimation Analysis (scFEA) Try the below web server!
  ☆143Updated 2 years ago
• igrabski / sc-SHC
  Significance analysis for clustering single-cell RNA-sequencing data
  ☆123Updated last year
• theislab / zellkonverter
  Conversion between scRNA-seq objects
  ☆198Updated 3 weeks ago
• saezlab / liana
  LIANA: a LIgand-receptor ANalysis frAmework
  ☆230Updated last year
• aertslab / AUCell
  AUCell: score single cells with gene regulatory networks
  ☆182Updated last year
• aertslab / scenicplus
  SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) a…
  ☆245Updated 2 weeks ago
• YosefLab / Compass
  In-Silico Modeling of Metabolic Heterogeneity using Single-Cell Transcriptomes
  ☆120Updated 3 months ago
• BlishLab / scriabin
  Analysis of cell-cell communication at single-cell resolution
  ☆106Updated last year
• theislab / kBET
  An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
  ☆169Updated 2 years ago
• livnatje / DIALOGUE
  DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map th…
  ☆117Updated 2 years ago
• welch-lab / MultiVelo
  Multi-omic velocity inference
  ☆116Updated last year
• theislab / scib-pipeline
  Snakemake pipeline that works with the scIB package to benchmark data integration methods.
  ☆81Updated last year
• swolock / scrublet
  Detect doublets in single-cell RNA-seq data
  ☆162Updated 5 years ago
• JiekaiLab / scDIOR
  scDIOR: Single cell data IO softwaRe
  ☆153Updated 3 years ago
• LewisLabUCSD / Ligand-Receptor-Pairs
  Compendium of available lists of ligand-receptor pairs and surface-secreted protein interactions.
  ☆149Updated 3 years ago
• aertslab / SCENICprotocol
  A scalable SCENIC workflow for single-cell gene regulatory network analysis
  ☆171Updated 3 years ago
• navinlabcode / CellTrek
  ☆129Updated 3 years ago
• cellgeni / schard
  reticulate-free single cell format conversion
  ☆206Updated last week
• icbi-lab / infercnvpy
  Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.
  ☆179Updated last week
• yelabucsf / scrna-parameter-estimation
  Direct estimation of mean and covariance from single cell RNA seq experiments
  ☆127Updated 8 months ago
• YMa-lab / CARD
  ☆129Updated last year
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆81Updated 11 months ago
• colomemaria / epiScanpy
  Episcanpy: Epigenomics Single Cell Analysis in Python
  ☆149Updated last year
• neurorestore / Augur
  Cell type prioritization in single-cell data
  ☆136Updated last year