Alternatives and similar repositories for solo

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

• SCCAF / sccaf
  Single-Cell Clustering Assessment Framework
  ☆105Updated last year
• theislab / anndata2ri
  Convert between AnnData and SingleCellExperiment
  ☆137Updated this week
• Hoohm / CITE-seq-Count
  A tool that allows to get UMI counts from a single cell protein assay
  ☆82Updated 3 months ago
• yelabucsf / scrna-parameter-estimation
  Direct estimation of mean and covariance from single cell RNA seq experiments
  ☆112Updated 2 months ago
• YosefLab / popV
  ☆80Updated last week
• BayraktarLab / cell2fate
  Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.
  ☆79Updated 4 months ago
• pinellolab / dictys
  Context specific and dynamic gene regulatory network reconstruction and analysis
  ☆120Updated 3 weeks ago
• ncborcherding / utility
  Collection of Tumor-Infiltrating Lymphocyte Single-Cell Experiments with TCR
  ☆90Updated last year
• aertslab / pycisTopic
  pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.
  ☆70Updated last week
• theislab / scCODA
  A Bayesian model for compositional single-cell data analysis
  ☆170Updated 2 years ago
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆63Updated this week
• theislab / scib-pipeline
  Snakemake pipeline that works with the scIB package to benchmark data integration methods.
  ☆75Updated 6 months ago
• BlishLab / scriabin
  Analysis of cell-cell communication at single-cell resolution
  ☆103Updated 10 months ago
• tanaylab / metacells
  Metacells - Single-cell RNA Sequencing Analysis
  ☆110Updated 10 months ago
• welch-lab / MultiVelo
  Multi-omic velocity inference
  ☆110Updated 9 months ago
• AllonKleinLab / SPRING_dev
  ☆69Updated last year
• CahanLab / singleCellNet
  SingleCellNet: classify single cells across species and platforms
  ☆138Updated last year
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆74Updated 5 months ago
• parashardhapola / scarf
  Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with mill…
  ☆101Updated 3 months ago
• interactivereport / cellxgene_VIP
  Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey a…
  ☆155Updated this week
• immunogenomics / symphony
  Efficient and precise single-cell reference atlas mapping with Symphony
  ☆105Updated 2 years ago
• zktuong / dandelion
  dandelion - A single cell BCR/TCR V(D)J-seq analysis package for 10X Chromium 5' data
  ☆117Updated 3 weeks ago
• saezlab / dorothea
  R package to access DoRothEA's regulons
  ☆149Updated last year
• saezlab / progeny
  R package for Pathway RespOnsive GENe activity inference
  ☆106Updated 2 years ago
• ShobiStassen / VIA
  trajectory inference
  ☆104Updated 6 months ago
• theislab / AutoGeneS
  ☆61Updated 4 years ago
• czbiohub-sf / tabula-sapiens
  Single Cell Transcriptomics of 25 Human Organs to Create a Tabula Sapiens
  ☆42Updated 2 years ago
• rnakato / ShortCake
  A docker image for single-cell analysis
  ☆88Updated 6 months ago
• phbradley / conga
  Clonotype Neighbor Graph Analysis
  ☆90Updated 3 weeks ago
• timoast / sinto
  Tools for single-cell data processing
  ☆125Updated last year