Alternatives and similar repositories for anndata2ri

Users that are interested in anndata2ri are comparing it to the libraries listed below

• SCCAF / sccaf
  Single-Cell Clustering Assessment Framework
  ☆105Updated last year
• theislab / scCODA
  A Bayesian model for compositional single-cell data analysis
  ☆176Updated 2 years ago
• yelabucsf / scrna-parameter-estimation
  Direct estimation of mean and covariance from single cell RNA seq experiments
  ☆118Updated 5 months ago
• theislab / scib-pipeline
  Snakemake pipeline that works with the scIB package to benchmark data integration methods.
  ☆77Updated 8 months ago
• rajewsky-lab / novosparc
  ☆131Updated last year
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆74Updated 7 months ago
• GregorySchwartz / too-many-cells
  Cluster single cells and analyze cell clade relationships with colorful visualizations.
  ☆113Updated 11 months ago
• ShobiStassen / VIA
  trajectory inference
  ☆105Updated 8 months ago
• aertslab / AUCell
  AUCell: score single cells with gene regulatory networks
  ☆169Updated last year
• colomemaria / epiScanpy
  Episcanpy: Epigenomics Single Cell Analysis in Python
  ☆147Updated 10 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…
  ☆104Updated 5 months ago
• pinellolab / dictys
  Context specific and dynamic gene regulatory network reconstruction and analysis
  ☆122Updated 3 weeks ago
• dpeerlab / SEACells
  SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data
  ☆168Updated 6 months ago
• jfnavarro / st_pipeline
  ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method …
  ☆87Updated 7 months ago
• tanaylab / metacells
  Metacells - Single-cell RNA Sequencing Analysis
  ☆111Updated last year
• theislab / zellkonverter
  Conversion between scRNA-seq objects
  ☆187Updated last month
• timoast / sinto
  Tools for single-cell data processing
  ☆127Updated last year
• zktuong / dandelion
  dandelion - A single cell BCR/TCR V(D)J-seq analysis package for 10X Chromium 5' data
  ☆119Updated last week
• ncborcherding / utility
  Collection of Tumor-Infiltrating Lymphocyte Single-Cell Experiments with TCR
  ☆93Updated last week
• theislab / kBET
  An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
  ☆168Updated last year
• interactivereport / cellxgene_VIP
  Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey a…
  ☆157Updated last month
• calico / solo
  software to detect doublets
  ☆95Updated 9 months ago
• swolock / scrublet
  Detect doublets in single-cell RNA-seq data
  ☆157Updated 4 years ago
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆65Updated last month
• BayraktarLab / cell2fate
  Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.
  ☆79Updated 6 months ago
• BlishLab / scriabin
  Analysis of cell-cell communication at single-cell resolution
  ☆104Updated last year
• YosefLab / popV
  ☆83Updated this week
• prabhakarlab / Banksy
  BANKSY: spatial clustering
  ☆121Updated last month
• AllonMKlein / scrublet
  Detect doublets in single-cell RNA-seq data
  ☆86Updated 6 years ago
• JEFworks-Lab / STdeconvolve
  Reference-free cell-type deconvolution of multi-cellular spatially resolved transcriptomics data
  ☆144Updated 2 months ago