Alternatives and similar repositories for anndata2ri

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

• 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 4 months ago
• SCCAF / sccaf
  Single-Cell Clustering Assessment Framework
  ☆105Updated last year
• theislab / scCODA
  A Bayesian model for compositional single-cell data analysis
  ☆173Updated 2 years ago
• theislab / scib-pipeline
  Snakemake pipeline that works with the scIB package to benchmark data integration methods.
  ☆76Updated 7 months ago
• pinellolab / dictys
  Context specific and dynamic gene regulatory network reconstruction and analysis
  ☆121Updated last week
• colomemaria / epiScanpy
  Episcanpy: Epigenomics Single Cell Analysis in Python
  ☆145Updated 8 months ago
• saezlab / dorothea
  R package to access DoRothEA's regulons
  ☆149Updated last year
• GregorySchwartz / too-many-cells
  Cluster single cells and analyze cell clade relationships with colorful visualizations.
  ☆112Updated 9 months ago
• rajewsky-lab / novosparc
  ☆131Updated last year
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆74Updated 6 months ago
• aertslab / AUCell
  AUCell: score single cells with gene regulatory networks
  ☆164Updated 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 3 weeks ago
• zktuong / dandelion
  dandelion - A single cell BCR/TCR V(D)J-seq analysis package for 10X Chromium 5' data
  ☆118Updated 2 weeks ago
• calico / solo
  software to detect doublets
  ☆94Updated 7 months ago
• theislab / zellkonverter
  Conversion between scRNA-seq objects
  ☆184Updated 2 months ago
• dpeerlab / SEACells
  SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data
  ☆166Updated 4 months ago
• saezlab / progeny
  R package for Pathway RespOnsive GENe activity inference
  ☆107Updated 2 years ago
• theislab / kBET
  An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
  ☆167Updated last year
• ShobiStassen / VIA
  trajectory inference
  ☆104Updated 6 months ago
• AllonMKlein / scrublet
  Detect doublets in single-cell RNA-seq data
  ☆85Updated 6 years ago
• BlishLab / scriabin
  Analysis of cell-cell communication at single-cell resolution
  ☆104Updated 11 months ago
• scverse / scanpy_usage
  Scanpy use cases.
  ☆86Updated 4 years ago
• yelabucsf / scrna-parameter-estimation
  Direct estimation of mean and covariance from single cell RNA seq experiments
  ☆115Updated 3 months ago
• ncborcherding / utility
  Collection of Tumor-Infiltrating Lymphocyte Single-Cell Experiments with TCR
  ☆91Updated last week
• tanaylab / metacell
  Metacell - Single-cell mRNA Analysis
  ☆116Updated 7 months ago
• tanaylab / metacells
  Metacells - Single-cell RNA Sequencing Analysis
  ☆111Updated 10 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 …
  ☆85Updated 5 months ago
• Hoohm / CITE-seq-Count
  A tool that allows to get UMI counts from a single cell protein assay
  ☆82Updated 4 months ago
• JiekaiLab / scDIOR
  scDIOR: Single cell data IO softwaRe
  ☆145Updated 3 years ago
• JEFworks-Lab / STdeconvolve
  Reference-free cell-type deconvolution of multi-cellular spatially resolved transcriptomics data
  ☆140Updated 3 weeks ago