Alternatives and similar repositories for scvi-tools

Users that are interested in scvi-tools are comparing it to the libraries listed below

• theislab / single-cell-tutorial
  Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq an…
  ☆1,538Updated 3 years ago
• scverse / scanpy
  Single-cell analysis in Python. Scales to >100M cells.
  ☆2,313Updated last week
• theislab / single-cell-best-practices
  https://www.sc-best-practices.org
  ☆1,095Updated 3 weeks ago
• mdozmorov / scRNA-seq_notes
  A list of scRNA-seq analysis tools
  ☆767Updated last week
• aertslab / pySCENIC
  pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…
  ☆567Updated 6 months ago
• chanzuckerberg / cellxgene
  An interactive explorer for single-cell transcriptomics data
  ☆742Updated last week
• theislab / scvelo
  RNA Velocity generalized through dynamical modeling
  ☆481Updated 2 weeks ago
• scverse / anndata
  Annotated data.
  ☆696Updated last week
• calico / basenji
  Sequential regulatory activity predictions with deep convolutional neural networks.
  ☆461Updated 7 months ago
• aristoteleo / dynamo-release
  Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction …
  ☆480Updated 2 weeks ago
• bowang-lab / scGPT
  ☆1,424Updated last month
• scverse / PyDESeq2
  A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
  ☆710Updated 2 weeks ago
• openproblems-bio / openproblems
  Formalizing and benchmarking open problems in single-cell genomics
  ☆418Updated last month
• zqfang / GSEApy
  Gene Set Enrichment Analysis in Python
  ☆683Updated 3 weeks ago
• Starlitnightly / omicverse
  A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.
  ☆813Updated this week
• mikelove / awesome-multi-omics
  List of software packages for multi-omics analysis
  ☆883Updated last week
• OmicsML / awesome-deep-learning-single-cell-papers
  ☆831Updated 8 months ago
• agitter / single-cell-pseudotime
  An overview of algorithms for estimating pseudotime in single-cell RNA-seq data
  ☆435Updated this week
• mousepixels / sanbomics_scripts
  scripts and notebooks from sanbomics
  ☆456Updated last year
• hemberg-lab / scRNA.seq.course
  Analysis of single cell RNA-seq data course
  ☆677Updated 3 years ago
• morris-lab / CellOracle
  This is the alpha version of the CellOracle package
  ☆405Updated last year
• gao-lab / GLUE
  Graph-linked unified embedding for single-cell multi-omics data integration
  ☆442Updated last month
• hbctraining / scRNA-seq
  ☆596Updated 4 years ago
• saeyslab / nichenetr
  NicheNet: predict active ligand-target links between interacting cells
  ☆600Updated last month
• hbctraining / Intro-to-scRNAseq
  ☆639Updated last month
• theislab / scib
  Benchmarking analysis of data integration tools
  ☆400Updated 3 months ago
• seandavi / awesome-single-cell
  Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
  ☆3,619Updated last week
• theislab / scarches
  Reference mapping for single-cell genomics
  ☆396Updated last month
• sqjin / CellChat
  R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data
  ☆756Updated 2 years ago
• immunogenomics / harmony
  Fast, sensitive and accurate integration of single-cell data with Harmony
  ☆617Updated 2 months ago