Alternatives and similar repositories for SCTransformPy

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

• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆63Updated 3 weeks ago
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆74Updated 6 months ago
• lilab-bcb / harmony-pytorch
  ☆55Updated 3 months ago
• mossjacob / pyslingshot
  Python implementation of the Slingshot pseudotime algorithm
  ☆62Updated last year
• simonwm / tacco
  TACCO: Transfer of Annotations to Cells and their COmbinations
  ☆52Updated last year
• YosefLab / scib-metrics
  Accelerated, Python-only, single-cell integration benchmarking metrics
  ☆68Updated last week
• CSOgroup / cellcharter
  A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
  ☆130Updated 2 weeks ago
• drieslab / awesome-spatial-data-analysis
  Awesome list of tools and methods to perform spatial transcriptomic data analysis.
  ☆44Updated 4 years ago
• YosefLab / popV
  ☆82Updated last week
• dpeerlab / ENVI
  ☆50Updated 3 months ago
• wallet-maker / cytopus
  Single cell omics biology annotations
  ☆51Updated 4 months ago
• pinellolab / dictys
  Context specific and dynamic gene regulatory network reconstruction and analysis
  ☆121Updated last week
• aertslab / pycisTopic
  pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.
  ☆73Updated 3 weeks ago
• bowang-lab / DeepVelo
  ☆46Updated last year
• tanaylab / metacells
  Metacells - Single-cell RNA Sequencing Analysis
  ☆111Updated 10 months ago
• livnatje / DIALOGUE
  DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map th…
  ☆113Updated last year
• Moldia / Xenium_benchmarking
  Code used to benchmark Xenium
  ☆65Updated last year
• GuangyuWangLab2021 / cellDancer
  Predict RNA velocity through deep learning
  ☆70Updated last year
• welch-lab / MultiVelo
  Multi-omic velocity inference
  ☆110Updated 10 months ago
• digitalcytometry / cytospace
  CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data
  ☆133Updated 6 months ago
• icbi-lab / luca
  Single-cell Lung Cancer Atlas with 1.2M cells
  ☆66Updated 7 months ago
• almaan / stereoscope
  Spatial mapping of cell types by integration of transcriptomics data
  ☆93Updated 3 years ago
• theislab / spatial_scog_workshop_2022
  Tutorials for the SCOG Virtual Workshop ‘Spatial transcriptomics data analysis in Python’ - May 23-24, 2022
  ☆53Updated 3 years ago
• ShobiStassen / VIA
  trajectory inference
  ☆104Updated 6 months ago
• cistrome / MIRA
  Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.
  ☆63Updated last month
• raphael-group / paste2
  Probabilistic Alignment of Spatial Transcriptomics Experiments v.2
  ☆37Updated 5 months ago
• settylab / Mellon
  Non-parametric density inference for single-cell analysis.
  ☆72Updated 3 months ago
• BayraktarLab / cell2fate
  Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.
  ☆79Updated 5 months ago
• theislab / scib-pipeline
  Snakemake pipeline that works with the scIB package to benchmark data integration methods.
  ☆76Updated 7 months ago
• SCCAF / sccaf
  Single-Cell Clustering Assessment Framework
  ☆105Updated last year