Alternatives and similar repositories for scimilarity

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

• scverse / pertpy
  Single-cell perturbation analysis
  ☆196Updated last week
• sanderlab / scPerturb
  scPerturb: A resource and a python/R tool for single-cell perturbation data
  ☆140Updated 6 months ago
• theislab / scarches
  Reference mapping for single-cell genomics
  ☆381Updated last month
• saezlab / liana-py
  LIANA+: an all-in-one framework for cell-cell communication
  ☆227Updated last month
• theislab / scib
  Benchmarking analysis of data integration tools
  ☆373Updated 7 months ago
• scverse / decoupler
  Python package to perform enrichment analysis from omics data.
  ☆218Updated last week
• LewisLabUCSD / Ligand-Receptor-Pairs
  Compendium of available lists of ligand-receptor pairs and surface-secreted protein interactions.
  ☆137Updated 2 years ago
• scverse / scanpy-tutorials
  Scanpy Tutorials.
  ☆219Updated last week
• dpeerlab / spectra
  Supervised Pathway DEConvolution of InTerpretable Gene ProgRAms
  ☆173Updated last year
• morris-lab / CellOracle
  This is the alpha version of the CellOracle package
  ☆375Updated 7 months ago
• broadinstitute / Tangram
  Spatial alignment of single cell transcriptomic data.
  ☆317Updated last month
• theislab / sc-pert
  Models and datasets for perturbational single-cell omics
  ☆161Updated 3 years ago
• YosefLab / scib-metrics
  Accelerated, Python-only, single-cell integration benchmarking metrics
  ☆68Updated last week
• Teichlab / celltypist
  A tool for semi-automatic cell type classification
  ☆398Updated 3 weeks ago
• colomemaria / epiScanpy
  Episcanpy: Epigenomics Single Cell Analysis in Python
  ☆145Updated 8 months ago
• snap-stanford / SATURN
  ☆135Updated last year
• icbi-lab / infercnvpy
  Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.
  ☆166Updated last week
• scverse / SnapATAC2
  Single-cell epigenomics analysis tools
  ☆283Updated 3 weeks ago
• Winnie09 / GPTCelltype
  ☆207Updated last year
• calico / scBasset
  Sequence-based Modeling of single-cell ATAC-seq using Convolutional Neural Networks.
  ☆98Updated 7 months ago
• Teichlab / SpatialDE
  Test genes for Spatial Variation
  ☆175Updated last year
• cantinilab / scPRINT
  single cell foundation model
  ☆97Updated this week
• BiomedicalMachineLearning / stLearn
  A novel machine learning pipeline to analyse spatial transcriptomics data
  ☆226Updated last month
• JackieHanLab / TOSICA
  Transformer for One-Stop Interpretable Cell-type Annotation
  ☆144Updated last year
• dpeerlab / SEACells
  SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data
  ☆166Updated 4 months ago
• aertslab / scenicplus
  SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) a…
  ☆233Updated 7 months ago
• Teichlab / bbknn
  Batch balanced KNN
  ☆169Updated last year
• theislab / diffxpy
  Differential expression analysis for single-cell RNA-seq data.
  ☆202Updated 6 months ago
• changwn / scFEA
  single cell Flux Estimation Analysis (scFEA) Try the below web server!
  ☆128Updated last year
• ZhangLabGT / scMultiSim
  A simulator for single cell multi-omics and spatial omics data that provides ground truth to benchmark a wide range of methods.
  ☆59Updated 7 months ago