Alternatives and similar repositories for scFates

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

• pachterlab / concordex
  Identification of spatial homogeneous regions
  ☆21Updated last month
• wanglab-broad / CAST
  CAST package
  ☆41Updated last year
• theislab / spapros
  Python package for Probe set selection for targeted spatial transcriptomics.
  ☆47Updated 3 weeks ago
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆67Updated last month
• const-ae / pyLemur
  A Python implementation of the LEMUR algorithm for analyzing multi-condition single-cell RNA-seq data.
  ☆28Updated 11 months ago
• theislab / multimil
  Multimodal weakly supervised learning to identify disease-specific changes in single-cell atlases
  ☆35Updated 2 months ago
• rargelaguet / mouse_organogenesis_10x_multiome_publication
  Code to reproduce the analysis of "Decoding gene regulation in the mouse embryo using single-cell multi-omics""
  ☆40Updated 3 years ago
• almaan / eggplant
  ☆22Updated 3 years ago
• YosefLab / mrvi_archive
  Multi-resolution Variational Inference
  ☆22Updated 3 weeks ago
• potulabe / symphonypy
  Port of symphony algorithm of single-cell reference atlas mapping to Python
  ☆33Updated last month
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆76Updated 9 months ago
• AllonKleinLab / cospar
  ☆26Updated last year
• rajewsky-lab / spacemake
  ☆48Updated last week
• immunogenomics / cna
  Covarying neighborhood analysis (CNA) is a method for finding structure in- and conducting association analysis with multi-sample single-…
  ☆56Updated 6 months ago
• bendemeo / shannonca
  Information-based dimensionality reduction
  ☆29Updated 11 months ago
• raphael-group / CalicoST
  Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics
  ☆43Updated 3 months ago
• jzhoulab / quasildr
  Quasilinear data representations for single-cell omics data analysis
  ☆44Updated 2 years ago
• wallet-maker / cytopus
  Single cell omics biology annotations
  ☆50Updated 7 months ago
• doraadong / TraSig
  Inferring cell-cell interactions from pseudotime ordering of scRNA-Seq data
  ☆25Updated 2 years ago
• cistrome / MIRA
  Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.
  ☆66Updated 4 months ago
• Novartis / scar
  scAR (single-cell Ambient Remover) is a deep learning model for removal of the ambient signals in droplet-based single cell omics
  ☆56Updated last year
• ratschlab / scim
  Code for Universal Single-Cell Matching with Unpaired Feature Sets
  ☆21Updated 4 years ago
• PeterZZQ / CellPath
  ☆20Updated 3 years ago
• gerstung-lab / BaSISS
  Code for the "Spatial genomics maps the structure, nature and evolution of cancer clones" paper
  ☆27Updated 3 years ago
• haniffalab / webatlas-pipeline
  A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas
  ☆65Updated 5 months ago
• pinellolab / pychromVAR
  A python package for chromVAR
  ☆31Updated 2 years ago
• StatBiomed / SpatialDM
  Spatial direct messaging detected by bivariate Moran
  ☆31Updated 4 months ago
• saketkc / pySCTransform
  Python package to perform normalization and variance-stabilization of single-cell data
  ☆25Updated 4 months ago
• mvinyard / ArchR-h5ad
  Parse ArchR arrow files to anndata h5ad
  ☆15Updated last year
• kharchenkolab / scITD
  Single-Cell Analysis of Inter-Individual Variability by Interpretable Tensor Decomposition
  ☆62Updated last year