Alternatives and similar repositories for scFates

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

• theislab / spapros
  Python package for Probe set selection for targeted spatial transcriptomics.
  ☆48Updated 2 months ago
• pachterlab / concordex
  Identification of spatial homogeneous regions
  ☆21Updated 3 months ago
• wanglab-broad / CAST
  CAST package
  ☆42Updated last year
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆69Updated 2 months ago
• YosefLab / mrvi_archive
  Multi-resolution Variational Inference
  ☆22Updated last week
• const-ae / pyLemur
  A Python implementation of the LEMUR algorithm for analyzing multi-condition single-cell RNA-seq data.
  ☆27Updated last year
• potulabe / symphonypy
  Port of symphony algorithm of single-cell reference atlas mapping to Python
  ☆33Updated last month
• 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
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆80Updated 11 months ago
• JEFworks-Lab / veloviz
  RNA-velocity informed embeddings for visualizing cellular trajectories
  ☆44Updated 3 years ago
• bendemeo / shannonca
  Information-based dimensionality reduction
  ☆29Updated last year
• almaan / eggplant
  ☆22Updated 3 years ago
• rajewsky-lab / spacemake
  ☆48Updated this week
• saketkc / pySCTransform
  Python package to perform normalization and variance-stabilization of single-cell data
  ☆25Updated 6 months ago
• cistrome / MIRA
  Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.
  ☆67Updated 6 months ago
• immunogenomics / cna
  Covarying neighborhood analysis (CNA) is a method for finding structure in- and conducting association analysis with multi-sample single-…
  ☆56Updated 7 months ago
• AllonKleinLab / cospar
  ☆26Updated 2 years ago
• raphael-group / CalicoST
  Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics
  ☆46Updated 5 months ago
• loosolab / scanpro
  A modular tool for proportion analysis in single-cell sequencing data
  ☆24Updated 4 months ago
• PeterZZQ / CellPath
  ☆20Updated 3 years ago
• theislab / cross_system_integration
  ☆13Updated 4 months ago
• theislab / multimil
  Weakly supervised learning uncovers phenotypic signatures in single-cell data
  ☆38Updated last month
• raphael-group / STARCH
  Spatial Transcriptomics Algorithm Reconstructing Copy-number Heterogeneity
  ☆30Updated last year
• Novartis / scar
  scAR (single-cell Ambient Remover) is a deep learning model for removal of the ambient signals in droplet-based single cell omics
  ☆57Updated last year
• kharchenkolab / scITD
  Single-Cell Analysis of Inter-Individual Variability by Interpretable Tensor Decomposition
  ☆62Updated last year
• gifford-lab / prescient
  Codebase for PRESCIENT (Potential eneRgy undErlying Single Cell gradIENTs) for generative modeling of single-cell time-series.
  ☆52Updated last year
• mvinyard / ArchR-h5ad
  Parse ArchR arrow files to anndata h5ad
  ☆16Updated 2 years ago
• StatBiomed / SpatialDM
  Spatial direct messaging detected by bivariate Moran
  ☆32Updated 6 months ago
• doraadong / TraSig
  Inferring cell-cell interactions from pseudotime ordering of scRNA-Seq data
  ☆25Updated 3 years ago
• wallet-maker / cytopus
  Single cell omics biology annotations
  ☆51Updated 9 months ago