Teichlab / SpatialDE

Related projects: ⓘ

• pinellolab / scATAC-benchmarking
  Benchmarking computational single cell ATAC-seq methods
  ☆176Updated 3 years ago
• icbi-lab / infercnvpy
  Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.
  ☆132Updated this week
• colomemaria / epiScanpy
  Episcanpy: Epigenomics Single Cell Analysis in Python
  ☆140Updated 4 months ago
• digitalcytometry / ecotyper
  EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.
  ☆177Updated 5 months ago
• LewisLabUCSD / Ligand-Receptor-Pairs
  Compendium of available lists of ligand-receptor pairs and surface-secreted protein interactions.
  ☆119Updated last year
• swolock / scrublet
  Detect doublets in single-cell RNA-seq data
  ☆131Updated 3 years ago
• digitalcytometry / cytospace
  CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data
  ☆110Updated 4 months ago
• aertslab / SCENICprotocol
  A scalable SCENIC workflow for single-cell gene regulatory network analysis
  ☆138Updated last year
• theislab / diffxpy
  Differential expression analysis for single-cell RNA-seq data.
  ☆191Updated last year
• aertslab / scenicplus
  SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) a…
  ☆176Updated 2 weeks ago
• czbiohub-sf / tabula-muris
  Code and annotations for the Tabula Muris single-cell transcriptomic dataset.
  ☆185Updated last year
• theislab / kBET
  An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
  ☆153Updated 7 months ago
• cortes-ciriano-lab / SComatic
  A tool for detecting somatic variants in single cell data
  ☆152Updated this week
• JEFworks-Lab / STdeconvolve
  Reference-free cell-type deconvolution of multi-cellular spatially resolved transcriptomics data
  ☆100Updated 2 months ago
• saezlab / decoupler-py
  Python package to perform enrichment analysis from omics data.
  ☆154Updated last week
• changwn / scFEA
  single cell Flux Estimation Analysis (scFEA) Try the below web server!
  ☆93Updated 10 months ago
• velocyto-team / velocyto.py
  RNA velocity estimation in Python
  ☆159Updated last year
• saeyslab / multinichenetr
  MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell trans…
  ☆112Updated 2 weeks ago
• CahanLab / singleCellNet
  SingleCellNet: classify single cells across species and platforms
  ☆128Updated last year
• tabdelaal / scRNAseq_Benchmark
  Bench-marking classification tools for scRNA-seq data
  ☆181Updated 2 years ago
• dpeerlab / SEACells
  SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data
  ☆145Updated 2 months ago
• JiekaiLab / scDIOR
  scDIOR: Single cell data IO softwaRe
  ☆130Updated 2 years ago
• sunduanchen / Scissor
  Scissor package
  ☆176Updated 4 months ago
• zktuong / dandelion
  dandelion - A single cell BCR/TCR V(D)J-seq analysis package for 10X Chromium 5' data
  ☆103Updated this week
• theislab / anndata2ri
  Convert between AnnData and SingleCellExperiment
  ☆124Updated this week
• theislab / scCODA
  A Bayesian model for compositional single-cell data analysis
  ☆147Updated last year
• aertslab / cisTopic
  cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data
  ☆135Updated 5 months ago
• saezlab / dorothea
  R package to access DoRothEA's regulons
  ☆132Updated 6 months ago
• almaan / stereoscope
  Spatial mapping of cell types by integration of transcriptomics data
  ☆87Updated 2 years ago
• KrishnaswamyLab / SingleCellWorkshop
  ☆86Updated 3 years ago