scverse / ecosystem-packages

Related projects: ⓘ

• theislab / spapros
  Python package for Probe set selection for targeted spatial transcriptomics.
  ☆23Updated last week
• scverse / genomic-features
  Genomic Features in Python from BioConductor's AnnotationHub
  ☆19Updated this week
• LouisFaure / scFates
  a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.
  ☆49Updated 3 months ago
• klarman-cell-observatory / PowerAnalysisForSpatialOmics
  ☆23Updated last year
• saketkc / pySCTransform
  Python package to perform normalization and variance-stabilization of single-cell data
  ☆21Updated 2 years ago
• pachterlab / concordex
  Identification of spatial homogeneous regions
  ☆17Updated last week
• dcjones / proseg
  Probabilistic cell segmentation for in situ spatial transcriptomics
  ☆32Updated this week
• scverse / spatialdata-plot
  Static plotting for spatialdata
  ☆27Updated this week
• immunitastx / monkeybread
  Analyzing cellular niches in spatial transcriptomics data
  ☆25Updated 3 months ago
• BayraktarLab / cell2fate
  Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.
  ☆35Updated last week
• haniffalab / webatlas-pipeline
  A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas
  ☆40Updated last week
• theislab / interactive_plotting
  ☆21Updated 4 years ago
• MICS-Lab / novae
  Graph-based foundation model for spatial transcriptomics data.
  ☆14Updated this week
• quentinblampey / spatialdata_xenium_explorer
  Interoperability between SpatialData and the Xenium Explorer
  ☆14Updated last month
• scverse / anndataR
  AnnData interoperability in R
  ☆53Updated 2 weeks ago
• hubmapconsortium / spatial-transcriptomics-pipeline
  ☆28Updated 4 months ago
• scverse / pytometry
  Flow & mass cytometry analytics.
  ☆41Updated this week
• BiomedicalMachineLearning / stlearn_interactive
  Interactive applications of stlearn
  ☆15Updated last year
• ckmah / bento-tools
  A Python toolkit for subcellular analysis of spatial transcriptomics data
  ☆63Updated last week
• dpeerlab / ENVI
  ☆35Updated last month
• almaan / eggplant
  ☆20Updated 2 years 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
  ☆48Updated last month
• seqscope / ficture
  ☆19Updated last week
• damienArnol / svca
  ☆13Updated 5 years ago
• YosefLab / mrvi_archive
  Multi-resolution Variational Inference
  ☆22Updated last month
• saezlab / mistyR
  Multiview Intercellular SpaTial modeling framework
  ☆43Updated 5 months ago
• lilab-bcb / harmony-pytorch
  ☆47Updated 8 months ago
• gerstung-lab / BaSISS
  Code for the "Spatial genomics maps the structure, nature and evolution of cancer clones" paper
  ☆23Updated last year
• theislab / ncem_tutorials
  ☆11Updated 2 years ago
• camlab-bioml / astir
  astir | Automated cell identity from single-cell multiplexed imaging and proteomics 🖥🔬✨
  ☆48Updated 3 months ago