Alternatives and similar repositories for webatlas-pipeline

Users that are interested in webatlas-pipeline are comparing it to the libraries listed below

• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆67Updated last week
• nf-core / spatialxe
  ☆23Updated last week
• shuxiaoc / maxfuse
  ☆56Updated last year
• theislab / spapros
  Python package for Probe set selection for targeted spatial transcriptomics.
  ☆45Updated last week
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆74Updated 8 months ago
• CSOgroup / cellcharter
  A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
  ☆141Updated this week
• simonwm / tacco
  TACCO: Transfer of Annotations to Cells and their COmbinations
  ☆61Updated 2 months ago
• YosefLab / popV
  ☆83Updated this week
• LouisFaure / scFates
  a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.
  ☆61Updated 3 months ago
• BayraktarLab / cell2fate
  Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.
  ☆81Updated 7 months ago
• dcjones / proseg
  Probabilistic cell segmentation for in situ spatial transcriptomics
  ☆138Updated last week
• theislab / multimil
  Multimodal weakly supervised learning to identify disease-specific changes in single-cell atlases
  ☆35Updated last month
• YeoLab / bento-tools
  A Python toolkit for subcellular analysis of spatial transcriptomics data
  ☆83Updated 2 weeks ago
• parashardhapola / scarf
  Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with mill…
  ☆108Updated last week
• wanglab-broad / CAST
  CAST package
  ☆40Updated last year
• rajewsky-lab / spacemake
  ☆45Updated last week
• SCCAF / sccaf
  Single-Cell Clustering Assessment Framework
  ☆106Updated 2 years ago
• yelabucsf / scrna-parameter-estimation
  Direct estimation of mean and covariance from single cell RNA seq experiments
  ☆121Updated 6 months ago
• Nanostring-Biostats / CosMx-Analysis-Scratch-Space
  This repository is an exploratory resource to accelerate opensource analysis of CosMx® Spatial Molecular Imager (SMI) data. Contained her…
  ☆82Updated this week
• StatBiomed / SpatialDM
  Spatial direct messaging detected by bivariate Moran
  ☆31Updated 3 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
• drieslab / awesome-spatial-data-analysis
  Awesome list of tools and methods to perform spatial transcriptomic data analysis.
  ☆46Updated 4 years ago
• dpeerlab / ENVI
  ☆50Updated last month
• Nanostring-Biostats / InSituType
  An R package for performing cell typing in SMI and other single cell data
  ☆43Updated 5 months ago
• aertslab / pycisTopic
  pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.
  ☆77Updated 2 months ago
• JCVenterInstitute / NSForest
  A machine learning method for the discovery of the minimum marker gene combinations for cell type identification from single-cell RNA seq…
  ☆66Updated 2 months ago
• calico / solo
  software to detect doublets
  ☆95Updated 10 months ago
• Teichlab / bin2cell
  Join subcellular Visium HD bins into cells
  ☆128Updated last week
• YosefLab / mrvi_archive
  Multi-resolution Variational Inference
  ☆22Updated this week
• theislab / spatial_scog_workshop_2022
  Tutorials for the SCOG Virtual Workshop ‘Spatial transcriptomics data analysis in Python’ - May 23-24, 2022
  ☆53Updated 3 years ago