Alternatives and similar repositories for cirrocumulus:

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

• haniffalab / webatlas-pipeline
  A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas
  ☆56Updated this week
• dcjones / proseg
  Probabilistic cell segmentation for in situ spatial transcriptomics
  ☆66Updated this week
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆59Updated 9 months ago
• theislab / spatial_scog_workshop_2022
  Tutorials for the SCOG Virtual Workshop ‘Spatial transcriptomics data analysis in Python’ - May 23-24, 2022
  ☆53Updated 2 years ago
• drieslab / awesome-spatial-data-analysis
  Awesome list of tools and methods to perform spatial transcriptomic data analysis.
  ☆40Updated 3 years ago
• BayraktarLab / cell2fate
  Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.
  ☆60Updated 6 months ago
• scverse / anndataR
  AnnData interoperability in R
  ☆71Updated this week
• PMBio / MuDataSeurat
  .h5mu files interface for Seurat
  ☆28Updated last year
• JEFworks-Lab / MERINGUE
  characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular dens…
  ☆68Updated 2 years ago
• JinmiaoChenLab / ezSingleCell2
  ☆54Updated last year
• icbi-lab / luca
  Single-cell Lung Cancer Atlas with 1.2M cells
  ☆59Updated 2 months ago
• jbergenstrahle / STUtility
  ☆47Updated 2 years ago
• rnakato / ShortCake
  A docker image for single-cell analysis
  ☆81Updated last month
• ncborcherding / utility
  Collection of Tumor-Infiltrating Lymphocyte Single-Cell Experiments with TCR
  ☆84Updated 8 months ago
• rajewsky-lab / spacemake
  ☆41Updated last week
• BodenmillerGroup / imcRtools
  An R package for handling and analysing imaging mass cytometry data
  ☆24Updated 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
  ☆52Updated 7 months ago
• immunogenomics / RA_Atlas_CITEseq
  RA Synovial Single-cell Multimodal Cell Atlas
  ☆12Updated last year
• saeyslab / napari-sparrow
  https://sparrow-pipeline.readthedocs.io/en/latest/
  ☆26Updated 2 weeks ago
• yelabucsf / scrna-parameter-estimation
  Direct estimation of mean and covariance from single cell RNA seq experiments
  ☆100Updated last month
• AllonKleinLab / SPRING_dev
  ☆67Updated 11 months ago
• SCCAF / sccaf
  Single-Cell Clustering Assessment Framework
  ☆99Updated last year
• theislab / spapros
  Python package for Probe set selection for targeted spatial transcriptomics.
  ☆35Updated 3 months ago
• Teichlab / sctk
  ☆35Updated 5 months ago
• chris-mcginnis-ucsf / MULTI-seq
  R implementation of MULTI-seq sample classification workflow
  ☆61Updated last year
• 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 2 years ago
• saezlab / progeny
  R package for Pathway RespOnsive GENe activity inference
  ☆100Updated 2 years ago
• HectorRDB / condiments
  Trajectory inference across multiple conditions with condiments: differential topology, progression, differentiation, and expression
  ☆26Updated 3 months ago
• SpatialTranscriptomicsResearch / st_pipeline
  ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method …
  ☆82Updated 3 years ago
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆63Updated last month