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
  ☆52Updated this week
• dcjones / proseg
  Probabilistic cell segmentation for in situ spatial transcriptomics
  ☆50Updated 2 weeks ago
• scverse / anndataR
  AnnData interoperability in R
  ☆67Updated this week
• guokai8 / scGSVA
  scGSVA: Perform GSVA for single cell RNA seq
  ☆52Updated 2 months ago
• jzhoulab / quasildr
  Quasilinear data representations for single-cell omics data analysis
  ☆42Updated last year
• Wei-BioMath / NeuronChat
  ☆32Updated last year
• JinmiaoChenLab / ezSingleCell2
  ☆52Updated last year
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆59Updated 7 months ago
• icbi-lab / luca
  Single-cell Lung Cancer Atlas with 1.2M cells
  ☆58Updated last month
• PMBio / MuDataSeurat
  .h5mu files interface for Seurat
  ☆28Updated last year
• CSOgroup / cellcharter
  A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
  ☆101Updated 3 weeks ago
• KlugerLab / GeneTrajectory
  R implementation of GeneTrajectory
  ☆51Updated 9 months ago
• prabhakarlab / Banksy
  BANKSY: spatial clustering
  ☆82Updated 5 months ago
• saezlab / progeny
  R package for Pathway RespOnsive GENe activity inference
  ☆98Updated last year
• jbergenstrahle / STUtility
  ☆47Updated last year
• BodenmillerGroup / imcRtools
  An R package for handling and analysing imaging mass cytometry data
  ☆22Updated 2 months ago
• drieslab / awesome-spatial-data-analysis
  Awesome list of tools and methods to perform spatial transcriptomic data analysis.
  ☆39Updated 3 years ago
• Nanostring-Biostats / SpatialDecon
  The SpatialDecon library implements the SpatialDecon algorithm for mixed cell deconvolution in spatial gene expression datasets. (This al…
  ☆35Updated last month
• HectorRDB / condiments
  Trajectory inference across multiple conditions with condiments: differential topology, progression, differentiation, and expression
  ☆26Updated last month
• SCCAF / sccaf
  Single-Cell Clustering Assessment Framework
  ☆97Updated last year
• raphael-group / STARCH
  Spatial Transcriptomics Algorithm Reconstructing Copy-number Heterogeneity
  ☆21Updated 6 months ago
• aerickso / SpatialInferCNV
  Clone Calling from Visium Spatial Transcriptomics of Cancer samples
  ☆60Updated 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
  ☆51Updated 5 months ago
• YosefLab / popV
  ☆65Updated this week
• edsgard / trendsceek
  Identify genes with spatial expression trends in single-cell gene expression data
  ☆50Updated 6 years ago
• theislab / scib-pipeline
  Snakemake pipeline that works with the scIB package to benchmark data integration methods.
  ☆67Updated last year
• msraredon / NICHES
  Niche Interactions and Cellular Heterogeneity in Extracellular Signaling
  ☆49Updated 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 2 years ago
• genecell / COSG
  Accurate and fast cell marker gene identification with COSG
  ☆40Updated last year
• Nanostring-Biostats / CellProfileLibrary
  ☆30Updated last month