Alternatives and similar repositories for Giotto:

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

• carmonalab / ProjecTILs
  Interpretation of cell states using reference single-cell maps
  ☆271Updated 3 weeks ago
• dmcable / spacexr
  Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …
  ☆363Updated 11 months ago
• saezlab / liana
  LIANA: a LIgand-receptor ANalysis frAmework
  ☆201Updated 9 months ago
• cellgeni / sceasy
  A package to help convert different single-cell data formats to each other
  ☆420Updated last year
• bnprks / BPCells
  Scaling Single Cell Analysis to Millions of Cells
  ☆205Updated this week
• IanevskiAleksandr / sc-type
  ☆261Updated 5 months ago
• welch-lab / liger
  R package for integrating and analyzing multiple single-cell datasets
  ☆412Updated this week
• constantAmateur / SoupX
  R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data
  ☆275Updated 2 years ago
• crazyhottommy / awesome_spatial_omics
  tools and notes for spatial omics
  ☆289Updated 2 months ago
• kstreet13 / slingshot
  Functions for identifying and characterizing continuous developmental trajectories in single-cell data.
  ☆291Updated last year
• MarcElosua / SPOTlight
  Spatial Transcriptomics Capture Location Deconvolution
  ☆178Updated last year
• theislab / zellkonverter
  Conversion between scRNA-seq objects
  ☆173Updated 3 weeks ago
• cellgeni / schard
  reticulate-free single cell format conversion
  ☆145Updated 5 months ago
• plger / scDblFinder
  Methods for detecting doublets in single-cell sequencing data
  ☆191Updated last month
• MarioniLab / miloR
  R package implementation of Milo for testing for differential abundance in KNN graphs
  ☆371Updated 5 months ago
• broadinstitute / CellBender
  CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
  ☆326Updated 9 months ago
• saeyslab / multinichenetr
  MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell trans…
  ☆145Updated 3 months ago
• samuel-marsh / scCustomize
  R package with collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.
  ☆252Updated 2 weeks ago
• immunogenomics / presto
  Fast Wilcoxon and auROC
  ☆180Updated 6 months ago
• sunduanchen / Scissor
  Scissor package
  ☆218Updated 11 months ago
• saezlab / liana-py
  LIANA+: an all-in-one framework for cell-cell communication
  ☆205Updated 2 months ago
• satijalab / sctransform
  R package for modeling single cell UMI expression data using regularized negative binomial regression
  ☆222Updated last week
• saeyslab / nichenetr
  NicheNet: predict active ligand-target links between interacting cells
  ☆535Updated last week
• aertslab / SCENICprotocol
  A scalable SCENIC workflow for single-cell gene regulatory network analysis
  ☆157Updated 2 years ago
• Dragonmasterx87 / Interactive-3D-Plotting-in-Seurat-3.0.0
  This repository contains R code, with which you can create 3D UMAP and tSNE plots of Seurat analyzed scRNAseq data
  ☆121Updated 2 years ago
• dynverse / dynbenchmark
  Comparison of methods for trajectory inference on single-cell data 🥇
  ☆206Updated last year
• smorabit / hdWGCNA
  High dimensional weighted gene co-expression network analysis
  ☆404Updated last month
• dpeerlab / SEACells
  SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data
  ☆158Updated last month
• saezlab / decoupleR
  R package to infer biological activities from omics data using a collection of methods.
  ☆248Updated last month
• xuranw / MuSiC
  Multi-subject Single Cell Deconvolution
  ☆257Updated last year