Alternatives and similar repositories for Giotto

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

• kstreet13 / slingshot
  Functions for identifying and characterizing continuous developmental trajectories in single-cell data.
  ☆294Updated last year
• saezlab / liana
  LIANA: a LIgand-receptor ANalysis frAmework
  ☆204Updated 10 months ago
• carmonalab / ProjecTILs
  Interpretation of cell states using reference single-cell maps
  ☆276Updated 2 weeks ago
• dynverse / dynbenchmark
  Comparison of methods for trajectory inference on single-cell data 🥇
  ☆206Updated last year
• cellgeni / sceasy
  A package to help convert different single-cell data formats to each other
  ☆425Updated last year
• MarcElosua / SPOTlight
  Spatial Transcriptomics Capture Location Deconvolution
  ☆181Updated last week
• saezlab / liana-py
  LIANA+: an all-in-one framework for cell-cell communication
  ☆212Updated 3 months ago
• theislab / zellkonverter
  Conversion between scRNA-seq objects
  ☆174Updated last month
• MarioniLab / miloR
  R package implementation of Milo for testing for differential abundance in KNN graphs
  ☆380Updated 6 months ago
• welch-lab / liger
  R package for integrating and analyzing multiple single-cell datasets
  ☆413Updated last month
• cellgeni / schard
  reticulate-free single cell format conversion
  ☆154Updated 6 months ago
• dmcable / spacexr
  Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …
  ☆368Updated 3 weeks ago
• constantAmateur / SoupX
  R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data
  ☆279Updated 2 years ago
• saeyslab / multinichenetr
  MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell trans…
  ☆147Updated 4 months ago
• sunduanchen / Scissor
  Scissor package
  ☆222Updated last year
• broadinstitute / CellBender
  CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
  ☆331Updated 10 months ago
• ZJUFanLab / scCATCH
  Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
  ☆227Updated 2 years ago
• satijalab / seurat-data
  Dataset distribution for Seurat
  ☆139Updated 3 months ago
• aertslab / scenicplus
  SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) a…
  ☆224Updated 4 months ago
• IanevskiAleksandr / sc-type
  ☆266Updated 6 months ago
• bnprks / BPCells
  Scaling Single Cell Analysis to Millions of Cells
  ☆211Updated 2 weeks ago
• plger / scDblFinder
  Methods for detecting doublets in single-cell sequencing data
  ☆196Updated 2 months ago
• dpeerlab / SEACells
  SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data
  ☆160Updated 2 months ago
• digitalcytometry / ecotyper
  EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.
  ☆201Updated last year
• 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
• navinlabcode / copykat
  ☆237Updated 11 months ago
• BorchLab / escape
  Easy single cell analysis platform for enrichment
  ☆183Updated last week
• theislab / scCODA
  A Bayesian model for compositional single-cell data analysis
  ☆163Updated 2 years ago
• dynverse / dynmethods
  A collection of 50+ trajectory inference methods within a common interface 📥📤
  ☆128Updated last year
• theislab / kBET
  An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
  ☆162Updated last year