GitHub topics: cell-cell-communication
sqjin/CellChat 📦
R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data
Language: R - Size: 45.4 MB - Last synced at: 1 day ago - Pushed at: over 1 year ago - Stars: 699 - Forks: 157
saeyslab/nichenetr
NicheNet: predict active ligand-target links between interacting cells
Language: R - Size: 152 MB - Last synced at: 1 day ago - Pushed at: 5 days ago - Stars: 540 - Forks: 125
multitalk/awesome-cell-cell-communication
Collection of computational tools for cell-cell communication inference for single-cell and spatially resolved omics
Language: Jupyter Notebook - Size: 17.6 MB - Last synced at: 4 days ago - Pushed at: 19 days ago - Stars: 49 - Forks: 7
theislab/ncem
Learning cell communication from spatial graphs of cells
Language: Python - Size: 40.8 MB - Last synced at: about 17 hours ago - Pushed at: over 1 year ago - Stars: 110 - Forks: 14
jinworks/CellChat
R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
Language: R - Size: 71.5 MB - Last synced at: 9 days ago - Pushed at: about 2 months ago - Stars: 403 - Forks: 68
ZJUFanLab/SpaTalk
Knowledge-graph-based cell-cell communication inference for spatially resolved transcriptomic data
Language: R - Size: 9.83 MB - Last synced at: 4 days ago - Pushed at: 4 months ago - Stars: 71 - Forks: 18
saezlab/liana-py
LIANA+: an all-in-one framework for cell-cell communication
Language: Python - Size: 272 MB - Last synced at: 7 days ago - Pushed at: 4 months ago - Stars: 206 - Forks: 25
saezlab/liana
LIANA: a LIgand-receptor ANalysis frAmework
Language: R - Size: 82.3 MB - Last synced at: 12 days ago - Pushed at: 10 months ago - Stars: 202 - Forks: 34
multitalk/miRTalk
Extracellular vesicle-derived miRNA-mediated cell-cell communication inference for single-cell transcriptomic data
Language: HTML - Size: 77 MB - Last synced at: 4 days ago - Pushed at: about 2 months ago - Stars: 14 - Forks: 2
StatBiomed/SpatialDM
Spatial direct messaging detected by bivariate Moran
Language: Jupyter Notebook - Size: 51.1 MB - Last synced at: 22 days ago - Pushed at: about 1 month ago - Stars: 26 - Forks: 6
saeyslab/multinichenetr
MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data
Language: HTML - Size: 686 MB - Last synced at: about 1 month ago - Pushed at: 5 months ago - Stars: 144 - Forks: 17
multitalk/scCrossTalk
Infer and visualize cell-cell communication for single-cell RNA-seq data
Language: HTML - Size: 50.3 MB - Last synced at: 4 days ago - Pushed at: 5 months ago - Stars: 6 - Forks: 1
earmingol/cell2cell
User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
Language: Python - Size: 99.7 MB - Last synced at: 28 days ago - Pushed at: 12 months ago - Stars: 60 - Forks: 17
ZJUFanLab/CellTalkDB
A manually curated database of literature-supported ligand-receptor interactions in human and mouse
Language: R - Size: 18.5 MB - Last synced at: 4 days ago - Pushed at: 11 months ago - Stars: 30 - Forks: 5
JEFworks-Lab/MERINGUE
characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular densities
Language: R - Size: 89.8 MB - Last synced at: 2 months ago - Pushed at: almost 3 years ago - Stars: 69 - Forks: 5
CostaLab/CrossTalkeR
R package to do the Ligand Receptor Analysis Visualization
Language: Jupyter Notebook - Size: 173 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 42 - Forks: 10
Svvord/FastCCC
A permutation-free framework for scalable, robust, and reference-based cell-cell communication analysis in single cell transcriptomics studies
Language: Jupyter Notebook - Size: 22.1 MB - Last synced at: 4 days ago - Pushed at: 3 months ago - Stars: 5 - Forks: 1
ChanghanGitHub/exFINDER
Identifying external communication signals using single-cell transcriptomics data
Language: HTML - Size: 270 MB - Last synced at: about 1 month ago - Pushed at: 12 months ago - Stars: 20 - Forks: 1
SunXQlab/scMLnet
Single-cell RNA-seq data-based inference of multilayer inter- and intra-cellular signaling networks
Language: R - Size: 12.9 MB - Last synced at: about 1 month ago - Pushed at: almost 4 years ago - Stars: 26 - Forks: 8
skimlab/spatialCCC
Investigate cell-cell signaling, by analyzing ligand-receptor interactions in spatial transcriptomic data
Language: HTML - Size: 74 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 1 - Forks: 1
liuyifang/FlyPhoneDB
Source code for Liu, Y., Li, J. S. S., Rodiger, J., Comjean, A., Attrill, H., Antonazzo, G., ... & Perrimon, N. (2022). FlyPhoneDB: an integrated web-based resource for cell–cell communication prediction in Drosophila. Genetics, 220(3), iyab235.
Language: R - Size: 3.15 MB - Last synced at: about 2 months ago - Pushed at: 11 months ago - Stars: 6 - Forks: 7
LitingKu/SpaCCI
SpaCCI: Spatially Aware Cell-Cell Interaction Analysis
Language: R - Size: 15.7 MB - Last synced at: 7 months ago - Pushed at: 8 months ago - Stars: 0 - Forks: 0
lhc17/HoloNet
HoloNet. Reveal the holograph of functional communication events in spatial transcriptomics. Help understand how microenvironments shaping cellular phenotypes
Language: Python - Size: 6.47 MB - Last synced at: about 1 month ago - Pushed at: 9 months ago - Stars: 21 - Forks: 3
dalodriguez/ExPCom
Differential communication analysis for scRNAseq datasets based on expression products
Language: R - Size: 41.1 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 0 - Forks: 0
lasseignelab/230313_TS_CCCinHumanAD
This repo accompanies the Soelter et al., 2024 manuscript "Altered Glia-Neuron Communication in Alzheimer’s Disease Affects WNT, p53, and NFkB Signaling Determined by snRNA-seq"
Language: R - Size: 1.1 GB - Last synced at: 4 months ago - Pushed at: 12 months ago - Stars: 1 - Forks: 1
Jia-Zhao1998/20.440-Group_Project_JZ_APM
20.440 Group Project-Intercellular Communication in vivo
Language: Jupyter Notebook - Size: 31.6 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0
saezlab/ccc_protocols
LIANA x Tensor-cell2cell Protocols
Language: Jupyter Notebook - Size: 168 MB - Last synced at: about 2 months ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 3
SunXQlab/ESICCC
ESICCC: A systematic computational framework for evaluation, selection and integration of cell-cell communication inference methods
Language: R - Size: 23.4 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 11 - Forks: 1
theimagelab/entrain
Entrain: Predicting Environmental Regulators of Differentiation Trajectories
Language: R - Size: 63.9 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 0
WangShuxiong/SoptSC
SoptSC for single cell data analysis: unsupervised inference of clustering, cell lineage, pseudotime and cell-cell communication network from scRNA-seq data.
Language: MATLAB - Size: 62 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 19 - Forks: 5
ZJUFanLab/SpaTrio
Language: Python - Size: 74.5 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 4 - Forks: 1
auroramaurizio/periferal_nerve_injury
Bioinfo scripts for the analyses described in EXPERIMENTAL PROCEDURES section of "Structured wound angiogenesis instructs mesenchymal barrier compartments in the regenerating nerve" manuscript
Language: Jupyter Notebook - Size: 19.4 MB - Last synced at: 10 months ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 2
ZJUFanLab/scDeepTalk
Infer cell-cell communications based on feed-forward neural network
Language: R - Size: 14.4 MB - Last synced at: 4 days ago - Pushed at: over 4 years ago - Stars: 3 - Forks: 0
ccruizm/GBmap
Code used to create the core and extended GBmap, including downstream analyses (cell-cell interactions, spatial transcriptomics deconvolution) and how to produce the figures.
Language: Jupyter Notebook - Size: 98.8 MB - Last synced at: over 2 years ago - Pushed at: over 2 years ago - Stars: 9 - Forks: 0
SunXQlab/scMLnet2.0 Fork of YUZIXD/scMLnet2.0
scMLnet2.0: Single-cell RNA-seq data-based inference of multilayer inter- and intra-cellular signaling networks
Size: 15 MB - Last synced at: about 2 years ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 0
hmbaghdassarian/c2c_sim
Pipeline for simulating CCI dynamics across time
Language: Jupyter Notebook - Size: 12.8 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0
