cell-cell-communication

There are 35 repositories under cell-cell-communication topic.

  • sqjin/CellChat

    R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data

    Language:R64014727145

  • saeyslab/nichenetr

    NicheNet: predict active ligand-target links between interacting cells

    Language:R49014287117

  • jinworks/CellChat

    R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics

    Language:R298224952

  • saezlab/liana

    LIANA: a LIgand-receptor ANalysis frAmework

    Language:R182916231

  • saezlab/liana-py

    LIANA+: an all-in-one framework for cell-cell communication

    Language:Python169311021

  • saeyslab/multinichenetr

    MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data

    Language:HTML12539914

  • theislab/ncem

    Learning cell communication from spatial graphs of cells

    Language:Python10363513

  • ZJUFanLab/SpaTalk

    Knowledge-graph-based cell-cell communication inference for spatially resolved transcriptomic data

    Language:R6124318

  • JEFworks-Lab/MERINGUE

    characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular densities

    Language:R594145

  • earmingol/cell2cell

    User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins

    Language:Python5733712

  • 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 Notebook526411

  • CostaLab/CrossTalkeR

    R package to do the Ligand Receptor Analysis Visualization

    Language:Jupyter Notebook4162010

  • multitalk/awesome-cell-cell-communication

    Collection of computational tools for cell-cell communication inference for single-cell and spatially resolved omics

    Language:Jupyter Notebook28205

  • ZJUFanLab/CellTalkDB

    A manually curated database of literature-supported ligand-receptor interactions in human and mouse

    Language:R26245

  • SunXQlab/scMLnet

    Single-cell RNA-seq data-based inference of multilayer inter- and intra-cellular signaling networks

    Language:R25158

  • StatBiomed/SpatialDM

    Spatial direct messaging detected by bivariate Moran

    Language:Jupyter Notebook243175

  • lhc17/HoloNet

    HoloNet. Reveal the holograph of functional communication events in spatial transcriptomics. Help understand how microenvironments shaping cellular phenotypes

    Language:Python21193

  • 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:MATLAB21315

  • ChanghanGitHub/exFINDER

    Identifying external communication signals using single-cell transcriptomics data

    Language:HTML18221

  • SunXQlab/ESICCC

    ESICCC: A systematic computational framework for evaluation, selection and integration of cell-cell communication inference methods

    Language:R12211

  • theimagelab/entrain

    Entrain: Predicting Environmental Regulators of Differentiation Trajectories

    Language:R7100

  • ZJUFanLab/SpaTrio

    Language:Python7122

  • 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:R6237

  • multitalk/miRTalk

    Extracellular vesicle-derived miRNA-mediated cell-cell communication inference for single-cell transcriptomic data

    Language:HTML6111

  • multitalk/scCrossTalk

    Infer and visualize cell-cell communication for single-cell RNA-seq data

    Language:HTML5100

  • ZJUFanLab/scDeepTalk

    Infer cell-cell communications based on feed-forward neural network

    Language:R310

  • 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 Notebook1202

  • 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:R1301

  • saezlab/ccc_protocols

    LIANA x Tensor-cell2cell Protocols

    Language:Jupyter Notebook14163

  • skimlab/spatialCCC

    Investigate cell-cell signaling, by analyzing ligand-receptor interactions in spatial transcriptomic data

    Language:R1101

  • dalodriguez/ExPCom

    Differential communication analysis for scRNAseq datasets based on expression products

    Language:R0100

  • hmbaghdassarian/c2c_sim

    Pipeline for simulating CCI dynamics across time

    Language:Jupyter Notebook0200

  • Jia-Zhao1998/20.440-Group_Project_JZ_APM

    20.440 Group Project-Intercellular Communication in vivo

    Language:Jupyter Notebook10

  • LitingKu/SpaCCI

    SpaCCI: Spatially Aware Cell-Cell Interaction Analysis

    Language:R

  • SunXQlab/scMLnet2.0

    scMLnet2.0: Single-cell RNA-seq data-based inference of multilayer inter- and intra-cellular signaling networks

    Language:R00