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ICELLNET news:

Last package update: 2024-04-16 Last ligand-receptor interactions database update: 2023-11-08

ICELLNET v2.2.0 (2024-04-16):

  • Fix coding issue on sc.data.cleaning() function

ICELLNET v2.1.0 (2024-03-21):

  • Compatibility of ICELLNET functions with Seurat v5 and latest R versions (R> 4.1.x).

  • Update of LR.family.score() to reintroduce the "barplot" vizualisation option.

  • New use case study, showing how to identify cell type-specific interactions based on scRNAseq data.

  • Specific functions modifications:

    • sc.data.cleaning() and Perc_exp_infos() functions were adapted to work with Seurat v5 and latest R versions.
    • LR.family.score(): plot argument (previously TRUE or FALSE) can take NULL (no plot, returns a table), "heatmap" or "barplot" values, in order to provide corresponding vizualisations.
    • n=1 argument was set as default in gene.scaling() function.
    • CC.type and PC.type were set to "RNAseq"" as default in icellnet.score() function

ICELLNET v2.0.0 (2023-11-08):

  • New structure and extension of ICELLNET database to consider more subunits of ligand and receptors (enable 4 ligand subunits and 5 receptor subunits) - now contains 1669 interactions;

  • New classification of ICELLNET database: "Antigen binding" family renamed "HLA recognition"; "Adhesion molecules" renamed "Cell adhesion". New families includes "Wnt pathway" and "Innate immune".

  • Formatting functions provided to use CellphoneDB, matching the structure of ICELLNET databases: CellPhoneDB_convert()

  • Update of several functions to match the new structure of ICELLNET database: name.lr.couple(),ligand.average() (replacing previous ligand.average.RNAseq() and ligand.average.MA() functions), receptor.average() (replacing previous receptor.average.RNAseq() and receptor.average.MA() functions ), LR.viz(), icellnet.score(), icellnet.ind.score()

  • Update of several visualisation functions: LR.viz(), LR.family.score(), LR.family.score(), LR.heatmap(), LR.selection()

  • Specific functions modifications:

    • LR.viz(): can now display the pairwise interaction score of several interactions at a time, provided in "int" arguments (replace "couple" argument). Also possible to visualise directly a family of interactions when using "family" input argument. This function requires gene symbols as inputs and cannot be used with microarray probe names.
    • LR.family.score(): family (replacing my.family argument) and db.couple (replacing db.name.couple) arguments are not required (defaults values provided). Arguments "cluster_rows" and "cluster_columns" are added (used by ComplexHeatmap for heatmap visualisation)
    • name.lr.couple(): LR database becomes the only required input argument.
    • network.create(): not necessary anymore to rescale communication score from 1 to 10.

ICELLNET v1.3.0 (2023-06-29):

Updated functions with minor changes: Correction in gene.scaling() function. note() removed in sc_data_cleaning function. Correction of LR.family.score function when considering only one cell type. Vignette update. New package release.

ICELLNET v1.2.0 (2023-02-05):

ICELLNET can now handle spatial transcriptomic data! Allow to use other assay than "RNA" assay in Seurat objects, such as "SCT" or "Spatial" assays.

Update of ICELLNET database (2022-06-15):

ICELLNET database has been expanded to 1034 interactions, focusing on adding tumor microenvironment related interactions.

ICELLNET v1.0.0 - 2021-07-21:

  • ICELLNET ligand/receptor database include now 752 human ligand/receptor interactions, manually curated. In addition to immune checkpoints, cytokines, and chemokines, it now includes additional interactions from classified in an additional family "extracellular matrix", among others added interactions.
  • New release (version 1.0.0): New graphical representations to handle cell-cell communication studies from single-cell RNAseq datasets. See Exemple2_scRNAseq.md for details.

First ICELLNET version - 2021-03-30:

  • ICELLNET ligand/receptor database include now 543 human ligand/receptor interactions manually curated, with a particular interest on immune checkpoints, cytokines, and chemokines.
  • ICELLNET includes now new features to handle cell-cell communication studies from single-cell RNAseq datasets. See Vignette and use case Exemple2_scRNAseq.md for details.