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scDiffCom
View on CRAN: Click
here
Download and install scDiffCom package within the R console
Install from CRAN:
install.packages("scDiffCom")
Install from Github:
library("remotes")
install_github("cran/scDiffCom")
Install by package version:
library("remotes")
install_version("scDiffCom", "1.0.0")
Attach the package and use:
library("scDiffCom")
Maintained by
Cyril Lagger
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2021-08-17
Latest Update: 2021-08-17
Description:
Analysis tools to investigate changes in intercellular
communication from scRNA-seq data. Using a Seurat object as input,
the package infers which cell-cell interactions are present in the dataset
and how these interactions change between two conditions of interest
(e.g. young vs old). It relies on an internal database of ligand-receptor
interactions (available for human, mouse and rat) that have been gathered
from several published studies. Detection and differential analyses
rely on permutation tests. The package also contains several tools
to perform over-representation analysis and visualize the results. See
Lagger, C. et al. (2023) for a full
description of the methodology.
How to cite:
Cyril Lagger (2021). scDiffCom: Differential Analysis of Intercellular Communication from scRNA-Seq Data. R package version 1.0.0, https://cran.r-project.org/web/packages/scDiffCom. Accessed 07 Nov. 2024.
Previous versions and publish date:
0.1.0 (2021-08-17 09:20)
Other packages that cited scDiffCom R package
View scDiffCom citation profile
Other R packages that scDiffCom depends,
imports, suggests or enhances
Complete documentation for scDiffCom
Functions, R codes and Examples using
the scDiffCom R package
Some associated functions: BuildNetwork . BuildShiny . EraseRawCCI . FilterCCI . GetDistributions . GetParameters . GetTableCCI . GetTableORA . LRI_human . LRI_mouse . LRI_rat . PlotORA . ReduceGO . RunORA . gene_ontology_level . run_interaction_analysis . scDiffCom-class . seurat_sample_tms_liver . show-scDiffCom-method .
Some associated R codes: data.R . interaction_analysis.R . objects.R . utils_LRI.R . utils_cci.R . utils_filtering.R . utils_interactiveNetworks.R . utils_ora.R . utils_permutation.R . utils_preprocessing.R . utils_shiny.R . utils_validation.R . Full scDiffCom package functions and examples
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