Package: scDiffCom 1.1.1

scDiffCom: Differential Analysis of Intercellular Communication from scRNA-Seq Data

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) <doi:10.1038/s43587-023-00514-x> for a full description of the methodology.

Authors:Cyril Lagger [aut, cre], Eugen Ursu [aut], Anais Equey [ctb]

scDiffCom_1.1.1.tar.gz
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scDiffCom_1.1.1.tgz(r-4.4-any)scDiffCom_1.1.1.tgz(r-4.3-any)
scDiffCom_1.1.1.tar.gz(r-4.5-noble)scDiffCom_1.1.1.tar.gz(r-4.4-noble)
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scDiffCom.pdf |scDiffCom.html✨
scDiffCom/json (API)
NEWS

# Install 'scDiffCom' in R:
install.packages('scDiffCom', repos = c('https://cyrillagger.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/cyrillagger/scdiffcom/issues

Datasets:
  • LRI_human - A collection of human ligand-receptor interactions.
  • LRI_mouse - A collection of mouse ligand-receptor interactions.
  • LRI_rat - A collection of rat ligand-receptor interactions.
  • gene_ontology_level - All gene ontology terms annotated with their levels
  • seurat_sample_tms_liver - A down-sampled Seurat object to use for testing and benchmarking

On CRAN:

4.85 score 21 stars 17 scripts 232 downloads 12 exports 155 dependencies

Last updated 11 months agofrom:7877de2543. Checks:OK: 6 WARNING: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 04 2024
R-4.5-winOKNov 04 2024
R-4.5-linuxWARNINGNov 04 2024
R-4.4-winOKNov 04 2024
R-4.4-macOKNov 04 2024
R-4.3-winOKNov 04 2024
R-4.3-macOKNov 04 2024

Exports:BuildNetworkBuildShinyEraseRawCCIFilterCCIGetDistributionsGetParametersGetTableCCIGetTableORAPlotORAReduceGOrun_interaction_analysisRunORA

Dependencies:abindaskpassbase64encBHBiocGenericsbitopsbslibcachemcaToolscliclustercodetoolscolorspacecommonmarkcowplotcpp11crayoncrosstalkcurldata.tableDelayedArraydeldirdigestdotCall64dplyrdqrngevaluatefansifarverfastDummiesfastmapfitdistrplusFNNfontawesomefsfuturefuture.applygenericsggplot2ggrepelggridgesglobalsgluegoftestgplotsgridExtragtablegtoolsherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphIRangesirlbaisobandjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevalleidenlifecyclelistenvlmtestmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeminiUImunsellnlmeopensslparallellypatchworkpbapplypillarpkgconfigplotlyplyrpngpolyclipprogressrpromisespurrrR6RANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppProgressRcppTOMLreshape2reticulaterlangrmarkdownROCRrprojrootRSpectraRtsneS4ArraysS4VectorssassscalesscattermoresctransformSeuratSeuratObjectshinysitmosourcetoolsspspamSparseArrayspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrsurvivalsystensortibbletidyrtidyselecttinytexutf8uwotvctrsviridisLitewithrxfunxtableXVectoryamlzlibbioczoo

Readme and manuals

Help Manual

Help pageTopics
Display cell-type to cell-type interactive networksBuildNetwork BuildNetwork,scDiffCom-method
A shiny app to display scDiffCom resultsBuildShiny BuildShiny,scDiffCom-method
Create a copy of a scDiffCom object without 'cci_table_raw'EraseRawCCI EraseRawCCI,scDiffCom-method
Filter a scDiffCom object with new filtering parametersFilterCCI FilterCCI,scDiffCom-method
All gene ontology terms annotated with their levelsgene_ontology_level
Return the slot 'distributions' from a scDiffCom objectGetDistributions GetDistributions,scDiffCom-method
Return the slot 'parameters' from a scDiffCom objectGetParameters GetParameters,scDiffComBase-method
Return (a subset) of the slot 'cci_table_raw' or 'cci_table_detected' from a scDiffCom objectGetTableCCI GetTableCCI,scDiffCom-method
Return some or all ORA tables from the slot 'ora_table' from a scDiffCom objectGetTableORA GetTableORA,scDiffCom-method
A collection of human ligand-receptor interactions.LRI_human
A collection of mouse ligand-receptor interactions.LRI_mouse
A collection of rat ligand-receptor interactions.LRI_rat
Display top over-represented keywords from a category of interestPlotORA PlotORA,scDiffCom-method
Reduce scDiffCom GO TermsReduceGO ReduceGO,scDiffCom-method
Run (differential) intercellular communication analysisrun_interaction_analysis
Run over-representation analysisRunORA RunORA,scDiffCom-method
The scDiffCom ClassscDiffCom-class
A down-sampled Seurat object to use for testing and benchmarkingseurat_sample_tms_liver
Display a scDiffCom objectshow,scDiffCom-method