Package: scDiffCom 1.2.0

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_1.2.0.tar.gz
scDiffCom_1.2.0.zip(r-4.7)scDiffCom_1.2.0.zip(r-4.6)scDiffCom_1.2.0.zip(r-4.5)
scDiffCom_1.2.0.tgz(r-4.6-any)scDiffCom_1.2.0.tgz(r-4.5-any)
scDiffCom_1.2.0.tar.gz(r-4.7-any)scDiffCom_1.2.0.tar.gz(r-4.6-any)
scDiffCom_1.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
scDiffCom/json (API)
NEWS

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

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

Pkgdown/docs site:https://cyrillagger.github.io

Datasets:
  • gene_ontology_level - All gene ontology terms annotated with their levels
  • 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.
  • seurat_sample_tms_liver - A down-sampled Seurat object to use for testing and benchmarking

On CRAN:

Conda:

4.72 score 25 stars 21 scripts 271 downloads 12 exports 150 dependencies

Last updated from:febe137bcb. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK350
source / vignettesOK307
linux-release-x86_64OK339
macos-release-arm64OK449
macos-oldrel-arm64OK281
windows-develOK359
windows-releaseOK246
windows-oldrelOK249
wasm-releaseOK192

Exports:BuildNetworkBuildShinyEraseRawCCIFilterCCIGetDistributionsGetParametersGetTableCCIGetTableORAPlotORAReduceGOrun_interaction_analysisRunORA

Dependencies:abindaskpassbase64encBHBiocGenericsbitopsbslibcachemcaToolscliclustercodetoolscommonmarkcowplotcpp11crosstalkcurldata.tableDelayedArraydeldirdigestdotCall64dplyrdqrngevaluatefarverfastDummiesfastmapfitdistrplusFNNfontawesomefsfuturefuture.applygenericsggplot2ggrepelggridgesglobalsgluegoftestgplotsgridExtragtablegtoolsherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphIRangesirlbaisobandjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevallifecyclelistenvlmtestmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimeminiUInlmeopensslotelparallellypatchworkpbapplypillarpkgconfigplotlyplyrpngpolyclipprogressrpromisespurrrR6RANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppProgressRcppTOMLreshape2reticulaterlangrmarkdownROCRrprojrootRSpectraRtsneS4ArraysS4VectorsS7sassscalesscattermoresctransformSeuratSeuratObjectshinysitmosourcetoolsspspamSparseArrayspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrsurvivalsystensortibbletidyrtidyselecttinytexutf8uwotvctrsviridisLitewithrxfunxtableXVectoryamlzoo

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