Package: iTALK 0.1.1

iTALK: Characterize and Illustrate Intercellular Communication

iTALK, a computational approach to characterize, compare, and illustrate intercellular communication signals in the multicellular ecosystem using either bulk RNA sequencing data or single cell RNAseq data. iTALK can in principle be used to dissect the complexity, diversity, and dynamics of cell-cell communication from a wide range of cellular processes.

Authors:Zaoqu Liu [aut, cre], Yuanxin Wang [aut]

iTALK_0.1.1.tar.gz
iTALK_0.1.1.zip(r-4.7)iTALK_0.1.1.zip(r-4.6)iTALK_0.1.1.zip(r-4.5)
iTALK_0.1.1.tgz(r-4.6-any)iTALK_0.1.1.tgz(r-4.5-any)
iTALK_0.1.1.tar.gz(r-4.7-any)iTALK_0.1.1.tar.gz(r-4.6-any)
iTALK_0.1.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
iTALK/json (API)

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

Bug tracker:https://github.com/zaoqu-liu/italk/issues

Datasets:
  • database - Ligand-Receptor Interaction Database

On CRAN:

Conda:

rnasequencingsinglecellgeneexpressioncellbiology

4.19 score 77 scripts 16 exports 83 dependencies

Last updated from:b561893fcf (on main). Checks:7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64NOTE222
source / vignettesOK338
linux-release-x86_64NOTE214
macos-release-arm64NOTE161
macos-oldrel-arm64NOTE122
windows-develNOTE150
windows-releaseNOTE153
windows-oldrelNOTE159
wasm-releaseOK174

Exports:convert_expression_matrixconvert_species_biomartDEGDESeq2TestDESingleTestdetect_speciesedgeRTestFindLRLRPlotMASTTestMonocleTestNetViewrawParseSCDETestTimePlotWilcoxTest

Dependencies:AnnotationDbiaskpassBiobaseBiocFileCacheBiocGenericsbiomaRtBiostringsbitbit64blobcachemcirclizecliclustercolorspacecpp11crayoncurlDBIdbplyrdigestdplyrfarverfastmapfilelockgenericsggplot2GlobalOptionsgluegtablehmshttrhttr2igraphIRangesisobandjsonliteKEGGRESTlabelinglatticelifecyclemagrittrMatrixmemoisemimeopensslpbapplypillarpkgconfigpngprettyunitsprogresspurrrR.cacheR.methodsS3R.ooR.utilsR6randomcoloRrappdirsRColorBrewerRcpprlangRSQLiteRtsneS4VectorsS7scalesSeqinfoshapestringistringrsystibbletidyrtidyselectutf8V8vctrsviridisLitewithrxml2XVector

Quick Start Guide
Introduction | Installation | Load Package and Create Example Data | Workflow 1: Highly Expressed Gene Analysis | Step 1: Parse Expression Data | Step 2: Find Ligand-Receptor Pairs | Step 3: Visualize with Circos Plot | Step 4: Visualize with Network Plot | Workflow 2: Multi-Category Analysis | Workflow 3: Using the Ligand-Receptor Database | Summary | Session Info
Rendered fromquick-start.Rmdusingknitr::rmarkdown

Last update: 2026-01-23
Started: 2026-01-23

Visualization Guide
Introduction | Setup | LRPlot: Circos Visualization | Basic Circos Plot | Understanding the Circos Plot | Customized Circos Plot | NetView: Network Visualization | Basic Network Plot | Understanding the Network | Customized Network with Labels | DEG Data Visualization | Color Recommendations | Scientific Color Palettes | Publication-Ready Export | Tips and Best Practices | Session Info
Rendered fromvisualization.Rmdusingknitr::rmarkdown

Last update: 2026-01-23
Started: 2026-01-23

Algorithm and Statistical Methods
Overview | Ligand-Receptor Database | Database Structure | Database Sources | Statistical Methods for Differential Expression | Method Comparison | Wilcoxon Rank-Sum Test | DESeq2 Model | MAST Hurdle Model | L-R Pair Detection Algorithm | Workflow | Matching Algorithm | Multiple Testing Correction | Communication Strength Metrics | Expression-based Scoring | Fold Change-based Scoring | Network Construction | Computational Complexity | References | Session Info
Rendered fromalgorithm.Rmdusingknitr::rmarkdown

Last update: 2026-01-23
Started: 2026-01-23

Cross-Species Analysis
Introduction | Species Detection | Gene Naming Conventions | Automatic Detection | Detection Algorithm | Ortholog Mapping via BioMart | How It Works | BioMart Query Details | Caching System | Automatic Conversion in FindLR | Seamless Workflow | Disabling Auto-Conversion | Mapping Rates and Considerations | Typical Mapping Rates | One-to-Many Mappings | Unmapped Genes | Advanced Configuration | Using Different Ensembl Versions | Mirror Selection | SSL Configuration | Performance Benchmarks | Troubleshooting | Common Issues | Summary | Session Info
Rendered fromspecies-conversion.Rmdusingknitr::rmarkdown

Last update: 2026-01-23
Started: 2026-01-23