Package: liana 0.1.14.9000

liana: LIANA: a LIgand-receptor ANalysis frAmework

LIANA provides a number of methods and resources for ligand-receptor interaction inference from scRNA-seq data. This version is specifically designed for Seurat v4 and SeuratObject v4 compatibility. It includes improved Python environment handling and better integration with existing workflows.

Authors:Zaoqu Liu [cre, ctb], Daniel Dimitrov [aut], Charlotte Boys [aut], Martin Garrido Rodriguez [aut], Denes Turei [aut], James Nagai [aut]

liana_0.1.14.9000.tar.gz
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liana_0.1.14.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
liana/json (API)

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

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

Pkgdown/docs site:https://zaoqu-liu.github.io

On CRAN:

Conda:

scaterscransinglecellexperimentcomplexheatmapquarto

3.06 score 231 scripts 59 exports 180 dependencies

Last updated from:a14953e154 (on main). Checks:8 ERROR, 1 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64ERROR610
source / vignettesERROR514
linux-release-x86_64ERROR545
macos-release-arm64ERROR464
macos-oldrel-arm64ERROR431
windows-develERROR779
windows-releaseERROR504
windows-oldrelERROR840
wasm-releaseOK331

Exports:assign_lr_weightscalculate_ginicall_cellchatcall_connectomecall_italkcall_natmicall_scacall_squidpycellchat_formatDBchord_freqcompile_ligrecconn_formatDBdecomplexifydecompose_tensorfilter_nonabundant_celltypesFormatConnectomeFormatiTALKFormatSCAgenerate_homologsgenerate_lr_genesetgenerate_omnigenerate_orthologsget_abundance_summaryget_c2c_factorsget_connectomeget_curated_omniget_logfcget_lr_resourcesget_natmiget_scaheat_freqitalk_formatDBjoin_meansliana_aggregateliana_bysampleliana_callliana_defaultsliana_dotplotliana_heatmapliana_pipeliana_prepliana_tensor_c2cliana_wrapmean0minmaxplot_abundance_summaryplot_c2c_cellsplot_c2c_overviewplot_context_boxplotplot_context_heatplot_lr_heatmaprank_aggregaterank_methodrecomplexifysca_formatDBselect_resourceshow_homologeneshow_methodsshow_resources

Dependencies:abindaskpassassortheadbackportsbase64encbeachmatbeeswarmBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularbitbit64blobblusterbslibcachemCairocellrangercheckmatecirclizeclicliprclueclustercodetoolscolorspaceComplexHeatmapcpp11crayoncurlDBIDelayedArraydigestdoParalleldotCall64dplyrdqrngedgeRevaluatefarverfastmapFNNfontawesomeforeachformatRfsfutile.loggerfutile.optionsfuturefuture.applygenericsGenomicRangesGetoptLongggbeeswarmggplot2ggrastrggrepelGlobalOptionsglobalsgluegridExtragtableherehighrhmshtmltoolshttrhttr2igraphIRangesirlbaisobanditeratorsjquerylibjsonliteknitrlabelinglambda.rlaterlatticelifecyclelimmalistenvlocfitloggerlubridatemagrittrMatrixMatrixGenericsmatrixStatsmemoisemetapodmimeOmnipathRopensslparallellypheatmappillarpkgconfigpngprettyunitsprogressprogressrpurrrR.methodsS3R.ooR.utilsR6raggrappdirsRColorBrewerRcppRcppAnnoyRcppEigenRcppMLRcppProgressRcppTOMLreadrreadxlrematchreticulaterjsonrlangrmarkdownrprojrootRSpectraRSQLitersvdRtsnervestS4ArraysS4VectorsS7sassScaledMatrixscalesscaterscranscuttleselectrSeqinfosessioninfoSeuratObjectshapeSingleCellExperimentsitmosnowspspamSparseArraystatmodstringistringrSummarizedExperimentsyssystemfontstextshapingtibbletidyrtidyselecttimechangetinytextzdbutf8uwotvctrsviporviridisviridisLitevroomwithrxfunXMLxml2XVectoryamlzip

Readme and manuals

Help Manual

Help pageTopics
Helper function to assign weightsassign_lr_weights
Run CellChat with OmniPath function [[DEPRECATED]]call_cellchat
Function to call connectome with databases from OmniPath [[DEPRECATED]]call_connectome
Run iTALK with OmniPath data [[DEPRECATED]]call_italk
Call NATMI Pipeline from R with Resources Querried from OmniPath [[DEPRECATED]]call_natmi
Function to call SingleCellSignalR with databases from OmniPath [[DEPRECATED]]call_sca
Call Squidpy Pipeline via reticulate with OmniPath and format resultscall_squidpy
Frequency ChordDiagramchord_freq
Helper Function to 'decomplexify' ligands and receptors into individual subunitsdecomplexify
Wrapper function to run `cell2cell_tensor` decomposition on a prebuilt tensor.decompose_tensor
Filter nun-abundant cell typesfilter_nonabundant_celltypes
Helper function to filter and format connectomeFormatConnectome
Helper Function to Filter and format iTalk resultsFormatiTALK
Load NATMI results from folder and format appropriatelyFormatNatmi
Helper function to format SingleCellSignalR resultsFormatSCA
Function to generate a homologous OmniPath resourcegenerate_homologs
Generate a geneset resource for each LRgenerate_lr_geneset
Deprecated call to generate_homologsgenerate_orthologs
Returns tensor cell2cell resultsget_c2c_factors
Function to obtain connectome-like weightsget_connectome
Function to Generate the Curated (Default) LIANA resourceget_curated_omni
Function to obtain logFC weightsget_logfc
Helper function that returns the name of each intercell resource in OmniPathget_lr_resources
Function to obtain NATMI-like weightsget_natmi
Retrieves intercellular communication partners (ligands or receptors) from one ligand-receptor resource.get_partners
Helper Function to generate shuffled meansget_permutations
Function to obtain SingleCellSignalR-like scoresget_sca
Communication Frequency heatmap plotheat_freq
Function to Aggregate CCC Method Resultsliana_aggregate
Wrapper around `liana_wrap` to run liana for each sample.liana_bysample
Wrapper Function to obtain scores via liana_pipeliana_call
Function to pass Default Arguments for each methodliana_defaults
Liana dotplot interactions by source and target cellsliana_dotplot
Communication by cell type Heatmapliana_heatmap
LIANA message/warning helper function to allow for verbosityliana_message
Liana Pipe which runs DE analysis and merges needed information for LR inferenceliana_pipe
Function to handle different types of object as input and do basic quality checksliana_prep
Function to obtain different scoring schemesliana_scores
Wrapper function to run `cell2cell_tensor` with LIANA output.liana_tensor_c2c
LIANA wrapper functionliana_wrap
Helper Function which returns the value closest to 0min0
Helper min-max normalization functionminmax
Plot the product of loadings between the source and target loadings within a factorplot_c2c_cells
Function to plot an Overview of tensor-c2c resultsplot_c2c_overview
Generate boxplots with significanceplot_context_boxplot
Plot a Heatmap of context loadingsplot_context_heat
Function to plot a UMAP of context loadingsplot_lr_heatmap
Helper function to deal with tensor sparsity and liana's scores as in Pythonpreprocess_scores
Aggregate CCC Method results and by both magnitude and specificity ranksrank_aggregate
Helper function to rank each methodrank_method
Helper Function to Handle resource choicesselect_resource
Helper function to show available organisms via OmnipathR's homologene resourceshow_homologene
Helper Function to return the methods in LIANAshow_methods
Helper Function to return the Resources in LIANAshow_resources