Package: CACIMAR 1.0.0

CACIMAR: cross-species analysis of cell identities, markers and regulations

A toolkit to perform cross-species analysis based on scRNA-seq data. CACIMAR contains 5 main features. (1) identify Markers in each cluster. (2) Cell type annotaion (3) identify conserved markers. (4) identify conserved cell types. (5) identify conserved modules of regulatory networks.

Authors:Junyao Jiang [aut, cre]

CACIMAR_1.0.0.tar.gz
CACIMAR_1.0.0.zip(r-4.5)CACIMAR_1.0.0.zip(r-4.4)CACIMAR_1.0.0.zip(r-4.3)
CACIMAR_1.0.0.tgz(r-4.4-any)CACIMAR_1.0.0.tgz(r-4.3-any)
CACIMAR_1.0.0.tar.gz(r-4.5-noble)CACIMAR_1.0.0.tar.gz(r-4.4-noble)
CACIMAR_1.0.0.tgz(r-4.4-emscripten)
CACIMAR.pdf |CACIMAR.html✨
CACIMAR/json (API)

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

Peer review:

Bug tracker:https://github.com/jiang-junyao/cacimar/issues

Datasets:
  • OrthG_Hs_Ch - Orthologs genes database for homo sapiens and zebrafish
  • OrthG_Hs_Mm - Orthologs genes database for homo sapiens and mus musculus
  • OrthG_Hs_Zf - Orthologs genes database for homo sapiens and zebrafish
  • OrthG_Mm_Ch - Orthologs genes database for mus musculus and chicken
  • OrthG_Mm_Zf - Orthologs genes database for mus musculus and zebrafish
  • OrthG_Zf_Ch - Orthologs genes database for mus zebrafish and chicken

On CRAN:

cross-species-analysisscrna-seq

40 exports 11 stars 2.67 score 219 dependencies 6 scripts 170 downloads

Last updated 22 days agofrom:f6cb72d955. Checks:OK: 1 ERROR: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 02 2024
R-4.5-winERRORSep 02 2024
R-4.5-linuxERRORSep 02 2024
R-4.4-winERRORSep 02 2024
R-4.4-macERRORSep 02 2024
R-4.3-winERRORSep 02 2024
R-4.3-macERRORSep 02 2024

Exports:add_cellchat_probbuildHomDatabaseCACIMAR_colsCaculate_cell_pair_cci_scoreCaculate_cell_pair_cci_score2calculate_WeightsChordDiagramconserved_interaction_scorecreate_sankeyFormat_Markers_FracFormatConservedMarkersget_average_expressionHeatmap_CorIdentify_CellTypeIdentify_Conserved_CCIIdentify_Conserved_CCI1Identify_Conserved_CCI2identify_conserved_geneIdentify_Conserved_LRidentify_conserved_markeridentify_conserved_pairIdentify_ConservedCellTypesIdentify_ConservedMarkersIdentify_ConservedNetworksidentify_ct_ConservedNetworksIdentify_Markersidentify_network_relationshipsMake_ChordDiagram_dataMake_ChordDiagram_data2make_pheatmap_LR_datamake_pheatmap_LR_data1perform_CCI_analysispheatmap_LR_multipheatmap_LR1phylogenetic_tree_circlePlot_Celltype.Communicationplot_interaction_heatmapPlot_MarkersHeatmapPlot_phylogenetic_treePlot_Species_CellType_Tree

Dependencies:abindAnnotationDbiapeaplotaskpassbackportsbase64encBHBiobaseBiocFileCacheBiocGenericsbiomaRtBiostringsbitbit64bitopsblobbroombslibcachemcallrcaToolscellrangerclicliprclustercodetoolscolorspacecommonmarkconflictedcowplotcpp11crayoncrosstalkcurldata.tableDBIdbplyrdeldirdigestdotCall64dplyrdqrngdtplyrevaluatefansifarverfastDummiesfastmapfilelockfitdistrplusFNNfontawesomeforcatsfsfuturefuture.applygarglegenericsGenomeInfoDbGenomeInfoDbDataggfunggplot2ggplotifyggrepelggridgesggtreeglobalsgluegoftestgoogledrivegooglesheets4GPArotationgplotsgridExtragridGraphicsgtablegtoolshavenherehighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2icaidsigraphIRangesirlbaisobandjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglaterlatticelazyevalleidenlifecyclelistenvlmtestlubridatemagrittrMASSMatrixmatrixStatsmemoisemgcvmimeminiUImnormtmodelrmunsellnlmeopensslparallellypatchworkpbapplypheatmappillarpkgconfigplogrplotlyplyrpngpolyclipprettyunitsprocessxprogressprogressrpromisespspsychpurrrR6raggRANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppProgressRcppTOMLreadrreadxlrematchrematch2reprexreshape2reticulaterlangrmarkdownROCRrprojrootRSpectraRSQLiterstudioapiRtsnervestS4VectorssassscalesscattermoresctransformselectrSeuratSeuratObjectshinysitmosourcetoolsspspamspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrsurvivalsyssystemfontstensortextshapingtibbletidyrtidyselecttidytreetidyversetimechangetinytextreeiotzdbUCSC.utilsutf8uuiduwotvctrsviridisLitevroomwithrxfunxml2xtableXVectoryamlyulab.utilszlibbioczoo

Readme and manuals

Help Manual

Help pageTopics
filter cellchat CCC networksadd_cellchat_prob
Build homologous gene databasebuildHomDatabase
CACIMAR colors paletteCACIMAR_cols
Caculate conserved score of cell-cell interactionCaculate_cell_pair_cci_score
Caculate conserved score of cell-cell interaction for three speciesCaculate_cell_pair_cci_score2
Sum weight of cell-cell interactionscalculate_Weights
Make a ChordDiagramChordDiagram
Caculate conserved interaction score and Make data for ChordDiagramconserved_interaction_score
Create sankey plotcreate_sankey
Format marker genes for plottingFormat_Markers_Frac
Format Conserved markers to plot heatmapFormatConservedMarkers
Geometric mean of ligand and receptorget_average_expression
plot the heatmap of marker genes across different speciesHeatmap_Cor
Identify cell type of each clusterIdentify_CellType
TitleIdentify_Conserved_CCI
Identify conserved cell-cell interaction from two speciesIdentify_Conserved_CCI1
Identify conserved cell-cell interaction from three speciesIdentify_Conserved_CCI2
Identify conserved geneidentify_conserved_gene
Identify conserved ligand receptor interactionIdentify_Conserved_LR
Identify conserved markers in conserved celltypeidentify_conserved_marker
Identify conserved pairidentify_conserved_pair
Identify conserved cell types based on power of genes and orthologs databaseIdentify_ConservedCellTypes
Identify orthologs marker genes for two speciesIdentify_ConservedMarkers
Identify conserved regulatory networksIdentify_ConservedNetworks
Identify conserved cell type specific regulatory networksidentify_ct_ConservedNetworks
Identify markers of each clusterIdentify_Markers
Identify conserved node and edge in the networks Based on the Conservation analysis result from Identify_ConservedNetworks, this function further identify the conserved node and edge in the network(graph)identify_network_relationships
Make data fit for ChordDiagramMake_ChordDiagram_data
Make data fit for ChordDiagram for conserved cell types from three speciesMake_ChordDiagram_data2
Make ligand-receptor data for pheatmapmake_pheatmap_LR_data
Make ligand-receptor data for pheatmapmake_pheatmap_LR_data1
Orthologs genes database for homo sapiens and zebrafishOrthG_Hs_Ch
Orthologs genes database for homo sapiens and mus musculusOrthG_Hs_Mm
Orthologs genes database for homo sapiens and zebrafishOrthG_Hs_Zf
Orthologs genes database for mus musculus and chickenOrthG_Mm_Ch
Orthologs genes database for mus musculus and zebrafishOrthG_Mm_Zf
Orthologs genes database for mus zebrafish and chickenOrthG_Zf_Ch
Cell-cell interaction analysis with SingleCellSignalR algorithmperform_CCI_analysis
Create a pheatmap for average expression of ligand-receptor pairspheatmap_LR_multi
Create a pheatmap for average expression of ligand-receptor pairspheatmap_LR1
Plot communication between cell typesPlot_Celltype.Communication
Heapmap of cell-cell interactionplot_interaction_heatmap
Plot Markers in each cell typePlot_MarkersHeatmap
Plot phylogenetic treePlot_phylogenetic_tree
Plot Phylogenetic Tree of Different Species Cell TypesPlot_Species_CellType_Tree