Package: CiteFuse 1.19.0
Yingxin Lin
CiteFuse: CiteFuse: multi-modal analysis of CITE-seq data
CiteFuse pacakage implements a suite of methods and tools for CITE-seq data from pre-processing to integrative analytics, including doublet detection, network-based modality integration, cell type clustering, differential RNA and protein expression analysis, ADT evaluation, ligand-receptor interaction analysis, and interactive web-based visualisation of the analyses.
Authors:
CiteFuse_1.19.0.tar.gz
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CiteFuse.pdf |CiteFuse.html✨
CiteFuse/json (API)
NEWS
| # Install 'CiteFuse' in R: |
| install.packages('CiteFuse', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/sydneybiox/citefuse/issues
- CITEseq_example - A subset of ECCITE-seq data
- lr_pair_subset - A subset of Ligand Receptor Pairs
- sce_control_subset - A SingleCellExperiment of ECCITE-seq data
- sce_ctcl_subset - A SingleCellExperiment of ECCITE-seq data
On BioConductor:CiteFuse-1.19.0(bioc 3.21)CiteFuse-1.18.0(bioc 3.20)
singlecellgeneexpressionbioinformaticssingle-cell
Last updated 23 days agofrom:699f98c022. Checks:ERROR: 1 WARNING: 8. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | FAIL | Nov 14 2024 |
| R-4.5-win-x86_64 | WARNING | Nov 14 2024 |
| R-4.5-linux-x86_64 | WARNING | Nov 14 2024 |
| R-4.4-win-x86_64 | WARNING | Nov 14 2024 |
| R-4.4-mac-x86_64 | WARNING | Nov 14 2024 |
| R-4.4-mac-aarch64 | WARNING | Nov 14 2024 |
| R-4.3-win-x86_64 | WARNING | Nov 14 2024 |
| R-4.3-mac-x86_64 | WARNING | Nov 14 2024 |
| R-4.3-mac-aarch64 | WARNING | Nov 14 2024 |
Exports:CiteFusecrossSampleDoubletsDEbubblePlotDEcomparisonPlotDEgenesDEgenesCrossgeneADTnetworkigraphClusteringimportanceADTligandReceptorTestnormaliseExprsplotHTOpreprocessingreadFrom10XreducedDimSNFselectDEgenesspectralClusteringvisImportancevisLigandReceptorvisualiseDimvisualiseExprsvisualiseExprsListvisualiseKNNwithinSampleDoublets
Dependencies:abindaskpassassortheadbase64encbayesmbeachmatBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularblusterbslibcachemcliclustercodetoolscolorspacecompositionscowplotcpp11crayoncrosstalkcurldata.tabledbscanDelayedArrayDEoptimRdigestdplyrdqrngedgeRevaluatefansifarverfastmapFNNfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggforceggplot2ggraphggrepelggridgesgluegraphlayoutsgridExtragtablehighrhtmltoolshtmlwidgetshttrigraphIRangesirlbaisobandjquerylibjsonlitekernlabknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemetapodmgcvmimemixtoolsmunsellnlmeopensslpheatmappillarpkgconfigplotlyplyrpolyclippromisespurrrR6randomForestrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppProgressreshape2rhdf5rhdf5filtersRhdf5librlangrmarkdownrobustbaseRSpectrarsvdRtsneS4ArraysS4VectorssassScaledMatrixscalesscranscuttlesegmentedSingleCellExperimentsitmosnowSparseArraystatmodstringistringrSummarizedExperimentsurvivalsyssystemfontstensorAtibbletidygraphtidyrtidyselecttinytextweenrUCSC.utilsutf8uwotvctrsviridisviridisLitewithrxfunXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| CiteFuse | CiteFuse |
| A subset of ECCITE-seq data (control) | CITEseq_example |
| crossSampleDoublets | crossSampleDoublets |
| DEbubblePlot | DEbubblePlot |
| DEcomparisonPlot | DEcomparisonPlot |
| DEgenes | DEgenes |
| DEgenesCross | DEgenesCross |
| geneADTnetwork | geneADTnetwork |
| igraphClustering | igraphClustering |
| importanceADT | importanceADT |
| ligandReceptorTest | ligandReceptorTest |
| A subset of Ligand Receptor Pairs | lr_pair_subset |
| normaliseExprs | normaliseExprs |
| plotHTO | plotHTO |
| plotHTOSingle | plotHTOSingle |
| A function to preprocess the list of expression matrix | preprocessing |
| readFrom10X | readFrom10X |
| reducedDimSNF | reducedDimSNF |
| A SingleCellExperiment of ECCITE-seq data | sce_control_subset |
| A SingleCellExperiment of ECCITE-seq data | sce_ctcl_subset |
| selectDEgenes | selectDEgenes |
| spectralClustering | spectralClustering |
| visImportance | visImportance |
| visLigandReceptor | visLigandReceptor |
| visualiseDim | visualiseDim |
| visualiseExprs | visualiseExprs |
| visualiseExprsList | visualiseExprsList |
| visualiseKNN | visualiseKNN |
| withinSampleDoublets | withinSampleDoublets |
