Package: SingleCellSignalR 1.19.0
Jacques Colinge Developer
SingleCellSignalR: Cell Signalling Using Single Cell RNAseq Data Analysis
Allows single cell RNA seq data analysis, clustering, creates internal network and infers cell-cell interactions.
Authors:
SingleCellSignalR_1.19.0.tar.gz
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SingleCellSignalR.pdf |SingleCellSignalR.html✨
SingleCellSignalR/json (API)
NEWS
| # Install 'SingleCellSignalR' in R: |
| install.packages('SingleCellSignalR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- LRdb - Ligand/Receptor interactions data table
- PwC_ReactomeKEGG - Pathway Commons Reactome KEGG 2019-05-08
- example_dataset - Example dataset
- markers_default - A list of cell types markers
- mm2Hs - Mus Musculus (mm) to Homo Sapiense (Hs) Orthology table
On BioConductor:SingleCellSignalR-1.19.0(bioc 3.21)SingleCellSignalR-1.18.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
singlecellnetworkclusteringrnaseqclassification
Last updated 4 months agofrom:f0f49f1b5c. Checks:1 OK, 7 WARNING. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Feb 17 2025 |
| R-4.5-win | WARNING | Feb 17 2025 |
| R-4.5-mac | WARNING | Feb 17 2025 |
| R-4.5-linux | WARNING | Feb 17 2025 |
| R-4.4-win | WARNING | Feb 17 2025 |
| R-4.4-mac | WARNING | Feb 17 2025 |
| R-4.3-win | WARNING | Feb 17 2025 |
| R-4.3-mac | WARNING | Feb 17 2025 |
Exports:cell_classifiercell_signalingcluster_analysisclusteringdata_prepareexpression_plotexpression_plot_2inter_networkintra_networkLRscoremarkersmv_interactionssimplify_interactionsvisualize_interactions
Dependencies:abindaskpassassortheadbeachmatBHBiobaseBiocGenericsBiocManagerBiocNeighborsBiocParallelBiocSingularbitopsblustercaToolscirclizecliclustercodetoolscolorspacecpp11crayoncurldata.tableDelayedArraydqrngedgeRfarverforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGlobalOptionsgluegplotsgtablegtoolshttrigraphIRangesirlbaiteratorsjsonliteKernSmoothlabelinglambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmetapodmimemulttestmunsellopensslpheatmappkgconfigR6RColorBrewerRcpprlangrsvdRtsneS4ArraysS4VectorsScaledMatrixscalesscranscuttleshapeSingleCellExperimentsitmosnowSparseArraystatmodstringistringrSummarizedExperimentsurvivalsysUCSC.utilsvctrsviridisLiteXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Cell classifier | cell_classifier |
| Cell Signaling | cell_signaling |
| Cluster Analysis | cluster_analysis |
| Clustering | clustering |
| Data Prepare | data_prepare |
| Example dataset | example_dataset |
| Expression Plot | expression_plot |
| Expression Plot 2 | expression_plot_2 |
| inter network | inter_network |
| intra network | intra_network |
| Ligand/Receptor interactions data table | LRdb |
| Calculation of the LRscore | LRscore |
| Markers | markers |
| A list of cell types markers | markers_default |
| Mus Musculus (mm) to Homo Sapiense (Hs) Orthology table | mm2Hs |
| most variable interactions | mv_interactions |
| Pathway Commons Reactome KEGG 2019-05-08 | PwC_ReactomeKEGG |
| simplify_interactions | simplify_interactions |
| Visualize interactions | visualize_interactions |