Introduction | About scTGIF | Usage | Test data | Parameter setting : settingTGIF | Calculate attention maps and map-related gene functions: calcTGIF | HTML Report : reportTGIF | Session information
Package: scTGIF 1.27.0
Koki Tsuyuzaki
scTGIF: Cell type annotation for unannotated single-cell RNA-Seq data
scTGIF connects the cells and the related gene functions without cell type label.
Authors:
scTGIF_1.27.0.tar.gz
scTGIF_1.27.0.zip(r-4.7)scTGIF_1.27.0.zip(r-4.6)scTGIF_1.27.0.zip(r-4.5)
scTGIF_1.27.0.tgz(r-4.6-any)scTGIF_1.27.0.tgz(r-4.5-any)
scTGIF_1.27.0.tar.gz(r-4.7-any)scTGIF_1.27.0.tar.gz(r-4.6-any)
scTGIF_1.27.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
scTGIF/json (API)
| # Install 'scTGIF' in R: |
| install.packages('scTGIF', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- DistalLungEpithelium - Gene expression matrix of DistalLungEpithelium dataset containing five cluster.
- label.DistalLungEpithelium - Cellular label of DistalLungEpithelium dataset containing five cluster.
- pca.DistalLungEpithelium - The result of PCA of the DistalLungEpithelium dataset.
On BioConductor:scTGIF-1.27.0(bioc 3.24)scTGIF-1.26.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
dimensionreductionqualitycontrolsinglecellsoftwaregeneexpression
Last updated from:1b32e29119. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 208 | ||
| linux-devel-x86_64 | NOTE | 411 | ||
| source / vignettes | OK | 317 | ||
| linux-release-x86_64 | NOTE | 370 | ||
| macos-release-arm64 | NOTE | 250 | ||
| macos-oldrel-arm64 | NOTE | 233 | ||
| windows-devel | NOTE | 646 | ||
| windows-release | NOTE | 280 | ||
| windows-oldrel | NOTE | 679 | ||
| wasm-release | OK | 176 |
Exports:calcTGIFcellMarkerToGmtconvertRowIDreportTGIFsettingTGIF
Dependencies:abindannotateAnnotationDbiaskpassassertthatbabelgenebase64encBiobaseBiocGenericsBiocManagerBiocStyleBiostringsbitbit64blobbookdownbslibcachemclassclassIntcliclusterconcavemancpp11crayoncrosstalkcurldata.tableDBIDelayedArraydigestdotCall64dplyre1071entropyevaluatefarverfastmapfieldsfontawesomefsgenericsGenomicRangesggforceggplot2gluegraphGSEABasegtablehexbinhighrhtmltoolshtmlwidgetshttrigraphIRangesisobandjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglaterlatticelazyevallifecyclemagrittrmapsMASSMatrixMatrixGenericsmatrixStatsmemoisemimemisc3dmsigdbrnnTensoropensslotelpillarpkgconfigplot3DplotlypngpolyclippromisesproxypurrrR6RANNrappdirsRColorBrewerRcppRcppEigenrlangrmarkdownRSpectraRSQLiterTensors2S4ArraysS4VectorsS7sassscalesschexSeqinfosfSingleCellExperimentspamSparseArraystringistringrSummarizedExperimentsyssystemfontstagcloudtibbletidyrtidyselecttinytextweenrunitsutf8V8vctrsVicusviridisLitewithrwkxfunXMLxtableXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Cell type annotation for unannotated single-cell RNA-Seq data | scTGIF-package scTGIF |
| Function for connecting cellular patterns and functional patterns using jNMF | calcTGIF calcTGIF,SingleCellExperiment-method |
| A function to convert the CellMarker data to GMT files. | cellMarkerToGmt |
| A function to change the row names of a matrix. | convertRowID |
| Gene expression matrix of DistalLungEpithelium dataset containing five cluster. | DistalLungEpithelium |
| Cellular label of DistalLungEpithelium dataset containing five cluster. | label.DistalLungEpithelium |
| The result of PCA of the DistalLungEpithelium dataset. | pca.DistalLungEpithelium |
| Function for reporting the result of 'calcTGIF' function | reportTGIF reportTGIF,SingleCellExperiment-method |
| Paramter setting for scTGIF | settingTGIF settingTGIF,SingleCellExperiment-method |
