Introduction | Installation | Overview of the dataset | Assay types | scRNA-seq | scATAC-seq and Multiome | CITE-seq | Spatial transcriptomics | Annotations of the Tonsil Data Atlas | Interoperability with other frameworks | Session information | References
Package: HCATonsilData 1.11.0
Ramon Massoni-Badosa
HCATonsilData: Provide programmatic access to the tonsil cell atlas datasets
This package provides access to the scRNA-seq, scATAC-seq, multiome, CITE-seq and spatial transcriptomics (Visium) data generated by the tonsil cell atlas in the context of the Human Cell Atlas (HCA). The data is provided via the Bioconductor project in the form of SingleCellExperiments. Additionally, information on the whole compendium of identified cell types is provided in form of a glossary.
Authors:
HCATonsilData_1.11.0.tar.gz
HCATonsilData_1.11.0.tar.gz(r-4.7-any)HCATonsilData_1.11.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
HCATonsilData/json (API)
| # Install 'HCATonsilData' in R: |
| install.packages('HCATonsilData', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/massonix/hcatonsildata/issues
Datasets:
- annotations_dictionary - Annotation dictionary to keep track of annotations changes and versions
- colors_20230508 - Color palettes
- donor_metadata - Donor metadata
- NBC_MBC_annotation_df - Annotation dictionary for naive and memory B cells
On BioConductor:HCATonsilData-1.11.0(data/experiment 3.24)HCATonsilData-1.10.0(data/experiment 3.23)
singlecelldataexperimentdatarnaseqdataexperimenthubexpressiondataspatialdatadatapkg
Last updated from:5d3b6bc731. Checks:3 NOTE, 1 OK. Indexed: yes.
This is a data package. Data packages may be large and do not get checked across all platforms.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 224 | ||
| linux-devel | NOTE | 486 | ||
| source / vignettes | OK | 368 | ||
| linux-release | NOTE | 403 |
Exports:HCATonsilDatalistCellTypesTonsilData_cellinfoTonsilData_cellinfo_htmlTonsilData_glossaryupdateAnnotation
Dependencies:abindAnnotationDbiAnnotationHubaskpassbase64encBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsbiocmakeBiocManagerBiocVersionBiostringsbitbit64blobbslibcachemclicpp11crayoncurlDBIdbplyrDelayedArraydigestdir.expirydplyrevaluateExperimentHubfastmapfilelockfontawesomefsgenericsGenomicRangesglueh5mreadHDF5Arrayhighrhtmltoolshttrhttr2IRangesjquerylibjsonliteKEGGRESTknitrlatticelifecyclemagickmagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigpngpurrrR6rappdirsRcpprhdf5rhdf5filtersRhdf5librjsonrlangrmarkdownRSQLiteS4ArraysS4VectorssassSeqinfoSingleCellExperimentSparseArraySpatialExperimentstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexutf8vctrswithrxfunXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Annotation dictionary to keep track of annotations changes and versions | annotations_dictionary |
| Color palettes | colors_20230508 |
| Donor metadata | donor_metadata |
| Access the Tonsil Atlas data (RNA, ATAC, Multiome, CITE, Spatial) | HCATonsilData |
| List available cell types for a dataset of the tonsil cell atlas | listCellTypes |
| Annotation dictionary for naive and memory B cells (NBC-MBC) | NBC_MBC_annotation_df |
| TonsilData_cellinfo | TonsilData_cellinfo |
| TonsilData_cellinfo_html | TonsilData_cellinfo_html |
| TonsilData_glossary | TonsilData_glossary |
| Update cell type annotation | updateAnnotation |