Overview | Finding references | General-purpose references | Human primary cell atlas (HPCA) | Blueprint/ENCODE | Mouse RNA-seq | Immune references | Immunological Genome Project (ImmGen) | Database of Immune Cell Expression/eQTLs/Epigenomics (DICE) | Novershtern hematopoietic data | Monaco immune data | Adding new references | Session information | References
Package: celldex 1.22.0
Aaron Lun
celldex: Index of Reference Cell Type Datasets
Provides a collection of reference expression datasets with curated cell type labels, for use in procedures like automated annotation of single-cell data or deconvolution of bulk RNA-seq.
Authors:
celldex_1.22.0.tar.gz
celldex_1.22.0.tar.gz(r-4.7-any)celldex_1.22.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
celldex/json (API)
| # Install 'celldex' in R: |
| install.packages('celldex', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/ltla/celldex/issues
On BioConductor:celldex-1.23.0(data/experiment 3.24)celldex-1.22.0(data/experiment 3.23)
experimenthubexperimentdataexpressiondatasequencingdatarnaseqdatadatapkg
Last updated from:8fca92fc08 (on RELEASE_3_23). Checks:3 NOTE, 1 OK. Indexed: no.
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 | 174 | ||
| linux-devel | NOTE | 475 | ||
| source / vignettes | OK | 314 | ||
| linux-release | NOTE | 435 |
Exports:BlueprintEncodeDataDatabaseImmuneCellExpressionDatadefineTextQueryfetchLatestVersionfetchMetadatafetchReferenceHumanPrimaryCellAtlasDataImmGenDatalistReferenceslistVersionsMonacoImmuneDataMouseRNAseqDataNovershternHematopoieticDatasaveReferencesearchReferencessurveyReferences
Dependencies:abindalabaster.basealabaster.matrixalabaster.rangesalabaster.schemasalabaster.seAnnotationDbiAnnotationHubaskpassassortheadBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsbiocmakeBiocManagerBiocVersionBiostringsbitbit64blobcachemclicpp11crayoncurlDBIdbplyrDelayedArrayDelayedMatrixStatsdir.expirydplyrExperimentHubfastmapfilelockgenericsGenomicRangesgluegypsumh5mreadHDF5Arrayhttrhttr2IRangesjsonlitejsonvalidateKEGGRESTlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigpngpurrrR6rappdirsRcpprhdf5rhdf5filtersRhdf5librlangRSQLiteS4ArraysS4VectorsSeqinfoSparseArraysparseMatrixStatsstringistringrSummarizedExperimentsystibbletidyrtidyselectutf8V8vctrswithrXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Obtain human bulk RNA-seq data from Blueprint and ENCODE | BlueprintEncodeData |
| Obtain human bulk RNA-seq data from DICE | DatabaseImmuneCellExpressionData |
| Fetch a reference dataset | fetchMetadata fetchReference |
| Obtain the HPCA data | HumanPrimaryCellAtlasData |
| Obtain mouse bulk expression data from the Immunologic Genome Project | ImmGenData |
| List available references | fetchLatestVersion listReferences listVersions |
| Obtain bulk RNA-seq data of sorted human immune cells | MonacoImmuneData |
| Obtain mouse bulk expression data of sorted cell populations (RNA-seq) | MouseRNAseqData |
| Obtain bulk microarray expression for sorted hematopoietic cells | NovershternHematopoieticData |
| Save a reference dataset | saveReference |
| Search reference metadata | searchReferences |
| Survey reference metadata | surveyReferences |
