Dimension reduction | Clustering | Differential analysis | Differential abundance (DA) | Differential states (DS)
Package: HDCytoData 1.33.1
Lukas M. Weber
HDCytoData: Collection of high-dimensional cytometry benchmark datasets in Bioconductor object formats
Data package containing a set of publicly available high-dimensional cytometry benchmark datasets, formatted into SummarizedExperiment and flowSet Bioconductor object formats, including all required metadata. Row metadata includes sample IDs, group IDs, patient IDs, reference cell population or cluster labels (where available), and labels identifying 'spiked in' cells (where available). Column metadata includes channel names, protein marker names, and protein marker classes (cell type or cell state).
Authors:
HDCytoData_1.33.1.tar.gz
HDCytoData_1.33.1.tar.gz(r-4.7-any)HDCytoData_1.33.1.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
HDCytoData/json (API)
| # Install 'HDCytoData' in R: |
| install.packages('HDCytoData', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/lmweber/hdcytodata/issues
On BioConductor:HDCytoData-1.33.1(data/experiment 3.24)HDCytoData-1.32.1(data/experiment 3.23)
experimenthubexperimentdataexpressiondataflowcytometrydatasinglecelldatahomo_sapiens_dataimmunooncologydatadatapkg
Last updated from:ca8c9781c7. Checks:1 WARNING, 2 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 | WARNING | 206 | ||
| linux-devel | NOTE | 477 | ||
| source / vignettes | OK | 354 | ||
| linux-release | NOTE | 424 |
Exports:Bodenmiller_BCR_XL_flowSetBodenmiller_BCR_XL_SEKrieg_Anti_PD_1_flowSetKrieg_Anti_PD_1_SELevine_13dim_flowSetLevine_13dim_SELevine_32dim_flowSetLevine_32dim_SEMosmann_rare_flowSetMosmann_rare_SENilsson_rare_flowSetNilsson_rare_SESamusik_01_flowSetSamusik_01_SESamusik_all_flowSetSamusik_all_SEWeber_AML_sim_less_distinct_0.1pc_flowSetWeber_AML_sim_less_distinct_0.1pc_SEWeber_AML_sim_less_distinct_1pc_flowSetWeber_AML_sim_less_distinct_1pc_SEWeber_AML_sim_less_distinct_5pc_flowSetWeber_AML_sim_less_distinct_5pc_SEWeber_AML_sim_main_0.1pc_flowSetWeber_AML_sim_main_0.1pc_SEWeber_AML_sim_main_1pc_flowSetWeber_AML_sim_main_1pc_SEWeber_AML_sim_main_5pc_flowSetWeber_AML_sim_main_5pc_SEWeber_AML_sim_main_blasts_all_flowSetWeber_AML_sim_main_blasts_all_SEWeber_AML_sim_null_flowSetWeber_AML_sim_null_SEWeber_AML_sim_random_seeds_0.1pc_flowSetWeber_AML_sim_random_seeds_0.1pc_SEWeber_AML_sim_random_seeds_1pc_flowSetWeber_AML_sim_random_seeds_1pc_SEWeber_AML_sim_random_seeds_5pc_flowSetWeber_AML_sim_random_seeds_5pc_SEWeber_BCR_XL_sim_less_distinct_less_50pc_flowSetWeber_BCR_XL_sim_less_distinct_less_50pc_SEWeber_BCR_XL_sim_less_distinct_less_75pc_flowSetWeber_BCR_XL_sim_less_distinct_less_75pc_SEWeber_BCR_XL_sim_main_flowSetWeber_BCR_XL_sim_main_SEWeber_BCR_XL_sim_null_rep1_flowSetWeber_BCR_XL_sim_null_rep1_SEWeber_BCR_XL_sim_null_rep2_flowSetWeber_BCR_XL_sim_null_rep2_SEWeber_BCR_XL_sim_null_rep3_flowSetWeber_BCR_XL_sim_null_rep3_SEWeber_BCR_XL_sim_random_seeds_rep1_flowSetWeber_BCR_XL_sim_random_seeds_rep1_SEWeber_BCR_XL_sim_random_seeds_rep2_flowSetWeber_BCR_XL_sim_random_seeds_rep2_SEWeber_BCR_XL_sim_random_seeds_rep3_flowSetWeber_BCR_XL_sim_random_seeds_rep3_SE
Dependencies:abindAnnotationDbiAnnotationHubaskpassBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsbiocmakeBiocManagerBiocVersionBiostringsbitbit64blobcachemclicpp11crayoncurlcytolibDBIdbplyrDelayedArraydir.expirydplyrExperimentHubfastmapfilelockflowCoregenericsGenomicRangesgluehttrhttr2IRangesjsonliteKEGGRESTlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigpngpurrrR6rappdirsRcppRhdf5librlangRProtoBufLibRSQLiteS4ArraysS4VectorsSeqinfoSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectutf8vctrswithrXVectoryaml
Examples and use cases
Last update: 2021-01-25
Started: 2019-11-16
HDCytoData package
Overview | Datasets | Programmatic access to list of datasets | How to load data | Using the data | Transformation of raw data | Exploring the data | Contribution guidelines | Citation
Last update: 2020-01-20
Started: 2019-10-06
Contribution guidelines
Open GitHub issue | Prepare object files | Create pull request | Contact Bioconductor maintainers to upload .rda files | Acknowledgment of contributions | Code of conduct
Last update: 2019-11-22
Started: 2019-11-16
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| 'Bodenmiller_BCR_XL' dataset | Bodenmiller_BCR_XL Bodenmiller_BCR_XL_flowSet Bodenmiller_BCR_XL_SE |
| Data package of high-dimensional cytometry datasets | HDCytoData-package HDCytoData |
| 'Krieg_Anti_PD_1' dataset | Krieg_Anti_PD_1 Krieg_Anti_PD_1_flowSet Krieg_Anti_PD_1_SE |
| 'Levine_13dim' dataset | Levine_13dim Levine_13dim_flowSet Levine_13dim_SE |
| 'Levine_32dim' dataset | Levine_32dim Levine_32dim_flowSet Levine_32dim_SE |
| 'Mosmann_rare' dataset | Mosmann_rare Mosmann_rare_flowSet Mosmann_rare_SE |
| 'Nilsson_rare' dataset | Nilsson_rare Nilsson_rare_flowSet Nilsson_rare_SE |
| 'Samusik_01' dataset | Samusik_01 Samusik_01_flowSet Samusik_01_SE |
| 'Samusik_all' dataset | Samusik_all Samusik_all_flowSet Samusik_all_SE |
| 'Weber_AML_sim' semi-simulated datasets | Weber_AML_sim Weber_AML_sim_less_distinct Weber_AML_sim_less_distinct_0.1pc Weber_AML_sim_less_distinct_0.1pc_flowSet Weber_AML_sim_less_distinct_0.1pc_SE Weber_AML_sim_less_distinct_1pc Weber_AML_sim_less_distinct_1pc_flowSet Weber_AML_sim_less_distinct_1pc_SE Weber_AML_sim_less_distinct_5pc Weber_AML_sim_less_distinct_5pc_flowSet Weber_AML_sim_less_distinct_5pc_SE Weber_AML_sim_main Weber_AML_sim_main_0.1pc Weber_AML_sim_main_0.1pc_flowSet Weber_AML_sim_main_0.1pc_SE Weber_AML_sim_main_1pc Weber_AML_sim_main_1pc_flowSet Weber_AML_sim_main_1pc_SE Weber_AML_sim_main_5pc Weber_AML_sim_main_5pc_flowSet Weber_AML_sim_main_5pc_SE Weber_AML_sim_main_blasts_all Weber_AML_sim_main_blasts_all_flowSet Weber_AML_sim_main_blasts_all_SE Weber_AML_sim_null Weber_AML_sim_null_flowSet Weber_AML_sim_null_SE Weber_AML_sim_random_seeds Weber_AML_sim_random_seeds_0.1pc Weber_AML_sim_random_seeds_0.1pc_flowSet Weber_AML_sim_random_seeds_0.1pc_SE Weber_AML_sim_random_seeds_1pc Weber_AML_sim_random_seeds_1pc_flowSet Weber_AML_sim_random_seeds_1pc_SE Weber_AML_sim_random_seeds_5pc Weber_AML_sim_random_seeds_5pc_flowSet Weber_AML_sim_random_seeds_5pc_SE |
| 'Weber_BCR_XL_sim' semi-simulated datasets | Weber_BCR_XL_sim Weber_BCR_XL_sim_less_distinct Weber_BCR_XL_sim_less_distinct_less_50pc Weber_BCR_XL_sim_less_distinct_less_50pc_flowSet Weber_BCR_XL_sim_less_distinct_less_50pc_SE Weber_BCR_XL_sim_less_distinct_less_75pc Weber_BCR_XL_sim_less_distinct_less_75pc_flowSet Weber_BCR_XL_sim_less_distinct_less_75pc_SE Weber_BCR_XL_sim_main Weber_BCR_XL_sim_main_flowSet Weber_BCR_XL_sim_main_SE Weber_BCR_XL_sim_null Weber_BCR_XL_sim_null_rep1 Weber_BCR_XL_sim_null_rep1_flowSet Weber_BCR_XL_sim_null_rep1_SE Weber_BCR_XL_sim_null_rep2 Weber_BCR_XL_sim_null_rep2_flowSet Weber_BCR_XL_sim_null_rep2_SE Weber_BCR_XL_sim_null_rep3 Weber_BCR_XL_sim_null_rep3_flowSet Weber_BCR_XL_sim_null_rep3_SE Weber_BCR_XL_sim_random_seeds Weber_BCR_XL_sim_random_seeds_rep1 Weber_BCR_XL_sim_random_seeds_rep1_flowSet Weber_BCR_XL_sim_random_seeds_rep1_SE Weber_BCR_XL_sim_random_seeds_rep2 Weber_BCR_XL_sim_random_seeds_rep2_flowSet Weber_BCR_XL_sim_random_seeds_rep2_SE Weber_BCR_XL_sim_random_seeds_rep3 Weber_BCR_XL_sim_random_seeds_rep3_flowSet Weber_BCR_XL_sim_random_seeds_rep3_SE |