Installation | R packages | Access to MetaData | Access curated tuberculosis gene expression profile | Subset/Combine MultiAssayExperiment objects | Subset | Dataset integeration | Merge Studies with common gene symbols | Batch correction | Dataset subset | Select patients with Active TB and LTBI | Select other outcome of interests | Session Info
Package: curatedTBData 2.9.0
Xutao Wang
curatedTBData: Curation of existing tuberculosis transcriptomic studies
The curatedTBData is an R package that provides standardized, curated tuberculosis(TB) transcriptomic studies. The initial release of the package contains 49 studies. The curatedTBData package allows users to access tuberculosis trancriptomic efficiently and to make efficient comparison for different TB gene signatures across multiple datasets.
Authors:
curatedTBData_2.9.0.tar.gz
curatedTBData_2.9.0.tar.gz(r-4.7-any)curatedTBData_2.9.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
curatedTBData/json (API)
| # Install 'curatedTBData' in R: |
| install.packages('curatedTBData', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/compbiomed/curatedtbdata/issues
Datasets:
- DataSummary - Summarized tuberculosis studies included in the curatedTBData
- SignatureInfoTraining - Summarized results for tuberculosis gene signatures and their corresponding discovery/training studies
On BioConductor:curatedTBData-2.9.0(data/experiment 3.24)curatedTBData-2.8.0(data/experiment 3.23)
experimenthubgeohomo_sapiens_datadatapkg
Last updated from:3f32eb1679. Checks:3 WARNING, 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 | 176 | ||
| linux-devel | WARNING | 373 | ||
| source / vignettes | OK | 371 | ||
| linux-release | WARNING | 358 |
Exports:combine_objectscuratedTBDatasubset_curatedTBData
Dependencies:abindAnnotationDbiAnnotationHubaskpassBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocManagerBiocVersionBiostringsbitbit64blobcachemclicpp11crayoncurlDBIdbplyrDelayedArraydplyrExperimentHubfastmapfilelockgenericsGenomicRangesgluehttrhttr2IRangesjsonliteKEGGRESTlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeMultiAssayExperimentopensslpillarpkgconfigpngpurrrR6rappdirsrlangRSQLiteS4ArraysS4VectorsSeqinfoSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectutf8vctrswithrXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Select assay based on input list type | .select_assay |
| Subset curatedTBData based on single/multiple conditions | .subset_curatedTBData |
| Merge samples with common gene names from selected studies | combine_objects |
| Import curated Tuberculosis Data | curatedTBData |
| Summarized tuberculosis studies included in the curatedTBData | DataSummary |
| Summarized results for tuberculosis gene signatures and their corresponding discovery/training studies | SignatureInfoTraining |
| Subset curatedTBData based on single/multiple conditions | subset_curatedTBData |
| Update gene names from input data | update_gene_symbol |
