Package: davidTiling 1.53.1
Wolfgang Huber
davidTiling: Data and analysis scripts for David, Huber et al. yeast tiling array paper
This package contains the data for the paper by L. David et al. in PNAS 2006 (PMID 16569694): 8 CEL files of Affymetrix genechips, an ExpressionSet object with the raw feature data, a probe annotation data structure for the chip and the yeast genome annotation (GFF file) that was used. In addition, some custom-written analysis functions are provided, as well as R scripts in the scripts directory.
Authors:
davidTiling_1.53.1.tar.gz
davidTiling_1.53.1.tar.gz(r-4.7-any)davidTiling_1.53.1.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
davidTiling/json (API)
| # Install 'davidTiling' in R: |
| install.packages('davidTiling', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- gff - Genomic features of Saccharomyces cerevisiae
- probeAnno - An environment with probe mapping information for the Scerevisiae tiling array
- yeastFeatures - A data.frame with metadata about the features in SGD GFF files
On BioConductor:davidTiling-1.53.1(data/experiment 3.24)davidTiling-1.52.0(data/experiment 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
experimentdatagenomesaccharomyces_cerevisiae_datamicroarraydatareproducibleresearchdatapkg
Last updated from:c2d32bbb7c. Checks:1 ERROR, 2 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 | ERROR | 164 | ||
| linux-devel | WARNING | 299 | ||
| source / vignettes | OK | 256 | ||
| linux-release | WARNING | 242 |
Exports:getAllGOgetAttributeFieldgetDavidTilingDataGOHyperGscatterWithHistshowDens
Dependencies:affyaffyioannotateAnnotationDbiaskpassBiobaseBiocBaseUtilsBiocGenericsBiocManagerBiostringsbitbit64blobcachemclicpp11crayoncurlDBIfarverfastmapgenefiltergenericsggplot2glueGO.dbgtablehttrIRangesisobandjsonliteKEGGRESTlabelinglatticelifecyclelimmaMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpixmappkgconfigpngpreprocessCoreR6RColorBrewerrlangRSQLiteS4VectorsS7sandwichscalesSeqinfostatmodstrucchangesurvivalsystilingArrayvctrsviridisLitevsnwithrXMLxtableXVectorzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Dataset of class eSet with the raw 'CEL file' intensities | data:davidTiling davidTiling |
| Genomic features of Saccharomyces cerevisiae | data:gff gff |
| An environment with probe mapping information for the Scerevisiae tiling array | data:probeAnno probeAnno |
| Get all GO categories for a list of genes. | getAllGO |
| Extract the value of a certain field out of a character vector such as in the "attributes" column of a GFF table. | getAttributeField |
| Create the data set davidTiling. | getDavidTilingData |
| Hypergeometric test for GO category enrichment. | GOHyperG |
| Scatterplot with histograms of marginal distributions | scatterWithHist |
| Score segments | scoreSegments |
| Plot function for more than one density | showDens |
| A data.frame with metadata about the features in SGD GFF files | yeastFeatures |