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:Wolfgang Huber [aut, cre]

davidTiling_1.53.1.tar.gz
davidTiling_1.53.1.zip(r-4.7-any)davidTiling_1.53.1.zip(r-4.6-any)davidTiling_1.53.1.zip(r-4.5-any)
davidTiling_1.53.1.tgz(r-4.6-any)davidTiling_1.53.1.tgz(r-4.5-any)
davidTiling_1.53.1.tar.gz(r-4.7-any)davidTiling_1.53.1.tar.gz(r-4.6-any)
davidTiling_1.53.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
davidTiling/json (API)

# Install 'davidTiling' in R:

install.packages('davidTiling', repos = c('https://huber-group-embl.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/huber-group-embl/davidtiling/issues

Datasets:

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 CRAN:

experimentdata genome saccharomyces_cerevisiae_data microarraydata reproducibleresearch

2.26 score 6 scripts 6 exports 68 dependencies

Last updated from:c2d32bbb7c. Checks:7 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel	WARNING	274
source / vignettes	OK	283
linux-release	WARNING	232
macos-release	WARNING	187
macos-oldrel	WARNING	181
windows-devel	WARNING	148
windows-release	WARNING	165
windows-oldrel	WARNING	160
wasm-release	OK	158

Exports:getAllGO getAttributeField getDavidTilingData GOHyperG scatterWithHist showDens

Dependencies:affy affyio annotate AnnotationDbi askpass Biobase BiocBaseUtils BiocGenerics BiocManager Biostrings bit bit64 blob cachem cli cpp11 crayon curl DBI farver fastmap genefilter generics ggplot2 glue GO.db gtable httr IRanges isoband jsonlite KEGGREST labeling lattice lifecycle limma Matrix MatrixGenerics matrixStats memoise mime openssl pixmap pkgconfig png preprocessCore R6 RColorBrewer rlang RSQLite S4Vectors S7 sandwich scales Seqinfo statmod strucchange survival sys tilingArray vctrs viridisLite vsn withr XML xtable XVector zoo

Citation

Development and contributors

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