Package: gDNAinRNAseqData 1.13.0

Robert Castelo

gDNAinRNAseqData: RNA-seq data with different levels of gDNA contamination

Provides access to BAM files generated from RNA-seq data produced with different levels of gDNA contamination. It currently allows one to download a subset of the data published by Li et al., BMC Genomics, 23:554, 2022. This subset of data is formed by BAM files with about 100,000 alignments with three different levels of gDNA contamination.

Authors:Robert Castelo [aut, cre]

gDNAinRNAseqData_1.13.0.tar.gz
gDNAinRNAseqData_1.13.0.tar.gz(r-4.7-any)gDNAinRNAseqData_1.13.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
gDNAinRNAseqData/json (API)

# Install 'gDNAinRNAseqData' in R:

install.packages('gDNAinRNAseqData', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/functionalgenomics/gdnainrnaseqdata/issues

On BioConductor:gDNAinRNAseqData-1.13.0(data/experiment 3.24)gDNAinRNAseqData-1.12.0(data/experiment 3.23)

experimenthub experimentdata expressiondata sequencingdata rnaseqdata homo_sapiens_data datapkg

3.68 score 24 scripts 2 exports 71 dependencies

Last updated from:34e1e2aa52. Checks:1 NOTE, 3 OK. Indexed: yes.

This is a data package. Data packages may be large and do not get checked across all platforms.

Target	Result	Time
bioc-checks	NOTE	151
linux-devel	OK	324
source / vignettes	OK	249
linux-release	OK	281

Exports:LiYu22phenoData LiYu22subsetBAMfiles

Dependencies:AnnotationDbi AnnotationHub askpass BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocManager BiocParallel BiocVersion Biostrings bit bit64 bitops blob cachem cli codetools cpp11 crayon curl DBI dbplyr dplyr ExperimentHub fastmap filelock formatR futile.logger futile.options generics GenomicRanges glue httr httr2 IRanges jsonlite KEGGREST lambda.r lifecycle magrittr memoise mime openssl pillar pkgconfig png purrr R6 rappdirs RCurl Rhtslib rlang Rsamtools RSQLite S4Vectors Seqinfo snow stringi stringr sys tibble tidyr tidyselect utf8 vctrs withr XML XVector yaml

RNA-seq data with different levels of gDNA contamination

Retrieval of the gDNA contaminated RNA-seq data by Li et al. (2022) | Session information

Rendered fromgDNAinRNAseqData.Rmdusingknitr::rmarkdown

Last update: 2023-03-30
Started: 2023-03-24

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Development and contributors

Readme and manuals

Help Manual

Help page	Topics
RNA-seq data with different levels of gDNA contamination	gDNAinRNAseqData-package gDNAinRNAseqData LiYu22phenoData LiYu22subsetBAMfiles