Introduction | Basic design | Illustration | Comparative counts in a set of regions of interest | Larger scale sanity check | Statistical analyses of differential expression | Summary | Session data
Package: leeBamViews 1.49.0
VJ Carey
leeBamViews: leeBamViews -- multiple yeast RNAseq samples excerpted from Lee 2009
data from PMID 19096707; prototype for managing multiple NGS samples
Authors:
leeBamViews_1.49.0.tar.gz
leeBamViews_1.49.0.tar.gz(r-4.7-any)leeBamViews_1.49.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
leeBamViews/json (API)
| # Install 'leeBamViews' in R: |
| install.packages('leeBamViews', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
On BioConductor:leeBamViews-1.49.0(data/experiment 3.24)leeBamViews-1.48.0(data/experiment 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
experimentdatasaccharomyces_cerevisiae_datasequencingdatarnaseqdatasnpdatadatapkg
Last updated from:b5c21fdbf0. Checks:1 ERROR, 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 | ERROR | 162 | ||
| linux-devel | NOTE | 278 | ||
| source / vignettes | OK | 236 | ||
| linux-release | NOTE | 288 |
Exports:tabulateReadstotalReadCounts
Dependencies:askpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitopsBSgenomecigarillocodetoolscpp11crayoncurlformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangeshttrIRangesjsonlitelambda.rmatrixStatsmimeopensslR6RCurlrestfulrRhtslibrjsonRsamtoolsrtracklayerS4VectorsSeqinfosnowsysXMLXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| BamViews instance construction related to yeast RNA-seq | bs1 |
| supplemental data extract on RNA seq results in yeast | leeRPKM |
| supplemental data extracts on existing evidence of transcription in yeast | leeUnn |
| tabulate counts of alignments occurring in specified genomic regions | tabulateReads tabulateReads,BamViews,character_OR_NULL,logical,function-method tabulateReads,BamViews,character_OR_NULL,missing,missing-method tabulateReads,BamViews,missing,missing,missing-method |
| scan BAM files for total read counts | totalReadCounts totalReadCounts,BamViews-method |