Introduction | Building the sceUpstr object | Checking a finding of Harbison et al.
Package: harbChIP 1.50.0
VJ Carey
harbChIP: Experimental Data Package: harbChIP
data from a yeast ChIP-chip experiment
Authors:
harbChIP_1.50.0.tar.gz
harbChIP_1.50.0.tar.gz(r-4.7-any)harbChIP_1.50.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
harbChIP/json (API)
| # Install 'harbChIP' in R: |
| install.packages('harbChIP', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
On BioConductor:harbChIP-1.51.0(data/experiment 3.24)harbChIP-1.50.0(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_datasequencingdatadatapkg
Last updated from:30bc4a9e1c (on RELEASE_3_23). Checks:1 ERROR, 2 NOTE, 1 OK. Indexed: no.
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 | 118 | ||
| linux-devel | NOTE | 214 | ||
| source / vignettes | OK | 180 | ||
| linux-release | NOTE | 185 |
Exports:allhexbuildUpstreamSeqs2chkAllUSchkMotif4TFgetUpstreamkeysNmersorganismseqsshow
Dependencies:BiobaseBiocGenericsBiostringscrayongenericsIRangesS4VectorsSeqinfoXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| utility function: get all hexamers in upstream sequence for an ORF | allhex |
| workflow component - build an upstreamSeqs instance from a FASTA read | buildUpstreamSeqs2 |
| analyze relationship between motif frequency and binding intensity for selected motif and TF | chkAllUS chkMotif4TF |
| Experimental Data Package: harbChIP | harbChIP |
| Biostrings representations of S. cerevisiae upstream regions | sceUpstr |
| Class "upstreamSeqs" | getUpstream keys keys,upstreamSeqs-method Nmers Nmers,numeric,character,upstreamSeqs-method organism organism,upstreamSeqs-method seqs seqs,upstreamSeqs-method show,upstreamSeqs-method upstreamSeqs-class |
