Package: dagLogo 1.51.0

Jianhong Ou

dagLogo: dagLogo: a Bioconductor package for visualizing conserved amino acid sequence pattern in groups based on probability theory

Visualize significant conserved amino acid sequence pattern in groups based on probability theory.

Authors:Jianhong Ou, Haibo Liu, Alexey Stukalov, Niraj Nirala, Usha Acharya, Lihua Julie Zhu

# Install 'dagLogo' in R:

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

Datasets:

ecoli.proteome - An object of 'Proteome-class' representing the _Escherichia coli_ proteome.
proteome.example - An object of 'Proteome-class' representing the subset of _Drosophila melanogaster_ proteome.
seq.example - An object of 'dagPeptides-class' representing acetylated lysine-containing peptides.

On BioConductor:dagLogo-1.51.0(bioc 3.24)dagLogo-1.50.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

Last updated from:20ded966c2. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	198
linux-devel-x86_64	NOTE	490
source / vignettes	OK	341
linux-release-x86_64	NOTE	476
macos-release-arm64	NOTE	311
macos-oldrel-arm64	NOTE	257
windows-devel	NOTE	360
windows-release	NOTE	375
windows-oldrel	NOTE	407
wasm-release	OK	185

Jianhong Ou, Haibo Liu, Lihua Julie Zhu

Last update: 2020-08-27
Started: 2015-09-24

Help page	Topics
Add a custom coloring or grouping scheme.	addScheme
Get all predefined coloring and grouping schemes	availableSchemes
Build background models for DAU tests	buildBackgroundModel
clean up peptides	cleanPeptides
retrieve color setting for logo visualization	colorsets2
Class 'dagBackground'.	dagBackground dagBackground-class
Visualize daglogo using a heatmap.	dagHeatmap
Create sequence logo.	dagLogo
Class 'dagPeptides'. An S4 class to represent formatted, aligned peptides for dagLogo analysis.	dagPeptides dagPeptides-class
An object of 'Proteome-class' representing the _Escherichia coli_ proteome.	ecoli.proteome
Fetch protein/peptide sequences and create a 'dagPeptides-class' object.	fetchSequence
Format already aligned peptide sequences.	formatSequence
convert group name to a single character	nameHash
prepare proteome for background building	prepareProteome
Create an object of 'Proteome' Class.	prepareProteomeByFTP
Prepare a Proteome object for background building	prepareProteomeByUniProtWS
Class 'Proteome'.	Proteome Proteome-class
An object of 'Proteome-class' representing the subset of _Drosophila melanogaster_ proteome.	proteome.example
An object of 'dagPeptides-class' representing acetylated lysine-containing peptides.	seq.example
Differential usage test of amino acids or amino acid groups.	testDAU
Class 'testDAUresults'.	testDAUresults testDAUresults-class