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DepLogo (version 1.2.2)

Dependency Logo

Description

Plots dependency logos from a set of aligned input sequences.

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Version

Install

install.packages('DepLogo')

Monthly Downloads

220

Version

1.2.2

License

GPL-3

Maintainer

Jan Grau

Last Published

October 9th, 2025

Functions in DepLogo (1.2.2)

filterColumns

Filters data columns by some filter function
suggestColors

Suggests colors for symbols
revcom

Reverse complement
replaceColors

Replaces colors in DLData object
summary.DLData

Summarizing DLData objects
subLines

Plots weights as lines
subBoxes

Plots weights as boxplots
plotDeplogo

Plot a dependency logo
plotDepmatrix

Plots a matrix representation of dependency values
alphabet.dna

DNA alphabet
colorchart

Plots a colorchart representation of a set of sequences
Alphabet

built alphabet
deprects

Rectangles of averaged colors
plotBlocks

Plots blocks of data
partition

Paritions data by most inter-dependent positions
plotDeparcs

Plots a graph representation of dependency values
logo

Sequence logo
DLData

Create DLData object
getPWM

Position weight matrix from DLData object
getDeps

Compute dependencies between positions
filter.by.gaps

Filters columns (sequence positions) by gaps
alphabet.rna.gap

RNA alphabet with gaps
alphabet.protein

Amino acid alphabet
alphabet.protein.gap

Amino acid alphabet with gaps
alphabet.dna.gap

DNA alphabet with gaps
alphabet.rna

RNA alphabet
filter.by.conservation

Filters columns (sequence positions) by conservation
filter.by.dependencies

Filters columns (sequence positions) by dependency