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DepLogo (version 1.0)

Dependency Logo

Description

Plots dependency logos from a set of input sequences.

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Version

Install

install.packages('DepLogo')

Monthly Downloads

232

Version

1.0

License

GPL-3

Maintainer

Jan Grau

Last Published

March 13th, 2019

Functions in DepLogo (1.0)

logo

Sequence logo
plotBlocks

Plots blocks of data
getDeps

Compute dependencies between positions
plotDepmatrix

Plot a matrix representation of dependency values.
plotDeplogo

Plot a dependency logo
plotDeparcs

Plot a graph representation of dependency values.
filterColumns

Filter data columns by some filter function
filter.by.gaps

Filter columns (sequence positions) by gaps
replaceColors

Replace colors in DLData object
alphabet.protein.gap

Amino acid alphabet with gaps
filter.by.conservation

Filter columns (sequence positions) by conservation
revcom

Reverse complement
subBoxes

Plot weights as boxplots
filter.by.dependencies

Filter columns (sequence positions) by dependency
subLines

Plot weights as lines
partition

Parition data by most inter-dependent positions
getPWM

Position weight matrix from DLData object
suggestColors

Suggest colors for symbols
summary.DLData

Summarizing DLData objects
colorchart

Plot a colorchart representation of a set of sequences.
alphabet.rna

RNA alphabet
alphabet.protein

Amino acid alphabet
alphabet.dna.gap

DNA alphabet with gaps
alphabet.dna

DNA alphabet
alphabet.rna.gap

RNA alphabet with gaps
Alphabet

built alphabet
deprects

Rectangles of averaged colors
DLData

Create DLData object