Learn R Programming

DepLogo (version 1.2.1)

Dependency Logo

Description

Plots dependency logos from a set of aligned input sequences.

Copy Link

Version

Install

install.packages('DepLogo')

Monthly Downloads

253

Version

1.2.1

License

GPL-3

Maintainer

Jan Grau

Last Published

February 15th, 2024

Functions in DepLogo (1.2.1)

filter.by.gaps

Filters columns (sequence positions) by gaps
plotDeparcs

Plots a graph representation of dependency values
plotDepmatrix

Plots a matrix representation of dependency values
plotBlocks

Plots blocks of data
plotDeplogo

Plot a dependency logo
partition

Paritions data by most inter-dependent positions
revcom

Reverse complement
logo

Sequence logo
replaceColors

Replaces colors in DLData object
filter.by.dependencies

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

Filters columns (sequence positions) by conservation
alphabet.dna.gap

DNA alphabet with gaps
getDeps

Compute dependencies between positions
getPWM

Position weight matrix from DLData object
subBoxes

Plots weights as boxplots
subLines

Plots weights as lines
suggestColors

Suggests colors for symbols
summary.DLData

Summarizing DLData objects
filterColumns

Filters data columns by some filter function
alphabet.rna

RNA alphabet
deprects

Rectangles of averaged colors
colorchart

Plots a colorchart representation of a set of sequences
DLData

Create DLData object
Alphabet

built alphabet
alphabet.protein

Amino acid alphabet
alphabet.protein.gap

Amino acid alphabet with gaps
alphabet.dna

DNA alphabet
alphabet.rna.gap

RNA alphabet with gaps