RDocumentation
Moon
Learn R
Search all packages and functions
DepLogo (version 1.2.1)
Dependency Logo
Description
Plots dependency logos from a set of aligned input sequences.
Copy Link
Copy
Link to current version
Version
Version
1.2.1
1.2
1.0
Down Chevron
Install
install.packages('DepLogo')
Monthly Downloads
238
Version
1.2.1
License
GPL-3
Maintainer
Jan Grau
Last Published
February 15th, 2024
Functions in DepLogo (1.2.1)
Search functions
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