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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
Version
1.2.1
1.2
1.0
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Install
install.packages('DepLogo')
Monthly Downloads
238
Version
1.0
License
GPL-3
Maintainer
Jan Grau
Last Published
March 13th, 2019
Functions in DepLogo (1.0)
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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