DepLogo v1.0
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Dependency Logo
Plots dependency logos from a set of input sequences.
Functions in DepLogo
| Name | Description | |
| 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 | |
| No Results! | ||
Vignettes of DepLogo
| Name | ||
| DepLogo.Rmd | ||
| annotated_deplogo.png | ||
| references.bib | ||
| No Results! | ||
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Details
| Type | Package |
| License | GPL-3 |
| NeedsCompilation | no |
| RoxygenNote | 6.0.1 |
| VignetteBuilder | knitr |
| Packaged | 2019-03-13 13:30:19 UTC; dev |
| Repository | CRAN |
| Date/Publication | 2019-03-13 16:23:27 UTC |
| suggests | knitr , testthat |
| Contributors | Jens Keilwagen, Martin Nettling |
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