Package: DNAshapeR 1.35.0

Tsu-Pei Chiu

DNAshapeR: High-throughput prediction of DNA shape features

DNAhapeR is an R/BioConductor package for ultra-fast, high-throughput predictions of DNA shape features. The package allows to predict, visualize and encode DNA shape features for statistical learning.

Authors:Tsu-Pei Chiu and Federico Comoglio

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DNAshapeR.pdf |DNAshapeR.html✨
DNAshapeR/json (API)
NEWS

# Install 'DNAshapeR' in R:

install.packages('DNAshapeR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Uses libs:

c++– GNU Standard C++ Library v3

On BioConductor:DNAshapeR-1.33.0(bioc 3.20)DNAshapeR-1.32.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

structuralprediction dna3dstructure software

4.59 score 39 scripts 216 downloads 7 exports 25 dependencies

Last updated 23 days agofrom:090780d23f. Checks:OK: 1 NOTE: 8. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 30 2024
R-4.5-win-x86_64	NOTE	Oct 30 2024
R-4.5-linux-x86_64	NOTE	Oct 30 2024
R-4.4-win-x86_64	NOTE	Oct 30 2024
R-4.4-mac-x86_64	NOTE	Oct 30 2024
R-4.4-mac-aarch64	NOTE	Oct 30 2024
R-4.3-win-x86_64	NOTE	Oct 30 2024
R-4.3-mac-x86_64	NOTE	Oct 30 2024
R-4.3-mac-aarch64	NOTE	Oct 30 2024

Exports:encodeSeqShape getFasta getShape heatShape plotShape readShape trackShape

Dependencies:askpass BiocGenerics Biostrings crayon curl dotCall64 fields GenomeInfoDb GenomeInfoDbData GenomicRanges httr IRanges jsonlite maps mime openssl R6 Rcpp S4Vectors spam sys UCSC.utils viridisLite XVector zlibbioc

Bioconductor Package Vignette

Tsu-Pei Chiu, Federico Comoglio and Remo Rohs

Rendered fromDNAshapeR.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2018-08-30
Started: 2015-10-22

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
DNAshapeR package for high-throughput prediction of DNA shape features	DNAshapeR-package
Convert fasta file to methylated file format	convertMethFile
encode Hbond	encodeKmerHbond
Encode k-mer DNA sequence features	encodeKMerSeq
Encode n-st order shape features DNAshapeR can be used to generate feature vectors for a user-defined model. The model can be a shape model. There are four structural parameters including MGW, Roll, ProT and HelT. The second order shape features are product terms of values for the same category of shape features at adjacent positions.	encodeNstOrderShape
Encode k-mer DNA sequence and n-th order DNA Shape features	encodeSeqShape
Extract fasta sequence given a set of genomic intervals and a reference genome.	getFasta
Predict DNA shape from a FASTA file	getShape
Plot heatmap of DNA shape features	heatShape
Min-Max normalization	normalize
Normalize n-st order shape features	normalizeShape
Plot metaprofiles of DNA shape features	plotShape
Read the position fasta file	readNonStandardFastaFile
Read (parse) DNA shape predictions	readShape
Plot track view of DNA shape features	trackShape