Package: dStruct 1.19.0

Krishna Choudhary

dStruct: Identifying differentially reactive regions from RNA structurome profiling data

dStruct identifies differentially reactive regions from RNA structurome profiling data. dStruct is compatible with a broad range of structurome profiling technologies, e.g., SHAPE-MaP, DMS-MaPseq, Structure-Seq, SHAPE-Seq, etc. See Choudhary et al., Genome Biology, 2019 for the underlying method.

Authors:Krishna Choudhary [aut, cre], Sharon Aviran [aut]

dStruct_1.19.0.tar.gz
dStruct_1.19.0.zip(r-4.7-any)dStruct_1.19.0.zip(r-4.6-any)dStruct_1.19.0.zip(r-4.5-any)
dStruct_1.19.0.tgz(r-4.6-any)dStruct_1.19.0.tgz(r-4.5-any)
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dStruct_1.19.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
dStruct/json (API)

# Install 'dStruct' in R:

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

Bug tracker:https://github.com/datamaster-kris/dstruct/issues

Datasets:

lai2019 - _Saccharomyces cerevisiae_ Structure-seq data
wan2014 - _Homo sapiens_ PARS data

On BioConductor:dStruct-1.19.0(bioc 3.24)dStruct-1.18.0(bioc 3.23)

statisticalmethod structuralprediction sequencing software

5.13 score 3 stars 15 scripts 381 downloads 3 mentions 11 exports 30 dependencies

Last updated from:952c5900dc. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	182
linux-devel	NOTE	258
source / vignettes	OK	223
linux-release	NOTE	275
macos-release	NOTE	136
macos-oldrel	NOTE	147
windows-devel	NOTE	130
windows-release	NOTE	119
windows-oldrel	NOTE	119
wasm-release	OK	136

Exports:calcDis dCombs dStruct dStructGuided dStructome getCombs getContigRegions getRegions normalizer plotDStructurome twoEightNormalize

Dependencies:BiocGenerics cli cpp11 farver generics ggplot2 glue gtable IRanges isoband labeling lattice lifecycle magrittr plyr purrr R6 RColorBrewer Rcpp reshape2 rlang S4Vectors S7 scales stringi stringr vctrs viridisLite withr zoo

Differential RNA structurome analysis using dStruct

Rendered fromdStruct.Rmdusingknitr::rmarkdown

Last update: 2021-05-23
Started: 2021-02-18

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Calculates d score.	calcDis
Assesses within-group or between-group variation.	dCombs
Performs de novo discovery of differentially reactive regions.	dStruct
Performs guided discovery of differentially reactive regions.	dStructGuided
Performs de novo or guided discovery of differentially reactive regions for transcriptome-wide data.	dStructome
Identifies subgroupings of replicates for assessing within-group and between-group variation.	getCombs
Identifies contiguous regions from a list of nucleotide indices.	getContigRegions
Constructs potential differentially reactive regions.	getRegions
_Saccharomyces cerevisiae_ Structure-seq data	lai2019
Returns normalizer for reactivity vector.	normalizer
Plots differentially reactive regions.	plotDStructurome
Normalizes reactivity vector.	twoEightNormalize
_Homo sapiens_ PARS data	wan2014