Package: RiboDiPA 1.21.0

Ji-Ping Wang

RiboDiPA: Differential pattern analysis for Ribo-seq data

This package performs differential pattern analysis for Ribo-seq data. It identifies genes with significantly different patterns in the ribosome footprint between two conditions. RiboDiPA contains five major components including bam file processing, P-site mapping, data binning, differential pattern analysis and footprint visualization.

Authors:Keren Li [aut], Matt Hope [aut], Xiaozhong Wang [aut], Ji-Ping Wang [aut, cre]

RiboDiPA_1.21.0.tar.gz
RiboDiPA_1.21.0.zip(r-4.7)RiboDiPA_1.21.0.zip(r-4.6)RiboDiPA_1.21.0.zip(r-4.5)
RiboDiPA_1.21.0.tgz(r-4.6-x86_64)RiboDiPA_1.21.0.tgz(r-4.6-arm64)RiboDiPA_1.21.0.tgz(r-4.5-x86_64)RiboDiPA_1.21.0.tgz(r-4.5-arm64)
RiboDiPA_1.21.0.tar.gz(r-4.7-arm64)RiboDiPA_1.21.0.tar.gz(r-4.7-x86_64)RiboDiPA_1.21.0.tar.gz(r-4.6-arm64)RiboDiPA_1.21.0.tar.gz(r-4.6-x86_64)
RiboDiPA_1.21.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
RiboDiPA/json (API)

# Install 'RiboDiPA' in R:

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

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

data.binned - An example of binned P-sites data
data.psite - An example of P-site coverage data
result.exon - An example of exon-level differential pattern analysis result
result.pst - An example of differential pattern analysis result

On BioConductor:RiboDiPA-1.21.0(bioc 3.24)RiboDiPA-1.20.0(bioc 3.23)

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

riboseq geneexpression generegulation differentialexpression sequencing coverage alignment rnaseq immunooncology qualitycontrol dataimport software normalization cpp

4.00 score 1 scripts 12 exports 138 dependencies

Last updated from:3960dad2f2. Checks:1 ERROR, 11 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	225
linux-devel-arm64	NOTE	640
linux-devel-x86_64	NOTE	788
source / vignettes	OK	561
linux-release-arm64	NOTE	702
linux-release-x86_64	NOTE	788
macos-release-arm64	NOTE	505
macos-release-x86_64	NOTE	1058
macos-oldrel-arm64	NOTE	450
macos-oldrel-x86_64	NOTE	855
windows-devel	NOTE	709
windows-release	NOTE	755
windows-oldrel	NOTE	721
wasm-release	OK	200

Exports:binTrack bpTrack dataBinning diffPatternTest diffPatternTestExon exonTrack normFactor plotTest plotTrack psiteCal psiteMapping RiboDiPA

Dependencies:abind AnnotationDbi askpass backports BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings bit bit64 bitops blob cachem callr checkmate cigarillo cli codetools cpp11 crayon curl data.table DBI dbplyr DelayedArray densEstBayes desc DESeq2 distributional doParallel dplyr elitism farver fastmap filelock foreach formatR futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gridExtra gtable hms httr httr2 inline IRanges isoband iterators jsonlite KEGGREST labeling lambda.r lattice lifecycle locfit loo magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime nlme numDeriv openssl otel pillar pkgbuild pkgconfig plyr png posterior prettyunits processx progress ps purrr QuickJSR qvalue R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen RcppParallel RCurl reldist reshape2 restfulr Rhtslib rjson rlang Rsamtools RSQLite rstan rstantools rtracklayer S4Arrays S4Vectors S7 scales Seqinfo snow SparseArray StanHeaders stringi stringr SummarizedExperiment sys tensorA tibble tidyr tidyselect txdbmaker UCSC.utils utf8 vctrs viridisLite withr XML xml2 XVector yaml

RiboDiPA R package

Rendered fromRiboDiPA.Rmdusingknitr::rmarkdown

Last update: 2021-12-29
Started: 2020-04-20

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Visualization: generating tracks for 'igvR' (per bin)	binTrack
Visualization: generating tracks for 'igvR' (per bp)	bpTrack
An example of binned P-sites data	data.binned
An example of P-site coverage data	data.psite
Data binning	dataBinning
Differential pattern analysis of Ribo-seq data	diffPatternTest
Main function for differential pattern analysis of exon-binned Ribo-seq data	diffPatternTestExon
Visualization: generating tracks for 'igvR' (per exon)	exonTrack
Size factors for normalization by sequencing depth	normFactor
Plotting ribosome footprint data from mapped P-sites at the bin level.	plotTest
Plotting ribosome footprint data at the mapped P-site level	plotTrack
P-site position of reads	psiteCal
P-site mapping	psiteMapping
An example of exon-level differential pattern analysis result	result.exon
An example of differential pattern analysis result	result.pst
A wrapper function for the RiboDiPA pipeline	RiboDiPA