Package: RiboDiPA 1.13.0

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_1.13.0.tar.gz
RiboDiPA_1.13.0.zip(r-4.5)RiboDiPA_1.13.0.zip(r-4.4)RiboDiPA_1.13.0.zip(r-4.3)
RiboDiPA_1.13.0.tgz(r-4.4-arm64)RiboDiPA_1.13.0.tgz(r-4.4-x86_64)RiboDiPA_1.13.0.tgz(r-4.3-arm64)RiboDiPA_1.13.0.tgz(r-4.3-x86_64)
RiboDiPA_1.13.0.tar.gz(r-4.5-noble)RiboDiPA_1.13.0.tar.gz(r-4.4-noble)
RiboDiPA_1.13.0.tgz(r-4.4-emscripten)RiboDiPA_1.13.0.tgz(r-4.3-emscripten)
RiboDiPA.pdf |RiboDiPA.html✨
RiboDiPA/json (API)
NEWS

# 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-1.13.0(bioc 3.20)RiboDiPA-1.12.0(bioc 3.19)

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

bioconductor-package

12 exports 0.71 score 140 dependencies

Last updated 2 months agofrom:0e3a4575b3

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

Dependencies:abind AnnotationDbi askpass backports BH Biobase BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings bit bit64 bitops blob cachem callr checkmate cli codetools colorspace cpp11 crayon curl data.table DBI dbplyr DelayedArray densEstBayes desc DESeq2 digest distributional doParallel dplyr elitism fansi farver fastmap filelock foreach formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData 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 munsell nlme numDeriv openssl pillar pkgbuild pkgconfig plogr 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 scales snow SparseArray StanHeaders stringi stringr SummarizedExperiment sys tensorA tibble tidyr tidyselect txdbmaker UCSC.utils utf8 vctrs viridisLite withr XML xml2 XVector yaml zlibbioc

RiboDiPA R package

Keren Li, Matthew Hope, Xiaozhong A. Wang, Ji-Ping Wang

Rendered fromRiboDiPA.Rmdusingknitr::rmarkdownon Jun 30 2024.

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