Package: ribosomeProfilingQC 1.25.1

Jianhong Ou

ribosomeProfilingQC: Ribosome Profiling Quality Control

Ribo-Seq (also named ribosome profiling or footprinting) measures translatome (unlike RNA-Seq, which sequences the transcriptome) by direct quantification of the ribosome-protected fragments (RPFs). This package provides the tools for quality assessment of ribosome profiling. In addition, it can preprocess Ribo-Seq data for subsequent differential analysis.

Authors:Jianhong Ou [aut, cre], Mariah Hoye [aut]

ribosomeProfilingQC_1.25.1.tar.gz
ribosomeProfilingQC_1.25.1.zip(r-4.7)ribosomeProfilingQC_1.25.1.zip(r-4.6)ribosomeProfilingQC_1.25.1.zip(r-4.5)
ribosomeProfilingQC_1.25.1.tgz(r-4.6-any)ribosomeProfilingQC_1.25.1.tgz(r-4.5-any)
ribosomeProfilingQC_1.25.1.tar.gz(r-4.7-any)ribosomeProfilingQC_1.25.1.tar.gz(r-4.6-any)
ribosomeProfilingQC_1.25.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ribosomeProfilingQC/json (API)

# Install 'ribosomeProfilingQC' in R:

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

On BioConductor:ribosomeProfilingQC-1.25.0(bioc 3.24)ribosomeProfilingQC-1.24.0(bioc 3.23)

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

riboseq sequencing generegulation qualitycontrol visualization coverage

4.45 score 14 scripts 404 downloads 1 mentions 36 exports 168 dependencies

Last updated from:5623c88a81. Checks:1 WARNING, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	303
linux-devel-x86_64	OK	696
source / vignettes	OK	516
linux-release-x86_64	OK	692
macos-release-arm64	OK	343
macos-oldrel-arm64	OK	337
windows-devel	OK	564
windows-release	OK	571
windows-oldrel	OK	580
wasm-release	OK	254

Exports:assignReadingFrame codonBias codonUsage countReads coverageDepth coverageRates cvgd estimatePsite filterCDS FLOSS frameCounts getFPKM getORFscore getPsiteCoordinates metaPlot normalizeTEbyLoess normBy normByRUVs PAmotif plotDistance2Codon plotFrameDensity plotSpliceEvent plotTE plotTranscript prepareCDS readsDistribution readsEndPlot readsLenToKeep ribosomeReleaseScore shiftReadsByFrame show simulateRPF spliceEvent strandPlot summaryReadsLength translationalEfficiency

Dependencies:abind ade4 AnnotationDbi aroma.light askpass base64enc BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel biomaRt Biostrings bit bit64 bitops blob BSgenome bslib cachem caTools cigarillo cli cluster codetools colourpicker commonmark cpp11 crayon curl DBI dbplyr DelayedArray deldir digest DirichletMultinomial dplyr EDASeq edgeR evaluate farver fastmap filelock fontawesome formatR fs futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggExtra ggfittext ggplot2 ggrepel glue gridtext gtable gtools highr hms htmltools htmlwidgets httpuv httr httr2 hwriter interp IRanges isoband jpeg jquerylib jsonlite KEGGREST knitr labeling lambda.r later lattice latticeExtra lifecycle limma litedown locfit magrittr markdown MASS Matrix MatrixGenerics matrixStats memoise mime miniUI motifStack openssl otel pillar pixmap pkgconfig png prettyunits progress promises purrr pwalign R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen RCurl restfulr Rhtslib rjson rlang rmarkdown Rsamtools RSQLite Rsubread rtracklayer RUVSeq S4Arrays S4Vectors S7 sass scales Seqinfo seqLogo shades shiny shinyjs ShortRead snow sourcetools sp SparseArray statmod stringi stringr SummarizedExperiment sys TFBSTools TFMPvalue tibble tidyr tidyselect tinytex txdbmaker UCSC.utils utf8 vctrs viridisLite withr xfun XML xml2 xtable XVector yaml

ribosomeProfilingQC Guide

Rendered fromribosomeProfilingQC.Rmdusingknitr::rmarkdown

Last update: 2025-05-02
Started: 2019-10-29

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Assign reading frame	assignReadingFrame
Codon usage bias	codonBias
Start or Stop codon usage	codonUsage
Extract counts for RPFs and RNAs	countReads
Extract coverage depth for gene level or transcript level	coverageDepth
Calculate coverage rate	coverageRates
Class '"cvgd"'	$,cvgd-method $<-,cvgd-method cvgd cvgd-class show,cvgd-method [[,cvgd,ANY,ANY-method [[<-,cvgd,ANY,ANY,ANY-method
Estimate P site position	estimatePsite
Filter CDS by size	filterCDS
Fragment Length Organization Similarity Score (FLOSS)	FLOSS
Extract counts for gene level or transcript level	frameCounts
Get FPKM values for counts	getFPKM
Calculate ORFscore	getORFscore
Get P site coordinates	getPsiteCoordinates
barplot by ggplot2	ggBar
Metagene analysis plot	metaPlot
Normalize the TE by Loess	normalizeTEbyLoess
Normalization by edgeR, DESeq2 or RUVSeq	normBy
Normalization by RUVSeq	normByRUVs
Metaplot of P site distribution	PAmotif
Metaplot of P site distribution	plotDistance2Codon
Plot density for each reading frame	plotFrameDensity
Plot splice event	plotSpliceEvent
Plot translational efficiency	plotTE
Plot reads P site abundance for a specific transcript	plotTranscript
Prepare CDS	prepareCDS
Plot reads distribution in genomic elements	readsDistribution
Plot start/stop windows	readsEndPlot
Get reads length to keep by cutoff percentage	readsLenToKeep
Ribosome Release Score (RRS)	ribosomeReleaseScore
Shift reads by reading frame	shiftReadsByFrame
Simulation function	simulateRPF
Get splicing events	spliceEvent
Plot the distribution of reads in sense and antisense strand	strandPlot
Summary the reads lengths	summaryReadsLength
Translational Efficiency	translationalEfficiency