Package: ribosomeProfilingQC 1.17.0

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]

# Install 'ribosomeProfilingQC' in R:

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

On BioConductor:ribosomeProfilingQC-1.17.0(bioc 3.20)ribosomeProfilingQC-1.16.0(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

36 exports 1.00 score 181 dependencies 1 mentions

Last updated 2 months agofrom:df792aa208

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 annotate AnnotationDbi aroma.light askpass base64enc BH Biobase BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel biomaRt Biostrings bit bit64 bitops blob BSgenome bslib cachem caTools cli clipr cluster CNEr codetools colorspace colourpicker commonmark cpp11 crayon curl DBI dbplyr DelayedArray deldir digest DirichletMultinomial dplyr EDASeq edgeR evaluate fansi farver fastmap filelock fontawesome formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggExtra ggfittext ggplot2 ggrepel glue GO.db 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 locfit magrittr markdown MASS Matrix MatrixGenerics matrixStats memoise mgcv mime miniUI motifStack munsell nlme openssl pillar pixmap pkgconfig plogr plyr png poweRlaw pracma prettyunits progress promises purrr pwalign R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen RCurl readr reshape2 restfulr Rhtslib rjson rlang rmarkdown Rsamtools RSQLite Rsubread rtracklayer RUVSeq S4Arrays S4Vectors sass scales seqLogo shades shiny shinyjs ShortRead snow sourcetools sp SparseArray statmod stringi stringr SummarizedExperiment sys TFBSTools TFMPvalue tibble tidyr tidyselect tinytex txdbmaker tzdb UCSC.utils utf8 vctrs viridisLite vroom withr xfun XML xml2 xtable XVector yaml zlibbioc

ribosomeProfilingQC Guide

Jianhong Ou, Mariah Hoye

Rendered fromribosomeProfilingQC.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2024-04-12
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