Package: RiboProfiling 1.37.0

A. Popa

RiboProfiling: Ribosome Profiling Data Analysis: from BAM to Data Representation and Interpretation

Starting with a BAM file, this package provides the necessary functions for quality assessment, read start position recalibration, the counting of reads on CDS, 3'UTR, and 5'UTR, plotting of count data: pairs, log fold-change, codon frequency and coverage assessment, principal component analysis on codon coverage.

Authors:Alexandra Popa

RiboProfiling_1.37.0.tar.gz
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RiboProfiling.pdf |RiboProfiling.html✨
RiboProfiling/json (API)
NEWS

# Install 'RiboProfiling' in R:

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

Datasets:

cdsPosTransc - Per transcript relative position of start and end codons for dataset ctrlGAlignments
codonDataCtrl - Codon frequency and coverage in ORFs on chromosome 1, for dataset ctrlGAlignments
codonIndexCovCtrl - The read coverage for each codon in ORFs on chromosome 1, for dataset ctrlGAlignments
ctrlGAlignments - Ribosome profiling data on chr1 in human primary BJ fibroblasts control data: PMID: 23594524.

On BioConductor:RiboProfiling-1.37.0(bioc 3.21)RiboProfiling-1.36.0(bioc 3.20)

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

riboseq sequencing coverage alignment qualitycontrol software principalcomponent

4.30 score 8 scripts 371 downloads 11 mentions 12 exports 157 dependencies

Last updated 2 months agofrom:c7c7bd6d2b. Checks:OK: 1 WARNING: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 19 2024
R-4.5-win	WARNING	Dec 19 2024
R-4.5-linux	WARNING	Dec 19 2024
R-4.4-win	WARNING	Dec 19 2024
R-4.4-mac	WARNING	Dec 19 2024
R-4.3-win	WARNING	Dec 19 2024
R-4.3-mac	WARNING	Dec 19 2024

Exports:aroundPromoter codonInfo codonPCA countShiftReads countsPlot histMatchLength orfRelativePos plotSummarizedCov printPCA readStartCov readsToStartOrEnd riboSeqFromBAM

Dependencies:abind AnnotationDbi AnnotationFilter askpass backports base64enc BH Biobase BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel biomaRt Biostrings biovizBase bit bit64 bitops blob BSgenome bslib cachem checkmate chron cli cluster codetools colorspace cpp11 crayon curl data.table DBI dbplyr DelayedArray dichromat digest dplyr ensembldb evaluate fansi farver fastmap filelock fontawesome forcats foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges GGally ggbio ggplot2 ggstats glue graph gridExtra gsubfn gtable highr Hmisc hms htmlTable htmltools htmlwidgets httr httr2 IRanges isoband jquerylib jsonlite KEGGREST knitr labeling lambda.r lattice lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme nnet openssl OrganismDbi patchwork pillar pkgconfig plogr plyr png prettyunits progress ProtGenerics proto purrr R6 rappdirs RBGL RColorBrewer Rcpp RCurl reshape2 restfulr Rhtslib rjson rlang rmarkdown rpart Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors sass scales snow SparseArray sqldf stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex txdbmaker UCSC.utils utf8 VariantAnnotation vctrs viridis viridisLite withr xfun XML xml2 XVector yaml zlibbioc

Analysing Ribo-Seq data with the "RiboProfiling" package

Rendered fromRiboProfiling.Rnwusingknitr::knitron Dec 19 2024.

Last update: 2017-12-11
Started: 2015-10-07

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Returns the flank size around the TSS for the x % CDSs	aroundPromoter
Per transcript relative position of start and end codons for dataset ctrlGAlignments	cdsPosTransc
Codon frequency and coverage in ORFs on chromosome 1, for dataset ctrlGAlignments	codonDataCtrl
The read coverage for each codon in ORFs on chromosome 1, for dataset ctrlGAlignments	codonIndexCovCtrl
Associates the read counts on codons with the codon type for each ORF.	codonInfo
PCA graphs on codon coverage	codonPCA
Apply an offset on the read start along the transcript and returns the coverage on the 5pUTR, CDS, 3pUTR, as well as a matrix of codon coverage per ORF.	countShiftReads
Graphs of sample read counts (quality assesment)	countsPlot
Ribosome profiling data on chr1 in human primary BJ fibroblasts control data: PMID: 23594524.	ctrlGAlignments
Histogram of match length distribution of reads.	histMatchLength
Relative position of the start and stop codon along the transcript	orfRelativePos
Plots the summarized coverage in a specified range (e.g. around TSS) for the specified match sizes	plotSummarizedCov
Plots the PCA scatterplots produced by codonPCA function.	printPCA
Read start coverage around the TSS on the predifined CDSs	readStartCov
Reads in GAlignments converted to either Read Start (5') or End (3') Positions	readsToStartOrEnd
RiboProfiling.	RiboProfiling-package RiboProfiling
Starting from a BAM file path: quality plots, shift ribosome position, coverage on multiple transcript features and on codons.	riboSeqFromBAM