RiboProfiling specifications

Information


Unique identifier OMICS_12936
Name RiboProfiling
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data RiboProfiling can start with a path to a ribo-seq (or other type of) BAM to be analyzed. A list of multiple BAM files can also be provided. BAM files from either bowtie/tophat, STAR, and Lifescope (Solid), single- and paired-end have been validated.
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.10.0
Stability Stable
Requirements
plyr, grid, BiocGenerics, IRanges, GenomicRanges, Rsamtools, testthat, S4Vectors, GenomeInfoDb, Biostrings, rtracklayer, BiocStyle, GenomicAlignments, SummarizedExperiment, ggplot2, BSgenome.Hsapiens.UCSC.hg19, GenomicFeatures, data.table, knitr, sqldf, reshape2, TxDb.Hsapiens.UCSC.hg19.knownGene, ggbio, R(>=3.2.2)
Maintained Yes

Versioning


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Documentation


Maintainer


  • person_outline Alexandra Popa <>

Publication for RiboProfiling

RiboProfiling in publications

 (4)
PMCID: 5725899
PMID: 29228904
DOI: 10.1186/s12864-017-4362-6

[…] we observed a strong 3-nt periodicity in 29-nt footprints, with up to 12-nt upstream of the aug start site covered by ribosome footprints (12-nt offset) (fig. ). similar offsets were obtained using riboprofiling [], a bioconductor package for processing ribo-seq data (additional file : figure s1). unlike rna-seq reads that sometimes contain reads aligning to intronic regions, ribosome […]

PMCID: 5314775
PMID: 27923997
DOI: 10.1093/nar/gkw1190

[…] of multiple splice isoforms and repetitive regions and rfoot () uses riboseq data to predict non-ribosome protected rna sites. additional riboseq specific pipelines include proteoformer () and riboprofiling ()., while the use of ribosome profiling has been reviewed extensively, see (–), this review focuses on how riboseq has been used to characterize the mechanisms of initiation, […]

PMCID: 4494051
PMID: 26002864
DOI: 10.1093/gbe/evv098

[…] this would explain their lack of ribosomal association in the profiling data despite evidence for protein presence in other studies. all five genes showing moderate evidence for translation based on riboprofiling were also upgraded based on strong literature evidence for protein translation. annotates each addition gene based both on ribosomal profiling evidence for translation, and on total […]

PMCID: 4359382
PMID: 25233276
DOI: 10.7554/eLife.03523.027

[…] bar graph counting the number of blastp and blastx hits in lncrna-noribo, lncrna-ribo, and codrna, separately, for each species., it is unclear why the starved conditions () were used in the yeast riboprofiling data. starvation represses translation and therefore makes the data unreliable as a marker of translation. this should therefore be redone, perhaps with the rich media conditions of , […]


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RiboProfiling institution(s)
Institut de Pharmacologie Moléculaire et Cellulaire, University Nice Sophia Antipolis and CNRS, Sophia- Antipolis, Nice, France

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