Package: ribor 1.19.0

Michael Geng

ribor: An R Interface for Ribo Files

The ribor package provides an R Interface for .ribo files. It provides functionality to read the .ribo file, which is of HDF5 format, and performs common analyses on its contents.

Authors:Michael Geng [cre, aut], Hakan Ozadam [aut], Can Cenik [aut]

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ribor.pdf |ribor.html✨
ribor/json (API)
NEWS

# Install 'ribor' in R:
install.packages('ribor', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

On BioConductor:ribor-1.19.0(bioc 3.21)ribor-1.18.0(bioc 3.20)

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

softwareinfrastructure

4.51 score 32 scripts 134 downloads 39 exports 43 dependencies

Last updated 23 days agofrom:390801c0da. Checks:OK: 1 NOTE: 4 WARNING: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 31 2024
R-4.5-winNOTEOct 31 2024
R-4.5-linuxNOTEOct 31 2024
R-4.4-winNOTEOct 31 2024
R-4.4-macWARNINGOct 31 2024
R-4.3-winNOTEOct 31 2024
R-4.3-macWARNINGOct 31 2024

Exports:alias_hashexperiment_infoexperimentsformat_versionget_coverageget_experimentsget_infoget_internal_region_coordinatesget_internal_region_lengthsget_length_distributionget_metadataget_metageneget_original_region_coordinatesget_original_region_lengthsget_reference_namesget_region_coordinatesget_region_countsget_region_lengthsget_rnaseqget_tidy_metagenehas_metadataleft_spanlength_maxlength_minlength_offsetmetagene_radiusoriginal_hashpathplot_length_distributionplot_metageneplot_region_countsreferencerename_defaultrename_transcriptsRiboright_spanset_aliasesshowtranscript_info

Dependencies:BiocGenericsclicolorspacecpp11dplyrfansifarvergenericsggplot2gluegtablehashisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigpurrrR6RColorBrewerrhdf5rhdf5filtersRhdf5librlangS4Vectorsscalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithryaml

A Walk-through of RiboR

Michael Geng, Hakan Ozadam, Can Cenik

Rendered fromribor.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2021-05-14
Started: 2019-11-23

Readme and manuals

Help Manual

Help pageTopics
Retrieves the coverage data for a given transcriptget_coverage
Provides a list of experiments from a .ribo fileget_experiments
Get information about the .ribo fileget_info
Retrieves the region stop and start coordinatesget_internal_region_coordinates
Returns the overall length of each region with UTR Junctionsget_internal_region_lengths
Retrieves the length distribution of a given regionget_length_distribution
Retrieves the metadata of an experimentget_metadata
Retrieves the metagene data from a .ribo fileget_metagene
Retrieves the region stop and start coordinatesget_original_region_coordinates
Returns the overall length of each regionget_original_region_lengths
Retrieves a list of reference namesget_reference_names
Retrieves the region stop and start coordinatesget_region_coordinates
Retrieves the region counts from a .ribo fileget_region_counts
Returns the overall length of each region with UTR Junctionsget_region_lengths
Information on the RNA-Seq data of the experiments, if anyget_rnaseq
Retrieves the metagene data in a tidy formatget_tidy_metagene
Plots the length distributionplot_length_distribution
Plots the metagene coverage dataplot_metagene
Plots the region counts of UTR5, CDS, and UTR3plot_region_counts
Rename function for appris transcriptome naming conventionrename_default
Renames the transcriptsrename_transcripts
Ribo Classalias_hash alias_hash,Ribo-method experiments experiments,Ribo-method experiment_info experiment_info,Ribo-method format_version format_version,Ribo-method has_metadata has_metadata,Ribo-method left_span left_span,Ribo-method length_max length_max,Ribo-method length_min length_min,Ribo-method length_offset length_offset,Ribo-method metagene_radius metagene_radius,Ribo-method original_hash original_hash,Ribo-method path path,Ribo-method reference reference,Ribo-method Ribo Ribo-class right_span right_span,Ribo-method show,Ribo-method transcript_info transcript_info,Ribo-method
ribor: A package for reading .ribo filesribor
Set the aliases of a ribo objectset_aliases