Package: ribor 1.25.0

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]

ribor_1.25.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ribor/json (API)

# Install 'ribor' in R:

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

On BioConductor:ribor-1.25.0(bioc 3.24)ribor-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.

software infrastructure

4.64 score 44 scripts 370 downloads 39 exports 39 dependencies

Last updated from:aad8c146fd. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	160
linux-devel-x86_64	NOTE	275
source / vignettes	OK	241
linux-release-x86_64	NOTE	212
macos-release-arm64	NOTE	159
macos-oldrel-arm64	NOTE	118
windows-devel	NOTE	146
windows-release	NOTE	136
windows-oldrel	NOTE	157
wasm-release	OK	124

Exports:alias_hash experiment_info experiments format_version get_coverage get_experiments get_info get_internal_region_coordinates get_internal_region_lengths get_length_distribution get_metadata get_metagene get_original_region_coordinates get_original_region_lengths get_reference_names get_region_coordinates get_region_counts get_region_lengths get_rnaseq get_tidy_metagene has_metadata left_span length_max length_min length_offset metagene_radius original_hash path plot_length_distribution plot_metagene plot_region_counts reference rename_default rename_transcripts Ribo right_span set_aliases show transcript_info

Dependencies:BiocGenerics biocmake cli cpp11 dir.expiry dplyr farver filelock generics ggplot2 glue gtable hash isoband labeling lifecycle magrittr pillar pkgconfig purrr R6 RColorBrewer rhdf5 rhdf5filters Rhdf5lib rlang S4Vectors S7 scales stringi stringr tibble tidyr tidyselect utf8 vctrs viridisLite withr yaml

A Walk-through of RiboR

Rendered fromribor.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Retrieves the coverage data for a given transcript	get_coverage
Provides a list of experiments from a .ribo file	get_experiments
Get information about the .ribo file	get_info
Retrieves the region stop and start coordinates	get_internal_region_coordinates
Returns the overall length of each region with UTR Junctions	get_internal_region_lengths
Retrieves the length distribution of a given region	get_length_distribution
Retrieves the metadata of an experiment	get_metadata
Retrieves the metagene data from a .ribo file	get_metagene
Retrieves the region stop and start coordinates	get_original_region_coordinates
Returns the overall length of each region	get_original_region_lengths
Retrieves a list of reference names	get_reference_names
Retrieves the region stop and start coordinates	get_region_coordinates
Retrieves the region counts from a .ribo file	get_region_counts
Returns the overall length of each region with UTR Junctions	get_region_lengths
Information on the RNA-Seq data of the experiments, if any	get_rnaseq
Retrieves the metagene data in a tidy format	get_tidy_metagene
Plots the length distribution	plot_length_distribution
Plots the metagene coverage data	plot_metagene
Plots the region counts of UTR5, CDS, and UTR3	plot_region_counts
Rename function for appris transcriptome naming convention	rename_default
Renames the transcripts	rename_transcripts
Ribo Class	alias_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 files	ribor
Set the aliases of a ribo object	set_aliases