Package: bridger2 0.1.0

bridger2: Genome-Wide RNA Degradation Analysis Using BRIC-Seq Data

BRIC-seq is a genome-wide approach for determining RNA stability in mammalian cells. This package provides a series of functions for performing quality check of your BRIC-seq data, calculation of RNA half-life for each transcript and comparison of RNA half-lives between two conditions.

Authors:Naoto Imamachi [aut, cre]

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bridger2.pdf |bridger2.html✨
bridger2/json (API)

# Install 'bridger2' in R:

install.packages('bridger2', repos = c('https://imamachi-n.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/imamachi-n/bridger2/issues

Datasets:

RNA_halflife_comparison - Test BRIC-seq dataset for RNA half-life comparison
RNA_halflife_comparison_HK - Test BRIC-seq dataset for RNA half-life comparison using House-keeping genes.
RNA_halflife_grubbs_test - Test BRIC-seq dataset for p-value estimation using grubbs test
halflife_table - BRIC-seq result dataset for p-value estimation using grubbs test

On CRAN:

bioinformatics bric-seq half-life ngs rna rpkm-values

3.43 score 3 stars 18 scripts 241 downloads 14 exports 82 dependencies

Last updated 8 years agofrom:18640622a6. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 18 2024
R-4.5-win	OK	Nov 18 2024
R-4.5-linux	OK	Nov 18 2024
R-4.4-win	OK	Nov 18 2024
R-4.4-mac	OK	Nov 18 2024
R-4.3-win	OK	Nov 18 2024
R-4.3-mac	OK	Nov 18 2024

Exports:BridgeRCore BridgeRDatasetChecker BridgeRDataSetFromMatrix BridgeRDataSetFromRaw BridgeReport BridgeRGrubbsTest BridgeRHalfLifeCalc3models BridgeRHalfLifeCalcR2Select BridgeRNormalization BridgeRNormalizationFactors BridgeRNormalizationFactorsHK BridgeRPvalueEvaluation BridgeRResultChecker CalcHalflifeDeviation

Dependencies:askpass base64enc BSDA bslib cachem class cli colorspace commonmark cpp11 crayon crosstalk curl data.table digest dplyr e1071 evaluate fansi farver fastmap fontawesome fs generics ggplot2 glue gtable highr htmltools htmlwidgets httpuv httr isoband jquerylib jsonlite knitr labeling later lattice lazyeval lifecycle magrittr MASS Matrix memoise mgcv mime munsell nlme openssl outliers pillar pkgconfig plotly promises proxy purrr R6 rappdirs RColorBrewer Rcpp rlang rmarkdown sass scales shiny shinydashboard sourcetools stringi stringr sys tibble tidyr tidyselect tinytex utf8 vctrs viridisLite withr xfun xtable yaml

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
BridgeR basic function for calculating RNA half-life from BRIC-seq data	BridgeRCore
BRIC-seq Dataset checker	BridgeRDatasetChecker
Calculate relative RPKM expression from data.table format.	BridgeRDataSetFromMatrix
Calculate relative RPKM expression from raw data.	BridgeRDataSetFromRaw
Shinyapp reporting for drawing RNA decay curve.	BridgeReport
RNA half-life Grubbs test.	BridgeRGrubbsTest
Calculate RNA half-life for each gene using 3model method.	BridgeRHalfLifeCalc3models
Calculate RNA half-life for each gene using R2 selection method.	BridgeRHalfLifeCalcR2Select
Calculate the normalized RPKM for BRIC-seq dataset.	BridgeRNormalization
Calculate normalization factors for BRIC-seq datasets.	BridgeRNormalizationFactors
Calculate normalization factors from house-keeping genes.	BridgeRNormalizationFactorsHK
Calculate Fold-change of RNA half-life and p-value.	BridgeRPvalueEvaluation
BRIC-seq result checker	BridgeRResultChecker
Calculate RNA half-life SD.	CalcHalflifeDeviation
BRIC-seq result dataset for p-value estimation using grubbs test	halflife_table
test BRIC-seq dataset for RNA half-life comparison	RNA_halflife_comparison
test BRIC-seq dataset for RNA half-life comparison using House-keeping genes.	RNA_halflife_comparison_HK
test BRIC-seq dataset for p-value estimation using grubbs test	RNA_halflife_grubbs_test