metadf

metadf dataframe describing the data present in the cB file that
can be loaded with <code>data(cB_small)</code>. The contents are discussed
in great detail in the Getting_started vignette.

Several implementations of a novel Bayesian hierarchical statistical model of nucleotide
recoding RNA-seq experiments (NR-seq; TimeLapse-seq, SLAM-seq, TUC-seq, etc.)
for analyzing and comparing NR-seq datasets (see 'Vock and Simon' (2023) <doi:10.1261/rna.079451.122>).
NR-seq is a powerful extension of RNA-seq that provides information about the kinetics
of RNA metabolism (e.g., RNA degradation rate constants), which is notably lacking
in standard RNA-seq data. The statistical model makes maximal use of these high-throughput
datasets by sharing information across transcripts to significantly improve
uncertainty quantification and increase statistical power. 'bakR' includes a maximally
efficient implementation of this model for conservative initial investigations of datasets. 'bakR'
also provides more highly powered implementations using the probabilistic programming language
'Stan' to sample from the full posterior distribution. 'bakR' performs multiple-test
adjusted statistical inference with the output of these model implementations to
help biologists separate signal from background. Methods to automatically visualize key
results and detect batch effects are also provided.

Isaac Vock

bakR

Analyze and Compare Nucleotide Recoding RNA Sequencing Datasets

metadf function

A dataframe with 6 rows and 2 variables: row names are samples in the corresponding
cB<dl>
<dt>tl</dt>
<dd>time of s4U labeling, in hours</dd><dt>Exp_ID</dt>
<dd>numerical ID of reference and experimental conditions; 1 is reference and 2 is the single experimental condition</dd></dl>

Format

Example meatdf data frame — metadf

A dataframe with 6 rows and 2 variables: row names are samples in the corresponding
cB<dl>
<dt>tl</dt>
<dd>time of s4U labeling, in hours</dd>

<dt>Exp_ID</dt>
<dd>numerical ID of reference and experimental conditions; 1 is reference and 2 is the single experimental condition</dd>



</dl>

metadf: Example meatdf data frame

Description

Usage

Arguments

Format

Examples