Subset of fraction new estimates for dataset published by Luo et al. (2020).
Fraction new estimates, uncertainties, and read counts are included for 300
genes to keep the file size small.

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

fns function

A dataframe with 1,800 rows and 5 variables. Input to <code>bakRFndata</code><dl>
<dt>sample</dt>
<dd>Sample name</dd><dt>XF</dt>
<dd>Name of feature (e.g., ENSEMBL gene ID)</dd><dt>fn</dt>
<dd>Estimate of fraction of reads from feature that were new</dd><dt>se</dt>
<dd>Uncertainty in fraction new estimate (optional in bakRFnData)</dd><dt>n</dt>
<dd>Number of sequencing reads</dd>
</dl>

Format

Example fraction news (fns) data frame — fns

A dataframe with 1,800 rows and 5 variables. Input to <code>bakRFndata</code><dl>
<dt>sample</dt>
<dd>Sample name</dd>

<dt>XF</dt>
<dd>Name of feature (e.g., ENSEMBL gene ID)</dd>

<dt>fn</dt>
<dd>Estimate of fraction of reads from feature that were new</dd>

<dt>se</dt>
<dd>Uncertainty in fraction new estimate (optional in bakRFnData)</dd>

<dt>n</dt>
<dd>Number of sequencing reads</dd>


</dl>

fns: Example fraction news (fns) data frame

Description

Usage

Arguments

Format

References

Examples