cB_small

Subset of a cB file from the DCP2 dataset published in Luo et al. 2020.
The original file is large (69 MB), so the example cB file has been
downsampled and contains only 10 genes (rather than 25012). The columns
are described 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

cB_small function

A dataframe with 5788 rows and 5 variables; each row corresponds to a group of sequencing reads<dl>
<dt>sample</dt>
<dd>Sample name</dd><dt>TC</dt>
<dd>Number of T-to-C mutations</dd><dt>nT</dt>
<dd>Number of Ts</dd><dt>XF</dt>
<dd>Name of feature to which the group of reads map; usually a gene name</dd><dt>n</dt>
<dd>Number of identical sequencing reads</dd>
</dl>

Format

Example cB data frame — cB_small

A dataframe with 5788 rows and 5 variables; each row corresponds to a group of sequencing reads<dl>
<dt>sample</dt>
<dd>Sample name</dd>

<dt>TC</dt>
<dd>Number of T-to-C mutations</dd>

<dt>nT</dt>
<dd>Number of Ts</dd>

<dt>XF</dt>
<dd>Name of feature to which the group of reads map; usually a gene name</dd>

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


</dl>

cB_small: Example cB data frame

Description

Usage

Arguments

Format

References

Examples