GS_table

Subset of a GRAND-SLAM main output table from anlaysis of a dataset published in Luo et al. 2020.
Data for 300 randomly selected genes is included to keep 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

GS_table function

A dataframe with 300 rows and 63 variables; each row corresponds to GRAND-SLAM parameter
estimates for a single gene and 6 different samples (4 +s4U and 2 -s4U). Description of
all columns can be found on <a href="https://github.com/erhard-lab/gedi/wiki/GRAND-SLAM">GRAND-SLAM wiki</a>

Format

Example cB data frame — GS_table

A dataframe with 300 rows and 63 variables; each row corresponds to GRAND-SLAM parameter
estimates for a single gene and 6 different samples (4 +s4U and 2 -s4U). Description of
all columns can be found on <a href='https://github.com/erhard-lab/gedi/wiki/GRAND-SLAM'>GRAND-SLAM wiki</a>

GS_table: Example cB data frame

Description

Usage

Arguments

Format

References

Examples