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bakR
View on CRAN: Click
here
Download and install bakR package within the R console
Install from CRAN:
install.packages("bakR")
Install from Github:
library("remotes")
install_github("cran/bakR")
Install by package version:
library("remotes")
install_version("bakR", "1.0.1")
Attach the package and use:
library("bakR")
Maintained by
Isaac Vock
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2022-10-10
Latest Update: 2023-06-29
Description:
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) ).
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.
How to cite:
Isaac Vock (2022). bakR: Analyze and Compare Nucleotide Recoding RNA Sequencing Datasets. R package version 1.0.1, https://cran.r-project.org/web/packages/bakR
Previous versions and publish date:
Other packages that cited bakR R package
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Other R packages that bakR depends,
imports, suggests or enhances
Functions, R codes and Examples using
the bakR R package
Some associated functions: CorrectDropout . DissectMechanism . FnPCA . FnPCA2 . GS_table . GSprocessing . Heatmap_kdeg . NSSHeat . QC_checks . QuantifyDropout . Simulate_bakRData . Simulate_relative_bakRData . TL_stan . VisualizeDropout . avg_and_regularize . bakR-package . bakRData . bakRFit . bakRFnData . cB_small . cBprocess . fast_analysis . fn_process . fns . metadf . new_bakRData . new_bakRFnData . plotMA . plotVolcano . reliableFeatures . validate_bakRData . validate_bakRFnData .
Some associated R codes: Dropout_correction.R . Fast_analysis.R . Fitting_Models.R . GS_table_data.R . GSprocessing.R . NSSHeat.R . QC.R . Simulations.R . TL_stan.R . Visualizations.R . bakR-package.R . bakRData.R . cB_small_data.R . cBprocessing.R . fns_data.R . metadf_data.R . stanmodels.R . Full bakR package functions and examples
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