Package: bakR 1.0.1
bakR: Analyze and Compare Nucleotide Recoding RNA Sequencing Datasets
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.
Authors:
bakR_1.0.1.tar.gz
bakR_1.0.1.zip(r-4.5)bakR_1.0.1.zip(r-4.4)bakR_1.0.1.zip(r-4.3)
bakR_1.0.1.tgz(r-4.4-x86_64)bakR_1.0.1.tgz(r-4.4-arm64)bakR_1.0.1.tgz(r-4.3-x86_64)bakR_1.0.1.tgz(r-4.3-arm64)
bakR_1.0.1.tar.gz(r-4.5-noble)bakR_1.0.1.tar.gz(r-4.4-noble)
bakR.pdf |bakR.html✨
bakR/json (API)
NEWS
# Install 'bakR' in R: |
install.packages('bakR', repos = c('https://simonlabcode.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/simonlabcode/bakr/issues
Last updated 3 days agofrom:77950c1070. Checks:OK: 1 NOTE: 8. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 20 2024 |
R-4.5-win-x86_64 | NOTE | Nov 20 2024 |
R-4.5-linux-x86_64 | NOTE | Nov 20 2024 |
R-4.4-win-x86_64 | NOTE | Nov 20 2024 |
R-4.4-mac-x86_64 | NOTE | Nov 20 2024 |
R-4.4-mac-aarch64 | NOTE | Nov 20 2024 |
R-4.3-win-x86_64 | NOTE | Nov 20 2024 |
R-4.3-mac-x86_64 | NOTE | Nov 20 2024 |
R-4.3-mac-aarch64 | NOTE | Nov 20 2024 |
Exports:bakRDatabakRFitbakRFnDatacBprocessCorrectDropoutDissectMechanismfast_analysisfn_processFnPCAFnPCA2GSprocessingHeatmap_kdegNSSHeatplotMAplotVolcanoQC_checksQuantifyDropoutreliableFeaturesSimulate_bakRDataSimulate_relative_bakRDataVisualizeDropout
Dependencies:abindbackportsbase64encBHbslibcachemcallrcheckmatecliclustercolorspacecpp11data.tabledescdigestdistributionaldplyrevaluatefansifarverfastmapfontawesomeforeignFormulafsgenericsggplot2gluegridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetsinlineisobandjquerylibjsonliteknitrlabelinglatticelifecycleloomagrittrMASSMatrixmatrixStatsmemoisemgcvmimemunsellnlmennetnumDerivpillarpkgbuildpkgconfigposteriorprocessxpspurrrQuickJSRR6rappdirsRColorBrewerRcppRcppEigenRcppParallelrlangrmarkdownrpartrstanrstantoolsrstudioapisassscalesStanHeadersstringistringrtensorAtibbletidyrtidyselecttinytexutf8vctrsviridisviridisLitewithrxfunyaml
GRAND-SLAM output/fn estimates as bakR input
Rendered frombakR-Fn.Rmd
usingknitr::rmarkdown
on Nov 20 2024.Last update: 2023-06-27
Started: 2023-06-27
bakR for people in a hurry
Rendered frombakR-Quickstart.Rmd
usingknitr::rmarkdown
on Nov 20 2024.Last update: 2023-06-27
Started: 2023-06-27
Differential synthesis analysis with bakR and DESeq2
Rendered fromDifferential-Synth.Rmd
usingknitr::rmarkdown
on Nov 20 2024.Last update: 2024-01-13
Started: 2023-06-27
Correcting for dropout
Rendered fromDropout.Rmd
usingknitr::rmarkdown
on Nov 20 2024.Last update: 2024-06-25
Started: 2023-06-27
Differential kinetic analysis with bakR
Rendered fromGetting-Started.Rmd
usingknitr::rmarkdown
on Nov 20 2024.Last update: 2023-06-29
Started: 2021-10-07
Steady-state quasi-independent mechanistic investigations
Rendered fromNSS.Rmd
usingknitr::rmarkdown
on Nov 20 2024.Last update: 2023-06-29
Started: 2023-06-27
Troubleshooting analyses of NR-seq data with bakR
Rendered fromTroubleshooting.Rmd
usingknitr::rmarkdown
on Nov 20 2024.Last update: 2023-06-27
Started: 2023-06-27