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MutSeqR - Analysis of Error-Corrected Sequencing Data for Mutation Detection

Standard methods for analysis of mutation data following error- corrected sequencing (ECS) for the purpose of mutagencity assessment. Functions include importing the mutation lists provided by a variant caller, and a set of analytical tools for statistical testing and visualization of mutation data; comparison to COSMIC and/or germline signatures; etc.

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sequencingsomaticmutationvisualizationgenomicvariationdrivermutationstatisticalmethodgenetarget

6.60 score 11 stars 8 scripts 224 downloads

BioTooltipR - Add Bio Tooltips to HTML Reports

Provides lightweight helpers for adding gene and chemical tooltips to 'R Markdown', 'Quarto', 'shiny', 'pkgdown', and other HTML outputs. The package emits small HTML spans with module-specific data attributes and attaches the browser-side 'bio-tooltips' JavaScript and CSS assets through 'htmltools'. Entity lookup and rendering are handled in the browser by 'bio-tooltips'; this package does not query biological databases from R during package checks.

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bioinformaticschemicalsgenesrmarkdowntooltiptooltip-librarytooltips

4.48 score 1 stars 357 downloads

MutSeqRData - Experimental Data for MutSeqR Examples

Experimental data for use with the MutSeqR vignette and examples. This dataset is taken from LeBlanc et al., 2022. 24 MutaMouse animals were exposed to one of three doses of benzo[a]pyrene or a vehicle control for 28 days by oral gavage. 28 days after the end of the exposure, bone marrow of the femurs was harvested from euthanized animals. DNA extraction was conducted via DNeasy Blood and Tissue kit. DNA samples were sequenced using TwinStrand's Duplex Sequencing on the Mouse Mutagenesis Panel at > 10,000 depth. The Mouse Mutagenesis Panel comprises 20 2.4kb genomic targets with one located on each mouse autosome (two on chromosome 1). Pre-processing of sequence reads was redone since publication using an updated version of TwinStrand's Mutagenesis App (v. 3.20.1) which produced tabular mutation data files for each sample. Data contained herein are only those required for running MutSeqR examples and vignette.

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experimenthubmus_musculus_datagenomesomaticsequencingdatadatapkg

4.00 score 1 stars 1 scripts