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Commits on Apr 19, 2023

• Add tidyverse to "Suggests" due to BioC build error

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Commits on Feb 16, 2022

• Update DESCRIPTION

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• Update README.md

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Commits on Jul 6, 2021

• Update README.md

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Commits on May 23, 2021

• Declared namespace of all global variables after BiocCheck

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• Declare namespace of all elements within scope of functions such as ggplot2, subset, etc. See https://ggplot2.tidyverse.org/articles/ggplot2-in-packages.html

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• Polished documentation reflecting the switch to IRanges for some of the tasks

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• Addressed Bioconductor reviewer comment 1.

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Commits on May 22, 2021

• Addressed Bioconductor reviewer comments 3-4.

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• Addressed Bioconductor reviewer comments 2, 5-7.

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Commits on Apr 12, 2021

• Documentation for datasets

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• Merge branch 'devel'

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• Added documentation for lai2019 and wan2014, increased tolerance for tests, bumped version and R dependency

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Commits on Apr 8, 2021

• Updated README

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• Regenerated the documentation files

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• Added examples to function documentation

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• Removed call to class() function and added description of output from getRegions

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• Changed T/F to TRUE/FALSE. Required by BiocCheck

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• Adding HTML of vignette

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• Update R version dependency based on BiocCheck

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• Rename data objects

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Commits on Apr 7, 2021

• suppress warnings

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• Changed all tests and code in vignette to single process, devtools build updates

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• Updated README

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• Delete unwanted license file

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• Delete unwanted project file

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• Delete unwanted hidden file

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• Subset Lai et al. data to keep only a dozen or so transcripts, add other files per Bioconductor guidelines

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• Added unit tests and minor edits to the vignette

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Commits on Apr 5, 2021

• Simplified with a definition of dScore

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• Updated object name for function component operating on vector input to the function. The component operating on matrix input is fine.

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Commits on Apr 4, 2021

• Updated to ensure both guided and de novo modes of dStructome return result table with rownames as serial natural numbers

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• Results from dStruct.guided are now labeled as pval and del_d

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• Rownames of result from dStructome in the guided mode were not series of integers. Now they are.

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• dStruct now reports effect size for each tested region in addition to the p-values.

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