tidybulk

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"Proportion of variance explained" values on reduce_dimensions() output

1

The base `prcomp()` function provides the Proportion of variance explained values after the PCA analysis. ``` pca

canholyavkin

test_gene_overrepresentation: visualising results

7

Do you have any recommendations for visualising the output of test_gene_overrepresentation? Can it/should it use a clusterprofiler viz method: https://yulab-smu.github.io/clusterProfiler-book/ or a ggplot2 one?

mblue9

Tis should work similarly to the function `s_` of tidySE

stemangiola

Use feature instead of transcript

1

Since tidy* packages were converted to feature vocabulary, at some point we should adapt tidybulk too. @mblue9 concerns?

stemangiola

Allow logFC shrinkage in DESeq

4

For gene ranking (for GSEA, for example) and visualizations (on volcano plots, for example), DESeq author Michael Love suggests shrinking of the effect sizes (log-fold changes) with the `lfcShrink` function...

antass

`tidybulk` Replace pivot_* with select_columns_*

3

I think subset_transcripts and subset_samples would be more clear and in line with tidyverse. @mblue9 concerns?

stemangiola

Feedback from talk: get_bibliography

1

@mblue9, FYI at the Monash talk I received very good feedback about get_bibliography. I was suggested to include what methods/functions are related to each bib citation, for giving the opportunity...

stemangiola

for scaling check the presence of a multiplier column

1

And do this in general when columns are created.

stemangiola

Improve documentation and package imports

20

This pull request picks up on @chilampoon's pull request #297 . In summary: - Polish roxygen2 function documentation (e.g inheriting from other packages when possible) - Improve coding style (e.g...

william-hutchison

stemangiola