Add a section/tab that walks people through how to use the program? And maybe explains what's going on?

In the Gene-wise tab, the heatmap download data.

Add feature downstream of DEG Table for Go-term Enrichment (or something similar)

For gene searches, add ability to search by more than the ParaSite description. Maybe GO terms? Or possibly more usefully the Hunt et al 2016 gene set terminology.

Must be in same order as plotted in the heatmap.
Rows = genes
Cols = CPM for each sample

Make suggested changes to Single/Multiple Comparisons panel

The output pdf looks a little squished. It would be good to increase the margin size. Also, if possible, add the titles to the graph that are seen when the plot appears on the web browser.

When accessing the browser via a PC computer in lab, I found that the datatable for gene selection stalls when dealing with large datasets.

<20 seconds later> Turns out the problem is with setting the default number of values to display at 25 - that's just too many. Reduce to 5 or 10. Do this for all the datatables, just for safety.

We currently offer users the option to download a log2cpm.csv file containing normalized, filtered data. But the count values that get used/displayed in the browser are actually additionally variance-stabilized - so the values that are included in the vDGEList. It might be better to replace the log2cpm.csv file with data pulled from the vDGEList - or make the vDGEList into an excel file that contains the data and annotations for the genes. Basically an genome-wide version of the .xslx file that users can already download from the Browse By Gene Mode.

For maximizing time on the free shinyapps.io server, the browser times out after several minutes of inactivity. Add a note for users so they don't think the app is broken when this happens.

Compare searched genes against list of genes in the vDEGList dataset; remove genes that are not present and inform the user.

Add a tutorials tab that includes an overview of a basic workflow for the RNA-seq browser, plus a "common Q&A" section.

WBPS17 will include updated gene models for some genes - see Bryant et al 2022 Curr Biol for details. Redo Kallisto alignments for S. ratti and S. stercoralis.

Relevant information includes: methods, citations, contact info

For gene expression plot, should the row-wise clustering assignments be information that users can export? Seems like it might be good information to have.

More annotations to pull from bioMart. Make sure that it's flexible so that when we add the S. ratti data, it pulls up S. stercoralis homologs.

This information should be added to any display/download the currently includes the C. elegans homologs

At the Select Life Stage Comparisons, add code that checks to see if the same life stage appears in both the target and contrast groups. If so, throw an (informative) error.

When deployed to shinyapp.io, the graph looks very very poorly sized. Unclear yet what the issue is.

Clustering should probably be performed only on the genes of interest, not the whole data set.

In the gene-wise browsing tab, the code hangs if you try and submit a new search without using the clear button first. This is particularly pernicious in the deployed version on ShinyApps.io, as it seems to stall the entire program such that all other responsive elements become non-functional.

To make the program more robust for users, this issue should probably be looked at more closely.

Wormbase Parasite v15 includes updated mRNA transcript FASTA files - redo Kallisto alignments with the newest versions. This will likely change the S. ratti BiomaRT call - it looks like the newest version now includes transcript numbers (e.g. .1/.2), similarly to other species.

Current font family in pdf plots is helvetica which is buggy for Windows users. Change to a more general sans-serif font face.

Add error messages, particularly to user input sections

• Set up contrast/target incorrectly (incorrect formatting)
• Misspell life stages
• Make sure input sections have example/help text

Switch from heatmap.2 to ggplot
shift gene names to left of plot

Somewhere on the deployed version there should be a clear statement on the version number.

Also, re-start version numbers relative to initial bioRxiv publication?

In the datatables for both GW and LS, sorting rows by the value in the adjusted p-value column isn't working as desired. May be related to the way the numbers are formatted.

When users download DGE tables, give them the option of filtering genes.

Options should include:

• Only upregulated or downregulated or not-sig diff genes
• Genes consistently upregulated/downregulated/not-sig across multiple comparisons
• Top x% of differentially expressed genes? Let users select that percentage?

Ways to do this: Have a pop up window triggered by clicking the download button that asks users what they want to download.

An easier way might be to add a Downloads panel; could use the name logic that responsively populates dropdown menus to determine what download options are available (when it comes to multiple comparisons).

In case users want a heatmap of all genes in the genome, they should be able to ask Search by Gene mode to display "everything"

Add S. papillosus RNA-seq data from Baskaran et al 2017. https://academic.oup.com/gbe/article/9/3/790/3060133

Add the data from other Strongyloides RNAseq experiments?
Options include:

• S. ratti (https://www.nature.com/articles/ng.3495)
• S. papillosus (https://academic.oup.com/gbe/article/9/3/790/3060133)
• S. venezuelensis (https://www.nature.com/articles/s41598-018-23514-z)

Recent updates to the generate_excel_file code have added some header text that is now too specific - it looks weird when users download gene expression tables. Fix by shifting the main text of those extra header rows outside of the common generate_excel_file function.

Currently, if you reinitialize the GW tab after being in the LS tab, it throws an error if you have previously used textAreaInput boxes, particularly for inputing Life Stage Contrasts.

This should be fixed with updateTextAreaInput, but it's not currently working; I'm not sure why not. Look to see if there is a way to clear (de-Truthy) the action buttons? That might solve the problem.

• freeze top row
• enable Y-scrolling
• add option to show only 5 rows at a time
• add group averages for target/contrasts

It's not clear when downloading data tables in the browser that the downloadable files are excel spreadsheets. Update the button text to reflect this.

When running browser in Browse by Life Stage mode, running into an out of memory error while calculating GSEA. See screenshot of shinyapps.io log

Should be wrapped in a conditionalPanel.