hallemlab/wild_worm_codon_adapter

Shiny Web app for automatic codon optimization based on codon usage in Strongyloides species, Pristionchus species, Brugia malayi, as well as user-provided custom codon lookup tables

wild_worm_codon_adapter's Issues

Add legend panel

Add legend panel to Analyze Sequences mode that tells users what GC, Sr_CAI, and Ce_CAI values are.

C. elegans cDNA from WormBase rather than ParaSite

There are discrepancies between the number of isoforms for some C. elegans genes in Wormbase versus ParaSite (e.g. unc-22). Since Wormbase is under stricter control for C. elegans, switch biomaRT call searching for 'Ce-' genes to Wormbase.

Also, change progress message to "searching for genes"

Add isoform name column to Analyze Sequences table

Add a column with the transcript name, to deal with cases when cDNA retrieval returns multiple isoforms for a single gene.

Error message Analyze Sequences mode visualization issue

Error messages in Analyze Sequences mode are overlaid on top of the download button. Make sure those two element don't overlap

Feature request: Validate sequence inputs

Add Error message if input textbox characters are not nucleotides (or amino acids)

Clearing file upload inputs doesn't clear values from memory

If someone accidentally loads a file using the loadlut or loadintron file uploaders, then hits clear, the values associated with loadlut and loadintron appear to still be in memory (they shouldn't be b/c there is reset code in place).

To fix this the best way may be to add reactive values triggered by the use of the loadlut/loadinton input elements, see: https://stackoverflow.com/questions/44278944/r-shiny-doesnt-reset-fileinput-and-and-keeps-it-in-memory

Alternatively, have the dropdown menu include a "custom" option and make users select that option AND upload the values.

Linear regression of S. ratti vs C. elegans plot

Print the R^2 value on the graph?

Feature request: More codon usage options?

Add option for selecting codon usage rules? E.g. CAI vs Percent Usage (allows S. stercoralis codons)

Downloadable example file w/ named list of cDNA sequences

For analysis mode, a recent merge added the assumption that an input with two columns and more than one row is a list of geneID/cDNA pairs. Add an example file that can be downloaded for users.

Add ability to search by transcript id

Seems like necessary functionality.

Upgrade README.md and About tab

Make both the README.md and the About tab in the browser generate from the same/similar .md files.

Feature request: user can provide an Amino Acid for optimization

Add Amino Acid sequence input option

case matching for geneIDs

Currently, a search for "srae_" genes won't work, but "SRAE" will. Maybe add something that uppercases all letters?

Also, add an error response for if none of the searched genes can be found - it's currently not working correctly.

Detect/ignore column names in user inputs

If a user inputs column names (e.g. geneID), code should ignore them. Not sure if this is actually feasible or necessary.

Error message optimize sequences mode

Add an error message for when non-nucleotide values are provided?

Intron insertion bug? (needs resolving)

In some cases, the intron insertion sites might be close enough that they'll be inserted right next to each other. Make sure they aren't overlapping in a weird way.