Misc updates/fixes

[onursumer]

Home Page:

• Blurb (further detailed in about) (Slack Barry or Mike): needs text. Method, Assay, Glossary, etc
• Change the blurb on front page from using bold to highlight the letters in the words that form the acronym to use underline instead
• Table: expandable table switch columns (order: pathogenic germline, biallelic, somatic mutant)
• Table: add penetrance and sort by penetrance (sort by highest level of penetrance if the gene is in multiple penetrance groups) sort by % Germline Biallelic
• Table: search by gene symbol only
• “Includes only likely driver mutations, or relevant copy number changes”
• Mouse over any frequency should show nominator + denominator
• Include all cancer types in expandable row (including zero)
• For freqs put - instead of 0 (0 out of 0)
• % somatic mutant -> % somatic driver, % pathongeic germline -> % germline pathogenic
• When row is expanded, remove row header Mutation frequencies etc
• What should tooltip be for biallelic %?
• Fetching INSIGHT(ful) mutations
• Left justify insight logo, right justify mskcc
• Hide sub table on search
• arrow not in the right spot for tooltip
• Percent of pathogenic germline carriers biallelic in the corresponding tumor -> Percent of pathogenic germline carriers biallelic in the corresponding tumor sample
• Somatic
• Move total # Samples to front in expanded table

Gene Page:

• Benign germline -> Rare Benign/VUS germline (less than 2% of the whole cohort?)
• Start y axis from 1 when using numbers
• Add some space for lollipops to show lines
• Y-Axis: Radio-button
• Benign + pathogenic germline different color in table
• Somatic row show - in biallelic
• Justify headers same as content
• Add cDNA change column (hgvsc from genome nexus)
• Variable number of decimal point digits in the tooltip (currently fixed to 4 digits)
• move the + sign (expander) at the end to % column on gene page
• make y and -y same scale (round up digits on ticks (no need for two digits))
• tool tip for Rare Benign/VUS Germline isn't precisely accurate
• when hover over (i) next to gnomAD/ClinVar column header, the cursor does not change to hand icon but rather to a column resizing icon

About Page:

• The citation in the About page should be updated to correct the title and its status.

Download Page

• link to github repos
• accession codes to paper

Data

• penetrance
• what defines a rare benign germline?

[jjgao]

updated checklist based on feedback from lab meeting.