Difference between revisions of "WormBase-Caltech Weekly Calls"
From WormBaseWiki
Jump to navigationJump to searchm (→June 10, 2021) |
|||
Line 58: | Line 58: | ||
*July 6th? | *July 6th? | ||
*Data freeze/upload date on the release schedule is July 12th | *Data freeze/upload date on the release schedule is July 12th | ||
+ | |||
+ | === CenGen bar plots === | ||
+ | *initially discussed to have the bar plot images going in as image data | ||
+ | *CenGen group wants interactive bar plots similar to the modENCODE bar plots currently displayed in the FPKM expression data section on the expression widget. That way users could hover over a bar plot and see the cell type, the expression value (TPM, in our case) and the proportion of cells of each neuron type expressing the gene. | ||
+ | *they can provide the underlying data and have the WB team generate interactive plots for each gene | ||
+ | *Sibyl said that this is feasible and we could: 1. bring the data files in OR 2. call the CenGen API on the fly | ||
+ | *the first approach may be more work but better in the long run as we store the data | ||
+ | *Will ping Hinxton and see how they can integrate the data |
Revision as of 16:30, 10 June 2021
Contents
Previous Years
2021 Meetings
June 3, 2021
Reserving meeting rooms
- Raymond encountering challenges with setting up regular meeting room reservations in Chen building
- We've been asked to make reservations one week in advance
- Need to use a room if we reserve it
Summer student(s)
- Anatomy function project with Raymond
- Many types of anatomy function data submitted via AFP
June 10, 2021
Variation-Gene Associations
- Some QC on AFP-extracted data led to the realization that at least some of the 'tm' variations aren't associated with genes on tazendra
- https://github.com/WormBase/author-first-pass/issues/204
- https://github.com/WormBase/website/issues/8262
- It looks like non-manually asserted variation-gene associations will be generated via the VEP pipeline during the build, so Caltech would need to get this information from each WB release
Confirm WS282 Upload Dates
- July 6th?
- Data freeze/upload date on the release schedule is July 12th
CenGen bar plots
- initially discussed to have the bar plot images going in as image data
- CenGen group wants interactive bar plots similar to the modENCODE bar plots currently displayed in the FPKM expression data section on the expression widget. That way users could hover over a bar plot and see the cell type, the expression value (TPM, in our case) and the proportion of cells of each neuron type expressing the gene.
- they can provide the underlying data and have the WB team generate interactive plots for each gene
- Sibyl said that this is feasible and we could: 1. bring the data files in OR 2. call the CenGen API on the fly
- the first approach may be more work but better in the long run as we store the data
- Will ping Hinxton and see how they can integrate the data