Difference between revisions of "WBConfCall 2020.12.17-Agenda and Minutes"
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** Todd has built a document based on Doug Howe's file | ** Todd has built a document based on Doug Howe's file | ||
** Todd will share his file | ** Todd will share his file | ||
+ | ** Kevin H: if we are pulling everything (of current importance) over to the Alliance in 2 years, we'll need to incorporate pipelines that run during or after our build pipelines | ||
+ | ** We can start with Todd's document and build off of that (keeping a centrally located file) |
Revision as of 17:16, 17 December 2020
Help Desk
Agenda
- WormBase Social Hour?
- WormBase list of data types to bring into the Alliance
- CeNGEN - C. elegans Neuronal Gene Expression Network
Minutes
- CeNGEN
- Will talk in January for integration into WormBase: who should be on that call?
- Eduardo, Raymond, Todd, Chris
- Eduardo has several ideas about how to integrate and display
- Has slides (for Alliance) with a breakdown of technology over time, species represented (mostly human and mouse)
- First C. elegans dataset in 2017; another in 2019 with re-annotation of 2017 dataset
- scRNA-seq data sets are in a big sparse matrix
- Data in raw FASTQ file --> read alignments --> unfiltered matrix --> barcode filtering --> filtered matrix
- Data deposited usually at SRA and ENA, but often not raw data, usually the already filtered matrix (sometimes even more processed than that)
- Human Cell Atlas Data Portal (data.humacellatlas.org) (only human and mouse; not interested in other species)
- COVID19 cell atlas (covid19cellatlas.org)
- CellXGene (https://cellxgene.cziscience.com/)
- Should be analyzing differential gene expression (but not using a t-test)
- What about the EBI gene expression atlas (gxa): https://www.ebi.ac.uk/gxa/sc/home
- FlyBase already collaborating with
- Maybe we can use the tools/infrastructure that EBI GXA has; we could curate into their platform and we can build off of what the GXA has
- http://europepmc.org/article/MED/31665515
- Will talk in January for integration into WormBase: who should be on that call?
- Alliance documentation of WormBase data types to pull in
- Todd has built a document based on Doug Howe's file
- Todd will share his file
- Kevin H: if we are pulling everything (of current importance) over to the Alliance in 2 years, we'll need to incorporate pipelines that run during or after our build pipelines
- We can start with Todd's document and build off of that (keeping a centrally located file)