chanzuckerberg / cellxgene-census

CZ CELLxGENE Discover Census
https://chanzuckerberg.github.io/cellxgene-census/
MIT License
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consider additional assays for Census schema #837

Open jahilton opened 8 months ago

jahilton commented 8 months ago

These assays are in CELLxGENE (some are still private) but not addressed yet by the Census schema as included or explicitly excluded

10x transcription profiling
SORT-seq
CEL-seq
in situ sequencing
untargeted ExSeq
targeted ExSeq
SPLiT-seq
sci-RNA-seq3
PhenoCycler
smFISH
jahilton commented 7 months ago

A survey of all existing assays, Published or Private, should occur at the time of review. We now also have mCT-seq.

BAevermann commented 7 months ago

We should definitely set up a review mechanism prior to stable releases. I am curious as to why some scRNA-seq data generating assays were left out, for example SPLiT-seq or CEL-seq from the above list. In addition, we need to denote Multiomic RNA vs ATAC in order to get the RNA into Census as soon as possible.

pablo-gar commented 7 months ago

We will do a full pass on EFO to generate and inclusion/exclusion list of all terms.