Investigate applicability on single cell datasets

daisybio / TF-Prioritizer

Bioinformatics pipeline to identify differentially active transcription factors between conditions using expression and epigenetic data

GNU General Public License v3.0

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Investigate applicability on single cell datasets #67

Open nictru opened 9 months ago

nictru commented 9 months ago

Credits to Katie Hoadley, who would be interested in using this on a dataset of hers

mlist commented 9 months ago

Fatemeh has already done work in this direction, e.g. https://pubmed.ncbi.nlm.nih.gov/33124660/ but generally a good idea to adapt our pipeline to sc data now that Nico knows that format as well ;-)

nictru commented 9 months ago

Some meeting notes:

Maybe @quirinmanz has some fitting datasets
Look into Fatemehs paper and potentially use this instead of DYNAMITE
We should investigate sample aggregation (peak mixing), if the current implementation makes sense in this context

quirinmanz commented 9 months ago

Not sure what exactly you need/are looking for? scATAQ-seq? I don't have one lying around, at the moment

nictru commented 9 months ago

We would require RNA-Seq and any kind of HM-ChIP-Seq, ATAC-Seq or DNAse-Seq data. Is not on top of our priority, if someone stumbles across such a dataset, leave a note here

quirinmanz commented 9 months ago

https://www.nature.com/articles/s41576-022-00509-1/tables/2 There will be more datasets available soon I think

mlist commented 9 months ago

how about this: https://support.10xgenomics.com/single-cell-multiome-atac-gex/datasets/1.0.0/pbmc_granulocyte_sorted_10k