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saeyslab / nichenetr

NicheNet: predict active ligand-target links between interacting cells
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Vignette on using Bulk RNA-seq data #70

Closed kanekalla closed 3 years ago

kanekalla commented 3 years ago

Hi there,

Thanks for the wonderful tool. Do you have a vignette to perform NicheNet analysis for flow-sorted Bulk RNA-seq data?

browaeysrobin commented 3 years ago

Hi @kanekalla

Unfortunately there is no vignette specifically for bulk RNA-seq and we have no plans (at least not short term) to make one.

In the FAQ page, I mention some tips to start from the basic vignette for bulk RNA-seq data: https://github.com/saeyslab/nichenetr/blob/master/vignettes/faq.md#can-i-use-nichenet-on-bulk-rnaseq-data-as-well-or-only-on-single-cell-data

The main point is that you just focus on the different steps in the NicheNet analysis pipeline and replace single-cell based analysis ways by a bulk RNA-seq counterpart (eg defining the geneset of interest by DE analysis via a dedicated bulk RNA-seq DE tool like EdgeR, DESeq2, limma).

kanekalla commented 3 years ago

Thank you @browaeysrobin