Closed kanekalla closed 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).
Thank you @browaeysrobin
Hi there,
Thanks for the wonderful tool. Do you have a vignette to perform NicheNet analysis for flow-sorted Bulk RNA-seq data?