search

jaleesr / TrendCatcher

TrendCatcher is an open source R-package that allows users to systematically analyze and visualize time course data. Please cite "Temporal transcriptomic analysis using TrendCatcher identifies early and persistent neutrophil activation in severe COVID-19" by Xinge Wang et al published in JCI Insight (2022) - https://insight.jci.org/articles/view/157255
9 stars 3 forks source link

guide for converting Seurat object to trendcatcher data? #7

Closed wwzhang closed 7 months ago

wwzhang commented 8 months ago

I can't find any info to do this? Could you share?

wangxinge commented 8 months ago

Dear @wwzhang, thanks for using TrendCatcher! You can find the detailed method in our manuscript Method section. Since each Seurat object's annotation is different, we suggest you to convert it into pseudo-bulk matrix first. Each row is a gene, each column is the pseudo-bulk gene expression count (you can round up as integers). Then change the column name based on the TrendCatcher requirement, then run the analysis.