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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
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Is only count table fitting the format of input? #8

Closed jamesbangbang1126 closed 7 months ago

jamesbangbang1126 commented 8 months ago

Hi! guys, Thank you for your great work. However, I am a little confused if TPM or FPKM, the kind of transformed expressions, could be the input of the function, ‘run_TrendCatcher’. If not, how could I use TPM or FPKM as input?

Thank u in advance.

wangxinge commented 8 months ago

Dear @jamesbangbang1126, thanks for using TrendCatcher! The ideal input for run_TrendCatcher function is the raw count table without batch effect. But if you need normalization or batch effect, you can check the source code of preprocess_TrendCatcher.R. Here we applied CPM normaliztion and ComBat_seq batch correction functions, then converted it back into integers.