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I have a whole-gene CRISPR screening of an assay at different time points. I created a table of the gene number and the count of its reads:

gene_id, count_t0, count_t1, count_t3
ABCA1       3        6          7

What would be a standard way to process such type of data to inference information on up-regulated/down-regulated genes.

I saw this tool: http://crispr-analyzer.dkfz.de/, but it requires my NGS raw data and these file are very large in my case. I'd expect that the information for analysis purposes can be derived solely from the counting table above.

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    $\begingroup$ Have you tried DESeq2? It's one of the options from the tool you linked to even. $\endgroup$
    – Devon Ryan
    Jan 14 '19 at 0:23

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