What are some good tools (in Python if possible) for creating gene co-expression networks from RNA seq data?
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asked May 11, 2020 at 20:59
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2 Answers
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After looking around, it seems like the Camoco library is suitable.
answered May 11, 2020 at 23:39
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it depends on the size of your data. If you have enough RAM available, then you may directly compute a correlation-based distance matrix using the cor() function (with method="spearman" or method="pearson"). But you may also give a try to Mutual Information distance using the Parmigene (https://cran.r-project.org/web/packages/parmigene/index.html) R package or partial correlations with the Corpcor (https://cran.r-project.org/web/packages/corpcor/index.html) R package. If you have a large expression matrix, remember to use the excellent data.table package and its fread() function.
answered May 12, 2020 at 7:10