What are some good tools (in Python if possible) for creating gene co-expression networks from RNA seq data?
After looking around, it seems like the Camoco library is suitable.
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.