GCB535
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greenelab
Materials for GCB535 at Penn.
By making the class streamlined, it may be that some students are "surfing" at a higher level rather than thinking carefully about what commands they are doing and what the...
otherwise, students can't load libraries probably worth mentioning in the prelab in case that's not clear
sklearn.cross_validation appears to be defunct, replaced with .model_selection eg., cel 6 should be: from sklearn.model_selection import train_test_split
We didn't really state this explicitly, it was so implied that I don't know why/how we had someone do this but we should tell student to completely prelabs AND in-class...
It looks like in this question, there are ties in the p-value adjustment, so that when a student sorts you might get different subsets in the list. We probably want...
In moving to mm10, some issues to fix: 1. For part III in-class, we meant to use the narrow replicated peak file from mm10, not broad peaks. That means for...
The nature reviews genetics paper (part 1 of the prelab) is not instantly downloadable (is behind a pay wall), so we should get it and post it so students can...
1. In-class Q3 states that H3K4me3 is associated with enhancers but the reading said that H3K4me1 was the enhancer mark. 2. The HW Q1 has H3K9ac as a repressive mark...
I noticed that students the mean of students were not as far along on this assignment as they were on motifs 1. Maybe worth revisiting this assignment, making sure we...
with the reduced memory and options for exploration, some students pick up a gigantic .bed file, then run the usual sort -k1,1 -k2,2n command which subsequently dies. I ended up...