ewallace / cryptowakeup_mscdatasci2020 Goto Github PK

In .Rmd format

I think there were some ORF ids inconsistent with different data files!

We should double-check - refer to FungiDB for new versions.

@DimmestP could you take a look?

• some on biology
• some on methods for motifs and gene expression data

We need to:

• add coding sequences and approximate 3'UTR sequences.
• write a function to shred a fasta file of sequences into k-mers and a data frame of k-mer counts.
• write a function to take reverse-complement equivalence classes of k-mers (collapse DNA)
• make k-mer count data frames for the relevant files.
• run a practice data analysis on that.

Give a short guide for gene ontology searches of Cryptococcus H99, for sanity checks.

Try"

• PANTHER on related JEC21 genes
• fungidb
• fungifun