Notes
Writing
Scripts, methods and second thoughts — mostly Python and R, applied to problems in biology. Each note is meant to be short enough to read and complete enough to run.
FiguresGenomicsMatplotlibMethodPythonTaxonomy
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2017
PythonGenomics
Genomic arrays
A small NumPy-backed class for accumulating features along a chromosome-length array, and a reminder about right-open intervals.
-
2016
PythonTaxonomy
Getting species lineage
Walking the NCBI Taxonomy tree to annotate a list of species with its full lineage, because nothing off the shelf quite fit.
-
2016
FiguresMethod
Plotting — dos and don'ts
A working checklist for figures, assembled from a PLoS Computational Biology piece and a few additions learned the hard way.
-
2016
PythonMatplotlib
Cartoon-like plots with matplotlib
Matplotlib's xkcd mode, used as an excuse to walk through annotation, shading and stripping a plot back to what carries the message.
