Marcus Fedarko fedarko

fedarko / align_q2_table_and_metadata.py

Last active July 25, 2019 05:51

Filter a QIIME 2 feature table and a metadata TSV file to shared samples

	#! /usr/bin/env python3
	import biom
	from qiime2 import Artifact, Metadata

	YOUR_QZA_TABLE_FILEPATH_GOES_HERE = "table.qza"
	YOUR_METADATA_FILEPATH_GOES_HERE = "metadata.tsv"

	# Load the table
	tbl_qza = Artifact.load(YOUR_QZA_TABLE_FILEPATH_GOES_HERE)
	t = tbl_qza.view(biom.Table)

fedarko / poisson-cat.py

Created April 17, 2019 22:18 — forked from mortonjt/poisson-cat.py

Closed form categorical Poisson regression

	import numpy as np
	import patsy
	import pandas as pd
	from biom import Table

	# This is the main function
	def poisson_cat(table, metadata, category, ref=None):
	""" Poisson differential abundance.

	Parameters