forstater’s gists

forstater / server.r

Created August 31, 2016 14:11 — forked from wch/server.r

Shiny example: dynamic input fields

	data_sets <- c("mtcars", "morley", "rock")

	shinyServer(function(input, output) {

	# Drop-down selection box for which data set
	output$choose_dataset <- renderUI({
	selectInput("dataset", "Data set", as.list(data_sets))
	})

	# Check boxes

forstater / jacobs_nanopore_functions.py

Last active August 9, 2016 23:30

Useful Functions for Analyzing Nanopore Data with MOSAIC

	'''

	:Author: Jacob Forstater <[email protected]> or <[email protected]>
	:Description: Various functions/workflow that help to process nanopore data

	Log:
	JF 20160809 initial public commit

	'''

forstater / multiStateFilter.py

Created June 28, 2016 20:23

Function to query and filter multistate events.

	'''
	Author: Jacob Forstater
	Description: Workflow to clean up multistate events
	- Filters out NStates <2
	- Filters out any event with StateResTime < minValue
	- Supplys this back as a 2D flattened Array

	Log:
	JF 20160602 initial version

forstater / calcBinSize.py

Created May 25, 2016 19:35

Script to calculate optimal bin sizing using minimization of integrated square area

	"""
	Script to calculate optimal bin size (bandwidth).

	:Created: 5/25/2016
	:Author: Jacob Forstater <jacob.forstater@nist.gov>
	:Reference: Shimazaki and Shinomoto. Histogram Binwidth Optimization Method. Neural Comput. v19 pp1503-1527 (2007)
	:Original Source: Modified from http://toyoizumilab.brain.riken.jp/hideaki/res/histogram.html

	:ChangeLog:
	.. line-block::

forstater / useful_pandas_snippets.py

Last active December 2, 2016 16:18 — forked from bsweger/useful_pandas_snippets.md

Useful Pandas Snippets

	# List unique values in a DataFrame column
	pd.unique(df.column_name.ravel())

	# Convert Series datatype to numeric, getting rid of any non-numeric values
	df['col'] = df['col'].astype(str).convert_objects(convert_numeric=True)

	# Grab DataFrame rows where column has certain values
	valuelist = ['value1', 'value2', 'value3']
	df = df[df.column.isin(valuelist)]

forstater / gist:9fb3f3fa8cc1828ce95a

Created February 11, 2016 16:50 — forked from why-not/gist:4582705

Pandas recipe. I find pandas indexing counter intuitive, perhaps my intuitions were shaped by many years in the imperative world. I am collecting some recipes to do things quickly in pandas & to jog my memory.

	"""quick way to create a data frame to try things out"""
	df = pd.DataFrame(np.random.randn(5, 4), columns=['a', 'b', 'c', 'd'])

	df['A'] """ will bring out a col """ df.ix[0] """will bring out a row, #0 in this case"""

	"""to get an array from a data frame or a series use values, note it is not a function here, so no parans ()"""
	point = df_allpoints[df_allpoints['names'] == given_point] # extract one point row.
	point = point['desc'].values[0] # get its descriptor in array form.

forstater / binaryConvert.py

Last active August 29, 2015 14:27 — forked from abalijepalli/binaryConvert.py

A Python gist to convert any data type supported by MOSAIC (https://github.com/usnistgov/mosaic) to a simple binary format.

	"""
	Extend the MOSAIC ConvertToCSV class to export arbitrary binary files.

	:Created: 02/25/2015
	:Author: Arvind Balijepalli <[email protected]>
	:ChangeLog:
	.. line-block::
	02/25/15 AB Initial version
	"""
	import mosaic.ConvertToCSV as conv

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