Andrew Fiore-Gartland, Ph.D.'s Projects
Software carpentry workshop at UW, January 2015
Bootstrap testing for a beta-binomial regression model.
Create modules of co-signaling cytokines for analysis of multiplexed cytokine data (e.g. Luminex)
Data Carpentry workshop materials
A package that for applying a fast implementation of Fisher's exact test to observations in a pandas DataFrame.
flowWorkspace
A package that is useful for clustering high-dimensional instances (e.g. T cell receptors) and testing whether clusters of instances are differentially abundant in two or more categorical conditions. The package provides d3/SVG rendering of scipy hierarchical clustering dendrograms with zooming, panning and tooltips. This uniquely allows for exploring large trees of datasets, conditioned on a categorical trait.
Parsing and HLA predicted binding affinities for the "A-list" and "B-list" HIV epitopes provided by LANL
Python-based HLA:peptide binding prediction cache and IEDB-tool wrapper
Survival analysis in Python
Nbconvert as a webservice (rendering ipynb to static HTML)
IPython notebooks and related material
Python package for computing and plotting sequence logos, with output as SVG or matplotlib
Flexible and powerful data analysis / manipulation library for Python, providing labeled data structures similar to R data.frame objects, statistical functions, and much more
Generate peptides to be used for epitope mapping, maximizing coverage of a sequence alignment.
A small package that efficiently computes distances between genetic sequences. Can accommodate similarity matrices, sequences of different lengths and custom metrics.
Package for performing genetic sieve analysis of breakthrough sequences from vaccine clinical trials.
Software Carpentry introduction to Python for novices using inflammation data.
Dockerfile specifying programs for processing RNA seq data
scikit-bio is an open-source, BSD-licensed, Python package providing data structures, algorithms, and educational resources for bioinformatics.
Python module containing optimized routines for computing genetic distances.
A template for small scientific python projects
Statistical Interactive Explorer of Vaccine Efficacy
Implementation of k-medoids clustering (PAM) accepts scipy.sparse distance matrix, using numba for efficiency