agartland Goto Github PK

2015-01-15-uw

Software carpentry workshop at UW, January 2015

betabinom_test

Bootstrap testing for a beta-binomial regression model.

cycluster

Create modules of co-signaling cytokines for analysis of multiplexed cytokine data (e.g. Luminex)

datacarpentry

Data Carpentry workshop materials

fishersapi

A package that for applying a fast implementation of Fisher's exact test to observations in a pandas DataFrame.

flowworkspace

flowWorkspace

hackday-rstudio

hierdiff

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.

hivablist

Parsing and HLA predicted binding affinities for the "A-list" and "B-list" HIV epitopes provided by LANL

hlapredcache

Python-based HLA:peptide binding prediction cache and IEDB-tool wrapper

incubator

lifelines

Survival analysis in Python

metadatavis

nbviewer

Nbconvert as a webservice (rendering ipynb to static HTML)

ncov_epitopes

notebooks

IPython notebooks and related material

palmotif

Python package for computing and plotting sequence logos, with output as SVG or matplotlib

pandas

Flexible and powerful data analysis / manipulation library for Python, providing labeled data structures similar to R data.frame objects, statistical functions, and much more

pte_design

Generate peptides to be used for epitope mapping, maximizing coverage of a sequence alignment.

pwseqdist

A small package that efficiently computes distances between genetic sequences. Can accommodate similarity matrices, sequences of different lengths and custom metrics.

pysieve

Package for performing genetic sieve analysis of breakthrough sequences from vaccine clinical trials.

python-novice-inflammation

Software Carpentry introduction to Python for novices using inflammation data.

python_container

pythontraining

rnaseq_prep

Dockerfile specifying programs for processing RNA seq data

scikit-bio

scikit-bio is an open-source, BSD-licensed, Python package providing data structures, algorithms, and educational resources for bioinformatics.

seqdistance

Python module containing optimized routines for computing genetic distances.

shablona

A template for small scientific python projects

sieve

Statistical Interactive Explorer of Vaccine Efficacy

sparse_kmedoids

Implementation of k-medoids clustering (PAM) accepts scipy.sparse distance matrix, using numba for efficiency