ericmjl/Network-Analysis-Made-Simple

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ericmjl/Network-Analysis-Made-Simple

ericmjl

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An introduction to network analysis and applied graph theory using Python and NetworkX

Network Analysis Made Simple

Welcome to the GitHub repository for Network Analysis Made Simple! This is a tutorial designed to teach you the basic and practical aspects of graph theory. It has been presented at multiple conferences (PyCon, SciPy, PyData, and ODSC) in a variety of formats (ranging from 1.5 hr to 4 hour long workshops). The material is designed for a live tutorial presentation, with the code available for you to reference afterwards.

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bayesian-stats-modelling-tutorial

How to do Bayesian statistical modelling using numpy and PyMC3

Jupyter Notebook

bayesian-analysis-recipes

A collection of Bayesian data analysis recipes using PyMC3

Jupyter Notebook

nxviz

Visualization Package for NetworkX

essays-on-data-science

In which I put together my thoughts on the practice of data science.

dl-workshop

Crash course to master gradient-based machine learning. Also secretly a JAX course in disguise!

Jupyter Notebook

bayesian-deep-learning-demystified

In which I try to demystify the fundamental concepts behind Bayesian deep learning.

data-testing-tutorial

A short tutorial for data scientists on how to write tests for code + data.

Jupyter Notebook

hiveplot

Hive Plots in using Python & matplotlib!

Jupyter Notebook

bayesian-stats-talk

Doing Bayesian statistics in Python!

Jupyter Notebook

protein-interaction-network

Computes a molecular graph for protein structures.

minimal-flask-example

The simplest complex example that I can think of to show main Flask app concepts.

causality

In which I play with the ideas surrounding causality

flu-sequence-predictor

An experimental deep learning & genotype network-based system for predicting new influenza protein sequences.

Jupyter Notebook

minimal-streamlit-example

A minimal example of how to use streamlit on Heroku

pyds-cli

Helping you manage your data science projects sanely.

llamabot

Pythonic class-based interface to LLMs

conda-envs

My conda environment YAML files

distributions

Central repository for my distributions figures

Jupyter Notebook

Circos

Jupyter Notebook

fundl

A pedagogical, functional-oriented deep learning library built on top of jax.

scikit-learn-tutorial

Jupyter Notebook

minimal-panel-app

A pedagogical implementation of panel apps served up on a remote machine.

Jupyter Notebook

bayesian-generalized-abcde-testing

PyCon 2019 talk on Bayesian multi-group testing.

Jupyter Notebook

pyflatten

A utility for flattening nested data structures into an array.

what-are-probability-distributions

PyCon 2020 Talk on "what probability distributions are"

principled-ds-workflow

Delivered at PyData Boston on 21 July 2020

resume

Building a resume using nothing but YAML files and Python. A prototype.

ericmjl.github.io

probability-distributions-with-python

A talk on what probability distributions are, using Python

graph-fingerprint

A package for using convolutional neural nets to learn a graph fingerprint.

Jupyter Notebook

iacs2017

Materials for IACS 2017 contest.

Jupyter Notebook

probabilistic-programming-tutorial

systems-microbiology-hiv

Machine learning and phylogenetics on HIV

Jupyter Notebook

graph-deep-learning-demystified

An attempt at demystifying graph deep learning

score-models

In which I learn about score functions and how they can be used to generate data.

Jupyter Notebook

website

Eric Ma's Personal Website

dotfiles

worship-manager

Open source software for worship coordinators and leaders.

testing-for-data-scientists

Slides for my talk on testing for data scientists.

matplotlib-tutorial

A short tutorial on how to make matplotlib plots.

Jupyter Notebook

target-prediction

In which I try to replicate the main findings of Ferrero, E., Dunham, I., & Sanseau, P. (2017), Journal of Translational Medicine, 15(1), 182.

Jupyter Notebook

normalizing-flows

Deeply learning about normalizing flows.

Jupyter Notebook

czbiohub

autograd-cupy

Autograd wrapper for CuPy

software-testing-open-source-and-data-science

Software Testing in Open Source and Data Science: A talk delivered at the Data Umbrella speaker series

curve-fitting-talk

"Fret not, it's curve fitting all the way down!

Jupyter Notebook

insight-data-challenges

Jupyter Notebook

influenza-reassortment-detector

Scripts for running the influenza reassortment detector

thesis

PhD thesis!!!!!

emailme

A Python module to email myself from Python scripts and the command line.

influenza-reassortment-analysis

dream-respiratory-viral-challenge

hiv-resistance-prediction

In which I try to use ML models to predict HIV resistance phenotypes.

Jupyter Notebook

internet-monitor

A Streamlit app that monitors internet locally

Primer-Design-Automator

A tool for automating my primer design workflow

beast-gpu-tutorial

A short website that describes how to create an Amazon AWS GPU instance that runs BEAST + BEAGLE.

habit-tracker

Personal Flask app for tracking a habit.

bayesian-measurement-paper

My academic 'rant' on why n=3 is not sufficient.

Jupyter Notebook

protein-convolutional-nets

Part of my thesis work. Doing convolutional neural nets on protein graphs to make predictions.

Jupyter Notebook

protein-systematic-characterization

All our protocols, data, analysis, and papers related to this project are stored here.

Jupyter Notebook

continuous-pull

A command-line utility to continuously pull Git repository locally.

computational-representations-message-passing

A short technical piece on how message passing on graphs can be simultaneously made efficient and easy to read.

influenza-global-reassortment

Jupyter notebooks and data - reproducible analysis from reassortment paper

Jupyter Notebook

math-for-programmers-exercises

My exercises answers from Jeremy Kun's book, Mathematics for Programmers.

Jupyter Notebook

nnet-HA

Toy project, in which I train a neural network to predict influenza virus host tropism.

Jupyter Notebook

small-group

A local web app I built to store information about our Bible Study small group and use it to divide us into smaller groups.

polcart

A small utility for converting between polar and cartesian units.

flu-gibson

A tool for designing primers to clone influenza polymerase segments from viral cDNA.

genomic-surveillance-whitepaper

Publicly written white paper on genomic surveillance.

flu-gibson-webui

A Flask-based UI for the FluGibson package.

easy-talk-slides-and-notes

Personal-Scripts-and-Functions

My repository of custom scripts and functions.

tensor-flow-tutorial

In which I teach myself TensorFlow.

Jupyter Notebook

Influenza-Reassortment-Simulation-and-Identification

Influenza-Network-Transmission-Model

Jupyter Notebook

imgdisplay

A Python command-line app for displaying photos as a slideshow in a directory.

mbtools

Molecular Biology Tools

boston-gov-data

Jupyter Notebook

generative-thinking

something cool happening here

pymc3-models

Default models built on top of PyMC3.

Influenza-RNA-Secondary-Structure-Prediction

reveal-nord-theme

A personal implementation of the Nord theme + other slide utilities for reveal.js slides.

cookiecutter-data-project

Opinionated and personalized cookie-cutter data project template

tensor-fun

Minimal tensor operations examples. Playing around with higher-dimensional tensors.

Jupyter Notebook

genotype-network

Genotype network software, collaboration with Kyle Yuan.

h9-pb2-global-analysis

Song-Sheet-Transposer

d3-graph

A repository for me to remember how to use d3's force-directed layout API.

blog-assistant

My personal blogging assistant, built on top of llamabot and GPT4.

epaper-badge

Code for ePaper display badge

autoencoders

Me playing around with autoencoders. For fun.

Jupyter Notebook

ecdf-guide

An interactive guide to ECDFs.

Jupyter Notebook

flask-sandbox

In which i futz around with Flask, trying to make a random web app that does something.

pandoc-recipes

A curated set of recipes that I've used with pandoc to make all sorts of documents.

pytorch-playground

In which I play around with PyTorch.

flu-assembler

In which I try to implement my own influenza genome assembler. For funzies.

Jupyter Notebook

autograd-sparse

Autograd wrapper for scipy.sparse

bluetooth-proximity-tracker-calibration

A repository containing all of the raw data and experiments done on the Raspberry Pi bluetooth tracker.

Jupyter Notebook

quarto-scipy24-exercises

cookiecutter-talk

A repository to bootstrap my writing using Markdown, Pandoc, HTML and Reveal.js