alevax Goto Github PK

alevax.github.io

My Ph.D Journal

cellbox

CellBox: Interpretable Machine Learning for Perturbation Biology

code_snippets

cpa

The Compositional Perturbation Autoencoder (CPA) is a deep generative framework to learn effects of perturbations at the single-cell level. CPA performs OOD predictions of unseen combinations of drugs, learns interpretable embeddings, estimates dose-response curves, and provides uncertainty estimates.

cvtex

XeTeX cv templates

datasciencecoursera

Coursera Data Scientist Toolbox project

datasharing

The Leek group guide to data sharing

gtex-single-nucleus-reference

Code repository for the snRNA-seq cross-tissue atlas project

isthmus-progenitors-at-cell

Code for the paper associated to "Isthmus progenitor cells contribute to homeostatic cellular turnover and support regeneration following intestinal injury"

lanyon

A content-first, sliding sidebar theme for Jekyll.

lineage_plasticity_in_crpc

NEPC human data manipulation. Jak/Stat paper on Science

medium

Code related to blog posts on my Medium page

nasb-microtask-viewer-shiny

programmingassignment2

Repository for Programming Assignment 2 for R Programming on Coursera

pythonnumericaldemos

Well-documented Python demonstrations for spatial data analytics, geostatistical and machine learning to support my courses.

pyviper

Porting of Protein Activity and Pathway Inference to single cell and Python.

resources

PyMC3 educational resources

rethinking-tensorflow-probability

Statistical Rethinking (2nd Ed) with Tensorflow Probability

schadendorf-pd1

code and data for Liu, Schilling, et al Nat Med 2019

searchin

[OLD version] - Systematic Elucidation and Assessment of Regulatory Cell-to-cell Interaction Networks (SEARCHIN)

single-cell-best-practices

https://www.sc-best-practices.org

stat_rethinking_2020

Statistical Rethinking Course Winter 2020/2021

statistical-rethinking-2020-jupyter

Following along with Statistical Rethinking text on Bayesian modeling by McElreath

statistical-rethinking-2023-python-notes

Lecture notes and python code to replicate models built throughout the course of Richard Mcelreath's 2023 Lecture Series 'Statistical Rethinking'. Relies on pymc

statistical_rethinking_with_brms_ggplot2_and_the_tidyverse_2_ed

The bookdown version lives here:

statrethinking_winter2019

Statistical Rethinking course at MPI-EVA from Dec 2018 through Feb 2019

thinkbayes2

Think Bayes 2

viking

Virtual-Inference of Kinase INhibiton by Gene regulatory networks (VIKING)

viperpy-data

Data Repository for VIPER analysis in Python