davidaknowles

dox

Determining the genetic basis of anthracycline-cardiotoxicity by molecular response QTL mapping in induced cardiomyocytes

dpvc

Dirichlet Process Variable Clustering

eagle

An R package for detecting Gene-by-Environment (GxE) interaction effects on the transcriptome using Allele Specific Expression quantified from RNA-seq

gamma_sgvb

gprn

Gaussian Process Regression Network code

leafcutter

Annotation-free quantification of RNA splicing. Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae Kyung Im, Jonathan K. Pritchard

pydt

Pitman Yor diffusion tree sampler

suez

R package for mapping response-expression QTLs

tensor_gp

Code for Tensor Gaussian Process Regression for predicting drug combination synergy, developed for the AstraZeneca-Sanger Drug Combination Prediction DREAM Challenge 2015: https://www.synapse.org/#!Synapse:syn4231880/wiki/235645

tf_net

A custom conv net for the DREAM ENCODE challenge

davidaknowles/leafcutter

Annotation-free quantification of RNA splicing. Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae Kyung Im, Jonathan K. Pritchard

davidaknowles/eagle

An R package for detecting Gene-by-Environment (GxE) interaction effects on the transcriptome using Allele Specific Expression quantified from RNA-seq

davidaknowles/pydt

Pitman Yor diffusion tree sampler

davidaknowles/suez

R package for mapping response-expression QTLs

davidaknowles/eagle1S

Re-implementation of EAGLE using Stan.

davidaknowles/lacrosse

lacrosse: LAtent ChaRacteristics Of Small-molecule SEnsitivity. David A Knowles, Gina Bouchard, Sylvia Plevritis.

davidaknowles/mamba.py

A simple and efficient Mamba implementation in pure PyTorch and MLX.

davidaknowles/pisquared

R package to estimate sharing between two arrays of p-values

davidaknowles/regtools

Integrate DNA-seq and RNA-seq data to identify mutations that are associated with regulatory effects on gene expression.

davidaknowles/splice_wave

davidaknowles/adaglm

davidaknowles/AeroPython

Classical Aerodynamics of potential flow using Python, for Prof. Barba's course at GW (1st version:Spring 2014, 2nd run:2015).

davidaknowles/brie

BRIE: Bayesian Regression for Isoform Estimate in Single Cells

davidaknowles/casopr

Continuous Annotation-aware Shrinkage Of Polygenic Risk

davidaknowles/davidaknowles.github.io

Github Pages homepage

davidaknowles/denoising-diffusion-pytorch

Implementation of Denoising Diffusion Probabilistic Model in Pytorch

davidaknowles/eagle2

Environment-ASE through Generalized LinEar modeling, v2

davidaknowles/git-gud

Material for a presentation I gave on ramping up with Git.

davidaknowles/gpu-finder

davidaknowles/idg_dream

Illuminating the Druggable Genome (IDG)-DREAM Challenge

davidaknowles/implicit

davidaknowles/Mini-Conf

Run a conference from your backyard.

davidaknowles/mlcb.github.io

Machine Learning in Computational Biology workshop site

davidaknowles/omen-light

davidaknowles/poolqtl

davidaknowles/poster_town

davidaknowles/pyro_vmm

davidaknowles/RefManageR

R package RefManageR

davidaknowles/SwabSeq

davidaknowles/v200

Proceedings of MLCB 2022