Shah Lab's repositories
ProteinDecayNoise-paper
This repo is related to the data that went into the paper associated with the thesis "Evaluating noise in protein decay"
ltee_massspec
Code for our paper studying metabolic effects of expression changes in the LTEE
LTEE_gene_expression_2
A repository for the second version of our LTEE gene expression paper
nnPUlearning
Non-negative Positive-Unlabeled (nnPU) and unbiased Positive-Unlabeled (uPU) learning reproductive code on MNIST and CIFAR10
start-site-predictor
Prediction of translation start sites using Machine Learning
Intragenomic_variation_mutation_bias
A repository presenting the results from our analysis on the effects of intragenomic mutation bias variation within budding yeasts.
RiboRet
An R package to keep our code for analyzing RiboRet data
XACT-seq
Code for processing XACT-seq data
contingency_entrenchment
Scripts for homology modeling and FoldX simulations
SMoPT
Stochastic Model of Protein Translation