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ashley_scripts

awesome-bayes

List of resources for bayesian inference

awesome-small-molecule-ml

bcbb

Incubator for useful bioinformatics code, primarily in Python and R

blk

unicode blocks can plot anything!!

chainlearn

Mini module with syntax sugar for pandas/sklearn

colab_biowrappers

Bio and chem tools wrapped in colabs

combat.py

python / numpy / pandas / patsy version of ComBat for removing batch effects.

datacleaner

A Python tool that automatically cleans data sets and readies them for analysis.

drug_sensitivity_relnets

Drug sensitivity prediction with lots of gene/drug/cell line interaction information.

embodi

Framework for large language model "embodiment", e.g. props some "sensors" and "actuators" on the LLM

fancyimpute

Multivariate imputation and matrix completion algorithms implemented in Python

genoracle

A simple python module for gene set annotation, enrichment testing, consultation of gene/pathway databases and ontologies.

gett

Genotype, expression, and trait toolset

gexpfoundation_hackathon

Code repository for our submission at BioxML hackathon, team LLM

hyperparameter.space

Personal blog

llm-for-clinical-variants

molxspec

ML models to convert molecules to ESI mass spectra and maybe back again

node2vec

ouija

Incorporating prior knowledge in single-cell trajectory learning using Bayesian nonlinear factor analysis

pandio

Access python pandas in an "awk-like" manner in the command line -- inspired by Rio

parsegeo

Python utilities to parse data from the gene expression omnibus

plsrecord

Lightweight data provenance record keeper

pyroconductor

A high-level interface to access commonly-used R tools from python using the low-level r2py

pytorch-openai-transformer-lm

A PyTorch implementation of OpenAI's finetuned transformer language model with a script to import the weights pre-trained by OpenAI

reeffitpaper

Paper for the RNA Ensemble Extraction from Footprinting Insights Technique

scikit-tensor

Python library for multilinear algebra and tensor factorizations

scimitar

Single Cell Inference of MorphIng Trajectories and their Associated Regulation (SCIMITAR)

scsuite

single-cell Scalable Unified Inference of Trajectory Ensembles

simppl

A simple probabilistic programming language