songlab-cal/flinty

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Python
Created over 3 years ago
Updated 10 months ago

songlab-cal/flinty

songlab-cal

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A Simple and Flexible Test of Sample Exchangeability with Applications to Statistical Genomics

tape

Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology.

gpn

Genomic Pre-trained Network

Jupyter Notebook

tape-neurips2019

Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology. (DEPRECATED)

factored-attention

This repository contains code for reproducing results in our paper Interpreting Potts and Transformer Protein Models Through the Lens of Simplified Attention

Jupyter Notebook

mogwai

rna-sieve

A library for the deconvolution of bulk cell samples using single-cell RNA expression data.

CPT

Cross-protein transfer learning for variant effect prediction

Jupyter Notebook

scquint

Jupyter Notebook

swga2

CherryML

Scalable Maximum Likelihood Estimation of Phylogenetic Models

scquint-analysis

MultiCluster

Software for three-way clustering of multi-tissue multi-individual gene expression data using semi-nonnegative tensor decomposition

contact-geometry

MOCHIS

One- and two-sample tests against general families of alternatives

HiDENSEC

Code for Tracing cancer evolution and heterogeneity using Hi-C

Jupyter Notebook

slc22a5

Variant effect prediction for SLC22A5 transporter gene using Potts models

Jupyter Notebook

EGGTART

Extensive GUI gives TASEP realization in real-time.