songlab-cal/HiDENSEC

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songlab-cal/HiDENSEC

songlab-cal

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Code for Tracing cancer evolution and heterogeneity using Hi-C

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

flinty

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

slc22a5

Variant effect prediction for SLC22A5 transporter gene using Potts models

Jupyter Notebook

EGGTART

Extensive GUI gives TASEP realization in real-time.