Projects in Awesome Lists by songlab-cal
A curated list of projects in awesome lists by songlab-cal .
https://github.com/songlab-cal/tape
Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology.
benchmark dataset deep-learning language-modeling protein-sequences protein-structure pytorch semi-supervised-learning
Last synced: 09 Apr 2025
https://github.com/songlab-cal/gpn
Genomic Pre-trained Network
dna genomics language-model variant-effect-prediction
Last synced: 07 May 2025
https://github.com/songlab-cal/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)
benchmark dataset deep-learning language-modeling protein-sequences protein-structure semi-supervised-learning
Last synced: 07 May 2025
https://github.com/songlab-cal/factored-attention
This repository contains code for reproducing results in our paper Interpreting Potts and Transformer Protein Models Through the Lens of Simplified Attention
Last synced: 07 May 2025
https://github.com/songlab-cal/rna-sieve
A library for the deconvolution of bulk cell samples using single-cell RNA expression data.
Last synced: 07 May 2025
https://github.com/songlab-cal/cherryml
Scalable Maximum Likelihood Estimation of Phylogenetic Models
Last synced: 07 May 2025
https://github.com/songlab-cal/cpt
Cross-protein transfer learning for variant effect prediction
Last synced: 07 May 2025
https://github.com/songlab-cal/traitgym
dna genomics variant-effect-prediction
Last synced: 07 May 2025
https://github.com/songlab-cal/multicluster
Software for three-way clustering of multi-tissue multi-individual gene expression data using semi-nonnegative tensor decomposition
Last synced: 07 May 2025
https://github.com/songlab-cal/mochis
One- and two-sample tests against general families of alternatives
Last synced: 07 May 2025
https://github.com/songlab-cal/slc22a5
Variant effect prediction for SLC22A5 transporter gene using Potts models
Last synced: 07 May 2025
https://github.com/songlab-cal/eggtart
Extensive GUI gives TASEP realization in real-time.
Last synced: 07 May 2025
https://github.com/songlab-cal/sgdp_ighv_trbv
Clustered and filtered reads after mapping for the SImons Diversity Genome Project.
Last synced: 07 May 2025
https://github.com/songlab-cal/forward-equivalent-trees
Efficiently simulating multi-type birth-death processes via forward-equivalent parameter mapping
Last synced: 07 May 2025
https://github.com/songlab-cal/flinty
A Simple and Flexible Test of Sample Exchangeability with Applications to Statistical Genomics
bioinformatics exchangeability genome-analysis hypothesis-testing non-parametric-statistics
Last synced: 07 May 2025
https://github.com/songlab-cal/epigenome_editing_2023
Code for training and analyzing models from the epigenome editing paper Batra et al.
Last synced: 07 May 2025
https://github.com/songlab-cal/stratpgs
Performance Inflation and Perturbation Sensitivity of PGSs
Last synced: 07 May 2025
https://github.com/songlab-cal/phylogpn
Code for "A Phylogenetic Approach to Genomic Language Modeling"
Last synced: 07 May 2025
https://github.com/songlab-cal/hidensec
Code for Tracing cancer evolution and heterogeneity using Hi-C
Last synced: 07 May 2025
https://github.com/songlab-cal/bcr-allelic-inclusion
Model code and data for BCR allelic inclusion paper
Last synced: 07 May 2025