Machine Learning for Genomics

EUGENe

Elucidating the Utility of Genomic Elements with Neural Nets

SeqData

Annotated sequence data

SeqPro

Genomic sequence preprocessing toolkit

EUGENe_paper

Code for generating the figures and results presented in the manuscript EUGENe: A Python toolkit for sequence activity prediction and analysis

SeqExplainer

Interpreting sequence-to-function machine learning models

awesome-dl4g

(Soon to be) community-curated list of software packages and data resources for deep learning for genomics (DL4G)

SeqDatasets

Datasets for benchmarking, testing and developing in EUGENe

MotifData

Motif representation and analysis toolkit in Python

tutorials

A set of tutorials for how to use all the tools in ML4GLand

UCSD_DL4B

The official GitHub repository of UCSD's DL4B working group

use_cases

Repository documenting applications of the ML4GLand suite on published datasets

.github

AI-ATAC

Dataset from the AI-TAC convoluional network for predicting mouse immune cell ATAC-seq signal

deAlmeida_DrosophilaS2_UMI-STARR-seq

UMI-STARR-seq in Drosophila Melongaster, both genome wide and oligo based

deBoer_random-promoters_GPRA

Quantified activity of millions of random yeast promoters with GPRAs

external

Code snippets and wrappers for use of external tools without forking repos

HepG2_U2AF2-eCLIP

Horlacher_HepG2_CLIP

Predicting protein-RNA interaction via sequence-to-signal learning from CLIP-seq data

K562_ATAC-seq

ENCODE K562_ATAC-seq dataset

K562_CTCF-ChIP-seq

K562_STARR-seq

pbmc3k_10X-Multiome

RNACompete2013

The 2013-RNAcompete dataset consists of 244 experiments for 207 RBPs using only weakly structured probes