Machine Learning for Genomics
A collection of tools for investigating how DNA encodes function with machine learning
Pinned Repositories
awesome-dl4g
(Soon to be) community-curated list of software packages and data resources for deep learning for genomics (DL4G)
EUGENe
Elucidating the Utility of Genomic Elements with Neural Nets
EUGENe_paper
Code for generating the figures and results presented in the manuscript EUGENe: A Python toolkit for sequence activity prediction and analysis
MotifData
Motif representation and analysis toolkit in Python
SeqData
Annotated sequence data
SeqDatasets
Datasets for benchmarking, testing and developing in EUGENe
SeqExplainer
Interpreting sequence-to-function machine learning models
SeqPro
Genomic sequence preprocessing toolkit
tutorials
A set of tutorials for how to use all the tools in ML4GLand
use_cases
Repository documenting applications of the ML4GLand suite on published datasets
Machine Learning for Genomics's Repositories
ML4GLand/EUGENe
Elucidating the Utility of Genomic Elements with Neural Nets
ML4GLand/SeqData
Annotated sequence data
ML4GLand/SeqPro
Genomic sequence preprocessing toolkit
ML4GLand/EUGENe_paper
Code for generating the figures and results presented in the manuscript EUGENe: A Python toolkit for sequence activity prediction and analysis
ML4GLand/SeqExplainer
Interpreting sequence-to-function machine learning models
ML4GLand/awesome-dl4g
(Soon to be) community-curated list of software packages and data resources for deep learning for genomics (DL4G)
ML4GLand/SeqDatasets
Datasets for benchmarking, testing and developing in EUGENe
ML4GLand/MotifData
Motif representation and analysis toolkit in Python
ML4GLand/tutorials
A set of tutorials for how to use all the tools in ML4GLand
ML4GLand/UCSD_DL4B
The official GitHub repository of UCSD's DL4B working group
ML4GLand/use_cases
Repository documenting applications of the ML4GLand suite on published datasets
ML4GLand/.github
ML4GLand/AI-ATAC
Dataset from the AI-TAC convoluional network for predicting mouse immune cell ATAC-seq signal
ML4GLand/deAlmeida_DrosophilaS2_UMI-STARR-seq
UMI-STARR-seq in Drosophila Melongaster, both genome wide and oligo based
ML4GLand/deBoer_random-promoters_GPRA
Quantified activity of millions of random yeast promoters with GPRAs
ML4GLand/external
Code snippets and wrappers for use of external tools without forking repos
ML4GLand/HepG2_U2AF2-eCLIP
ML4GLand/Horlacher_HepG2_CLIP
Predicting protein-RNA interaction via sequence-to-signal learning from CLIP-seq data
ML4GLand/K562_ATAC-seq
ENCODE K562_ATAC-seq dataset
ML4GLand/K562_CTCF-ChIP-seq
ML4GLand/K562_STARR-seq
ML4GLand/pbmc3k_10X-Multiome
ML4GLand/RNACompete2013
The 2013-RNAcompete dataset consists of 244 experiments for 207 RBPs using only weakly structured probes