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regulatory-genomics

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pinellolab /DNA-Diffusion

🧬 Generative modeling of regulatory DNA sequences with diffusion probabilistic models 💨

deep-learning genomics generative-model diffusion-models regulatory-genomics stable-diffusion diffusion-probabilistic-models

UpdatedMar 17, 2025
Python

ML4GLand /EUGENe

Elucidating the Utility of Genomic Elements with Neural Nets

python machine-learning bioinformatics deep-learning genomics regulatory-genomics

UpdatedDec 2, 2024
Jupyter Notebook

aertslab /CREsted

CREsted is a Python package for training sequence-based deep learning models on scATAC-seq data, for capturing enhancer code and for designing cell type-specific sequences.

deep-learning sequence-models single-cell-genomics scatac-seq regulatory-genomics scverse

UpdatedMar 24, 2025
Python

evanseitz /squid-nn

surrogate quantitative interpretability for deepnets

motif-analysis surrogate-modelling explainable-ai model-interpretability attribution-methods regulatory-genomics

UpdatedMar 21, 2025
Python

ML4GLand /SeqPro

Genomic sequence preprocessing toolkit

python data-science machine-learning bioinformatics regulatory-genomics

UpdatedMar 17, 2025
Python

meuleman /SynthSeqs

Data-driven design of context-specific regulatory elements

synthetic-biology computational-biology pytorch regulatory-genomics

UpdatedJun 18, 2024
Python

kundajelab /lsgkm-svr

lsgkm+gkmexplain with regression functionality. Builds off kundajelab/lsgkm (which has gkmexplain), which in turn builds off Dongwon-Lee/lsgkm (the original lsgkm repo)

regression svr regulatory-genomics gkm-svm

UpdatedDec 1, 2020
C

BrentLab /Dual_Threshold_Optimization

Dual Threshold Optimization compares two ranked lists of features (e.g. genes) to determine the rank threshold for each list that minimizes the hypergeometric p-value of the overlap of features. It then calculates a permutation based empirical p-value and an FDR

bioinformatics transcription-factors transcription-factor-binding transcriptional-regulatory-network regulatory-network geneset-enrichment-analysis transcription-factor-perturbation regulatory-genomics

UpdatedDec 5, 2024
Rust

ML4GLand /SeqExplainer

Interpreting sequence-to-function machine learning models

python machine-learning bioinformatics deep-learning interpretable-machine-learning regulatory-genomics

UpdatedJan 25, 2024
Jupyter Notebook

ML4GLand /tutorials

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

machine-learning tutorial regulatory-genomics

UpdatedFeb 6, 2025
Jupyter Notebook

evanseitz /squid-manuscript

squid repository for manuscript analysis

motif-analysis surrogate-modelling explainable-ai model-interpretability attribution-methods regulatory-genomics

UpdatedMar 5, 2024
Python

dzyim /awesome-regulatory-genomics-papers

A curated list of regulatory genomics papers and resources.

lists awesome genetics gene-expression epigenetics functional-genomics regulatory-genomics

UpdatedApr 3, 2023

kchu25 /MotifPvalue.jl

Threshold and p-value computations for Position Weight Matrices

bioinformatics genomics julia motif p-value transcription-factor-binding pwm motifs position-weight-matrix regulatory-genomics

UpdatedDec 15, 2021
Julia

anilprakash94 /neur_ally

Deep learning model for non-coding regulatory variants

deep-learning genomics artificial-intelligence variant-effect-prediction noncoding-mutations attention-network regulatory-genomics neurological

UpdatedSep 22, 2023
Python

ML4GLand /SeqDatasets

Datasets for benchmarking, testing and developing in EUGENe

python machine-learning datasets regulatory-genomics

UpdatedDec 2, 2024
Python

kchu25 /UnfoldCDL.jl

Deep Unfolded Convolutional Dictionary Learning for motif discovery.

machine-learning deep-learning julia motif-discovery interpretable-deep-learning convolutional-dictionary-learning interpretable-machine-learning motif-finding transcription-factor-binding-site regulatory-genomics deep-unfolding

UpdatedFeb 2, 2023
Julia

ML4GLand /use_cases

Repository documenting applications of the ML4GLand suite on published datasets

machine-learning bioinformatics use-cases regulatory-genomics

UpdatedJan 3, 2024
Jupyter Notebook

biocompute-objects /bco-public-website

A Hugo-based deployment of biocomputeobject.org

biology standards bioinformatics-pipeline workflows ngs-analysis science-communication hts-computations regulatory-genomics high-th

UpdatedSep 10, 2021
HTML

mireia-bioinfo /plotRegulome

R package for plotting Islet Regulome data.

plotting regulatory-genomics

UpdatedJun 30, 2024
HTML

micheleantonazzi /bioinformatics-project

Analyze the active regulatory region of DNA using FFNN and CNN

bioinformatics cnn ffnn regulatory-genomics

UpdatedMar 29, 2021
Python

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