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    62 repositories

    • TENet

      Public
      Python
      •0•1•0•0•Updated Sep 22, 2024Sep 22, 2024

    • variant-scorer

      Public
      A framework to score and analyze variant effects genome-wide using ChromBPNet models
      Python
      •
      MIT License
      •2•8•2•0•Updated Oct 18, 2024Oct 18, 2024

    • bpnet-refactor

      Public
      Python
      •
      MIT License
      •0•3•5•1•Updated Apr 7, 2024Apr 7, 2024

    • track-hubs

      Public
      Python
      •0•0•0•0•Updated Apr 1, 2023Apr 1, 2023

    • ENCODE_manual_liver

      Public
      Python
      •1•0•0•0•Updated Mar 31, 2023Mar 31, 2023

    • ENCODE_manual_adrenal

      Public
      Python
      •1•0•0•0•Updated Mar 31, 2023Mar 31, 2023

    • idr

      Public
      IDR
      Python
      •
      GNU General Public License v2.0
      •46•30•0•1•Updated Mar 30, 2023Mar 30, 2023

    • basepairmodels

      Public
      Python
      •
      MIT License
      •6•16•18•2•Updated Mar 24, 2023Mar 24, 2023

    • simdna

      Public
      A python library for creating simulated regulatory DNA sequences
      Python
      •
      MIT License
      •21•38•0•2•Updated Feb 22, 2023Feb 22, 2023

    • ENCODE_scatac

      Public
      Python
      •
      MIT License
      •1•8•0•0•Updated Jan 31, 2023Jan 31, 2023

    • coessentiality-browser

      Public
      Gene browser using coessentiality and related data
      Python
      •1•4•10•1•Updated Dec 8, 2022Dec 8, 2022

    • mseqgen

      Public
      Multi task batch generator for training deep learning models on CHIP-seq, CHIP-exo, CHIP-nexus, ATAC-seq, RNA-seq (or any other -seq)
      Python
      •
      MIT License
      •2•1•1•0•Updated Aug 12, 2022Aug 12, 2022

    • genomics-DL-archsandlosses

      Public
      A collection of Deep Learning architectures and loss functions from across the genomics literature
      Python
      •
      MIT License
      •0•1•0•0•Updated Jul 28, 2022Jul 28, 2022

    • coessentiality

      Public
      Companion to "A genome-wide almanac of co-essential modules assigns function to uncharacterized genes" (https://doi.org/10.1101/827071)
      Python
      •
      MIT License
      •9•27•3•1•Updated Jul 19, 2022Jul 19, 2022

    • atac_dnase_pipelines

      Public
      ATAC-seq and DNase-seq processing pipeline
      bioinformatics-pipelinednase-seqatac-seq
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •81•162•25•2•Updated Jun 21, 2022Jun 21, 2022

    • deeplift

      Public
      Public facing deeplift repo
      sensitivity-analysissaliency-mapinterpretabilityguided-backpropagationinterpretable-deep-learningdeepliftintegrated-gradients
      Python
      •
      MIT License
      •162•820•40•3•Updated Apr 28, 2022Apr 28, 2022

    • cultivator

      Public
      A tool for generating covariate-matched and diversity-maximizing subsets. Generally useful, for built with genomic applications in mind.
      Python
      •
      MIT License
      •0•0•0•0•Updated Apr 23, 2022Apr 23, 2022

    • kerasAC

      Public
      keras accessibility models: code to train, predict, interpret
      Python
      •
      MIT License
      •6•6•0•0•Updated Feb 3, 2022Feb 3, 2022

    • seqdataloader

      Public
      Sequence data label generation and ingestion into deep learning models
      Python
      •
      MIT License
      •3•12•4•0•Updated Nov 17, 2021Nov 17, 2021

    • yuzu

      Public
      yuzu is a compressed-sensing based approach for quickly calculating in-silico mutagenesis saliency.
      Python
      •
      MIT License
      •0•6•0•0•Updated Nov 9, 2021Nov 9, 2021

    • chip-seq-pipeline2

      Public
      ENCODE ChIP-seq pipeline
      Python
      •
      MIT License
      •123•0•0•0•Updated Oct 10, 2021Oct 10, 2021

    • dSMF-scripts

      Public
      Python
      •0•0•0•0•Updated Sep 15, 2021Sep 15, 2021

    • MPRA-DragoNN

      Public
      Code accompanying the paper "Deciphering regulatory DNA sequences and noncoding genetic variants using neural network models of massively parallel reporter assays"
      Python
      •
      MIT License
      •4•11•0•1•Updated Aug 26, 2021Aug 26, 2021

    • tronn

      Public
      Transcriptional Regulation (Optimized) Neural Nets (TRoNN)
      Python
      •
      MIT License
      •1•8•1•0•Updated Aug 4, 2021Aug 4, 2021

    • abstention

      Public
      Algorithms for abstention, calibration and domain adaptation to label shift.
      calibrationdomain-adaptationprior-probability-shiftabstentionlabel-shift
      Python
      •4•36•0•0•Updated Nov 14, 2020Nov 14, 2020

    • chip-nexus-pipeline

      Public
      ChIP-nexus pipeline
      Python
      •
      MIT License
      •1•6•1•1•Updated Nov 6, 2020Nov 6, 2020

    • ENCODE_downloader

      Public
      Downloader for ENCODE
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •11•31•7•1•Updated Oct 5, 2020Oct 5, 2020

    • model_input_tracks

      Public
      Generate non-sequence input tracks for deep learning models, such as GC content, enzymatic activity
      Python
      •0•0•0•0•Updated Sep 16, 2020Sep 16, 2020

    • keras-genomics

      Public
      Genomics layers for Keras 2
      Python
      •7•5•0•0•Updated Sep 9, 2020Sep 9, 2020

    • dnafrag

      Public
      Optimized storage for DNA fragmentation V-plots
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Jul 12, 2020Jul 12, 2020