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    19 repositories

    • LEPAE

      Public
      Learning Evidence of Pairwise Association from Epigenomic and TF binding data
      Python
      •
      GNU General Public License v2.0
      •0•0•0•0•Updated Nov 5, 2024Nov 5, 2024

    • inpsyght_states

      Public
      ChromHMM and ConsHMM state-based analysis for InPSYght samples
      Jupyter Notebook
      •0•0•0•0•Updated Aug 7, 2024Aug 7, 2024

    • full_stack_ChromHMM_annotations

      Public
      Data of genome annotation from full-stack ChromHMM model trained with 1032 datasets from 127 reference epigenomes
      Python
      •1•32•0•0•Updated Jul 9, 2024Jul 9, 2024

    • EpiVarIndividuals

      Public
      R
      •0•0•0•0•Updated Jun 23, 2024Jun 23, 2024

    • ernstlab.github.io

      Public
      HTML
      •0•0•0•0•Updated Jun 11, 2024Jun 11, 2024

    • ChromActivity

      Public
      ChromActivity is a computational framework for the annotation of regulatory activity genomewide, through integration of data from epigenomic maps and multiple functional characterization assays.
      Python
      •0•1•0•0•Updated Apr 18, 2024Apr 18, 2024

    • ENSAS

      Public
      Identifying associations of de novo noncoding variants with autism through integration of gene expression, sequence and sex information
      Python
      •1•0•0•0•Updated Feb 29, 2024Feb 29, 2024

    • SharprSeq

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Jan 31, 2024Jan 31, 2024

    • CMImpute

      Public
      Cross-species and tissue imputation of species-level DNA methylation samples across mammalian species.
      Python
      •0•2•0•0•Updated Dec 7, 2023Dec 7, 2023

    • ChromGene

      Public
      Gene-Based Modelling of Epigenomic Data
      Python
      •
      MIT License
      •1•6•0•1•Updated Sep 25, 2023Sep 25, 2023

    • mouse_fullStack_annotations

      Public
      mouse_fullStack_annotations
      Python
      •0•10•0•0•Updated Jun 29, 2023Jun 29, 2023

    • ConsHMM

      Public
      Java
      •5•16•0•0•Updated Mar 5, 2023Mar 5, 2023

    • csrep

      Public
      differential and summary chromatin states
      Python
      •0•5•0•0•Updated Nov 25, 2022Nov 25, 2022

    • LECIF

      Public
      Learning a genome-wide score of conservation at the functional genomics level between human and mouse
      Python
      •
      GNU General Public License v2.0
      •1•12•0•0•Updated Sep 23, 2022Sep 23, 2022

    • CNEP

      Public
      Constrained Non-Exonic Predictor (CNEP) provides a score of evidence that each base of the genome in a constrained non-exonic base from information within large-scale collections of epigenomic and transcription factor binding data.
      Java
      •
      GNU General Public License v2.0
      •1•3•0•0•Updated Jun 13, 2022Jun 13, 2022

    • ChromTime

      Public
      Modeling Spatio-temporal Dynamics of Chromatin Marks
      Python
      •
      GNU General Public License v3.0
      •2•12•2•0•Updated Aug 2, 2021Aug 2, 2021

    • ConsHMM_CoV

      Public
      0•2•0•0•Updated Jun 3, 2021Jun 3, 2021

    • X-CNN

      Public
      Computational method for fine-mapping chromatin interactions, e.g., Hi-C
      Python
      •
      MIT License
      •1•7•0•0•Updated Feb 21, 2020Feb 21, 2020

    • chip_db

      Public
      A lightweight database to deal with many ChIP-seq or similar whole-genome tracks. Allows for constant-time access of any position along the genome.
      Python
      •2•0•0•0•Updated Apr 20, 2018Apr 20, 2018