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    58 repositories

    • aryeelab.dfci.harvard.edu

      Public
      Aryee Lab Webpage
      JavaScript
      •
      MIT License
      •100•0•0•0•Updated Nov 4, 2024Nov 4, 2024

    • cohesin_extrusion_reproducibility

      Public
      Code repository to reproduce all results for Sept, et al. 2023
      R
      •
      MIT License
      •0•0•0•0•Updated Oct 14, 2024Oct 14, 2024

    • nanopore-tools

      Public
      Tools for Oxford Nanopore
      WDL
      •1•2•3•0•Updated Aug 21, 2024Aug 21, 2024

    • topology-tools

      Public
      Processing pipelines for HiC and other 3D genome tools
      WDL
      •1•3•3•0•Updated Mar 17, 2024Mar 17, 2024

    • extrusion-sim

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Feb 12, 2024Feb 12, 2024

    • neochromatin

      Public
      R
      •0•1•0•0•Updated Nov 5, 2023Nov 5, 2023

    • guideseq

      Public
      Analysis pipeline for the GUIDE-seq assay.
      Python
      •
      GNU Affero General Public License v3.0
      •55•76•37•0•Updated Jun 14, 2023Jun 14, 2023

    • population-offtargets

      Public
      0•0•0•0•Updated Jun 4, 2023Jun 4, 2023

    • block_methylation

      Public
      0•0•0•0•Updated May 22, 2023May 22, 2023

    • encode-chip-seq-pipeline2

      Public
      ENCODE ChIP-seq pipeline
      Python
      •
      MIT License
      •123•0•0•0•Updated May 18, 2023May 18, 2023

    • umi

      Public
      Preprocessing tools for unique molecular index (UMI) sequencing reads
      Python
      •
      MIT License
      •26•31•10•0•Updated Apr 25, 2023Apr 25, 2023

    • encode-hic-pipeline

      Public
      HiC uniform processing pipeline
      WDL
      •
      MIT License
      •24•0•0•0•Updated Feb 3, 2023Feb 3, 2023

    • knock-knock

      Public
      toolkit for analyzing genome editing experiments
      Python
      •
      GNU General Public License v3.0
      •10•0•0•0•Updated Jan 25, 2023Jan 25, 2023

    • broad-epi-cut-n-run

      Public
      Porting the 4d nucleosome Cut-and-Run pipeline to WDL
      WDL
      •1•0•0•0•Updated Jan 3, 2023Jan 3, 2023

    • seaseq

      Public
      Abraham's lab - ChipSeq Pipeline
      WDL
      •
      Apache License 2.0
      •5•0•0•0•Updated Dec 20, 2022Dec 20, 2022

    • pairtools

      Public
      CLI tools to process mapped Hi-C data
      Python
      •
      MIT License
      •32•0•0•0•Updated Dec 8, 2022Dec 8, 2022

    • nanoHiMe

      Public
      C
      •2•0•0•0•Updated Nov 4, 2022Nov 4, 2022

    • nanopolish

      Public
      Signal-level algorithms for MinION data
      C++
      •
      MIT License
      •159•0•0•0•Updated Jul 29, 2022Jul 29, 2022

    • hichipper

      Public
      A preprocessing and QC pipeline for HiChIP data
      bioinformaticsepigeneticschromatin-interactionhichip
      HTML
      •
      MIT License
      •12•34•47•0•Updated Jul 11, 2022Jul 11, 2022

    • cas-designer

      Public
      WDL
      •0•1•1•0•Updated Jul 23, 2021Jul 23, 2021

    • cromwell-monitor

      Public
      Generate stats for Cromwell task calls including resource utilization & estimated costs
      Python
      •9•0•0•0•Updated Jun 26, 2021Jun 26, 2021

    • hypometh-expression-biomarkers

      Public
      HTML
      •0•0•0•0•Updated Mar 31, 2021Mar 31, 2021

    • colon-dna-topology

      Public
      Shell
      •2•5•0•0•Updated Jan 3, 2021Jan 3, 2021

    • bisulfite-seq-tools

      Public
      Suite of tools to conduct methylation data analysis. Methods from this workspace can be used for alignment and quality control analysis for various protocols including Whole Genom Bisulfite Sequencing (WGBS), Reduced Representation Bisulfite Sequencing (RRBS) and Hybrid Selection Bisulfite Sequencing (HSBS).
      methylationcloud-computingbisulfite-sequencing
      HTML
      •2•18•0•0•Updated Nov 19, 2020Nov 19, 2020

    • pytest-wdl

      Public
      Docker container with pytest-wdl for testing WDL pipelines
      Dockerfile
      •0•0•0•0•Updated Oct 25, 2020Oct 25, 2020

    • geomx-dnd

      Public
      0•0•0•0•Updated Oct 25, 2020Oct 25, 2020

    • al-folio

      Public
      A beautiful, simple, clean, and responsive Jekyll theme for academics
      JavaScript
      •
      MIT License
      •11k•0•0•0•Updated Jul 14, 2020Jul 14, 2020

    • RNAseq_BE_editing

      Public
      Shell
      •1•1•0•0•Updated Mar 16, 2020Mar 16, 2020

    • DNAlandscapeR

      Public
      Shiny app that integrates ChIA-PET and other epigenetic tracks
      C++
      •2•3•5•0•Updated Nov 30, 2019Nov 30, 2019

    • nanopore-util

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Oct 22, 2019Oct 22, 2019