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    29 repositories

    • deepC

      Public
      A neural network framework for predicting the Hi-C chromatin interactions from megabase scale DNA sequence
      HTML
      •
      GNU General Public License v3.0
      •14•33•2•0•Updated Jan 19, 2026Jan 19, 2026

    • sasquatch

      Public
      Predicting the impact of regulatory SNPs from cell and tissue specific DNase-footprints
      R
      •
      GNU General Public License v3.0
      •3•9•2•0•Updated Mar 1, 2023Mar 1, 2023

    • mlv

      Public
      Python
      •
      GNU General Public License v3.0
      •1•2•5•12•Updated Dec 8, 2022Dec 8, 2022

    • deepHaem

      Public
      Implementation of a deep convolutional neural network for predicting chromatin features from DNA sequence
      Python
      •
      GNU General Public License v3.0
      •6•16•0•0•Updated Jan 13, 2022Jan 13, 2022

    • mlv-docs

      Public
      HTML
      •1•0•0•0•Updated Nov 24, 2021Nov 24, 2021

    • Downes_2021_LZTFL1_Covid

      Public
      Custom codes for data analysis.
      Perl
      •1•3•0•0•Updated Sep 2, 2021Sep 2, 2021

    • CCseqBasicS

      Public
      CCseqBasic - stable version of CCseqBasic analysis pipeline (getting updates when dev pipeline features get stable enough)
      Shell
      •
      MIT License
      •1•1•0•0•Updated May 11, 2021May 11, 2021

    • CIView

      Public
      JavaScript
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Feb 1, 2021Feb 1, 2021

    • Lanceotron-User-Docs

      Public
      HTML
      •
      GNU General Public License v3.0
      •1•0•1•0•Updated Dec 7, 2020Dec 7, 2020

    • MEV

      Public
      Python
      •0•0•0•0•Updated Sep 29, 2020Sep 29, 2020

    • TriC

      Public
      Scripts for the analysis of TriC experiments
      Perl
      •0•0•0•0•Updated Jun 26, 2020Jun 26, 2020

    • MLVPanel

      Public
      JavaScript
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated May 19, 2020May 19, 2020

    • CaptureCompare

      Public
      Post processing of captureC replicates
      Shell
      •
      Other
      •1•0•0•0•Updated Feb 27, 2020Feb 27, 2020

    • CCseqBasicM

      Public
      Current development version of Multithread CCseqBasic
      Shell
      •
      MIT License
      •0•0•0•0•Updated Jan 7, 2020Jan 7, 2020

    • NGseqBasic

      Public
      Mapping, filtering, and data hub visualisation pipeline for DNase, ATAC, ChIP data
      ngs-pipeline
      ngs-pipeline
      Shell
      •
      MIT License
      •2•10•0•0•Updated Dec 23, 2019Dec 23, 2019

    • plateScreen96

      Public
      CRISPR short indel genotype analyser for sequences, which have unique indices per well
      genotype96-well-plate
      genotype96-well-plate
      Shell
      •
      MIT License
      •1•0•1•0•Updated Sep 3, 2019Sep 3, 2019

    • zegamiutils

      Public
      Utility methods for Zegami
      Python
      •0•1•0•0•Updated Aug 15, 2019Aug 15, 2019

    • CCseqBasicF

      Public
      CCseqBasic - freeze version with CF3 CF4 CF5 run modes (to run with different duplicate filtering options)
      Shell
      •
      MIT License
      •1•1•0•0•Updated Jun 3, 2019Jun 3, 2019

    • variantApp

      Public
      to investigate if your regions of interest have variant-calling potential
      Shell
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Mar 22, 2019Mar 22, 2019

    • CCseqBasic4

      Public
      CaptureC analysis pipeline with "proper duplicate filtering" (VS04) - for long read lengths.
      Shell
      •
      MIT License
      •1•0•0•0•Updated Jan 24, 2019Jan 24, 2019

    • CCseqBasic3

      Public
      CaptureC analysis pipeline with "lenient duplicate filtering" (VS03) - for short read lengths.
      Perl
      •
      MIT License
      •1•0•0•0•Updated Jan 24, 2019Jan 24, 2019

    • captureC

      Public
      CaptureC analysis code by James Davies - to serve as supplements to the publication.
      capturec
      capturec
      MIT License
      •5•1•0•0•Updated Jan 24, 2019Jan 24, 2019

    • PYRAMIDmetadata

      Public
      The real metadata files of pyramid. - the editing of the metadata will happen here, after we have done the "first round" of filling the files manually.
      0•0•0•0•Updated Jun 21, 2018Jun 21, 2018

    • GEObuilder

      Public
      GEO auto-archiver for NGseqBasic pipe (and other data types)
      Shell
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Jun 5, 2018Jun 5, 2018

    • pythonPileupModules

      Public
      Jupyter Notebook
      •1•0•0•0•Updated Feb 13, 2018Feb 13, 2018

    • nxtSeqCat

      Public
      Concatenation of multilane output of an Illumina NextSeq
      Perl
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Nov 8, 2017Nov 8, 2017

    • macs2hubber

      Public
      Macs2 wrapper, which automatically makes data hub from the output files
      Shell
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Oct 25, 2017Oct 25, 2017

    • RonsUtilityBox

      Public
      (Hopefully) useful scripts for genomics
      miscellaneous-scripts
      miscellaneous-scripts
      Python
      •2•0•0•0•Updated Oct 25, 2017Oct 25, 2017

    • LowInputCaptureC

      Public
      CaptureC analysis script, including options for stringent duplicate removal in low-input Capture-C experiments
      Perl
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Jun 15, 2017Jun 15, 2017
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