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    29 repositories

    • nextflow-radiantkit

      Public
      Nextflow pipeline for the processing of GPSeq YFISH data
      Nextflow
      •
      MIT License
      •2•0•0•0•Updated Aug 4, 2025Aug 4, 2025

    • nextflow-gpseq

      Public
      Nextflow pipeline for processing of GPSeq data
      R
      •
      MIT License
      •2•0•0•0•Updated Aug 4, 2025Aug 4, 2025

    • fish_probe_design

      Public
      Shell
      •
      MIT License
      •2•4•0•1•Updated Jul 11, 2025Jul 11, 2025

    • radiantkit

      Public
      Analysis of YFISH image for GPSeq
      Python
      •
      MIT License
      •1•1•2•0•Updated Jun 9, 2025Jun 9, 2025

    • .github

      Public
      bicrolabs
      0•0•0•0•Updated May 9, 2025May 9, 2025

    • nextflow-gpseqyfish

      Public
      Nextflow pipeline for the processing of GPSeq YFISH data
      Nextflow
      •2•0•0•0•Updated Dec 12, 2024Dec 12, 2024

    • UpStreamPipeline

      Public
      Fork of UpStreamPipelines for ChIP, CUT&RUN, ATAC analysis from the Hughes Lab
      HTML
      •
      MIT License
      •1•0•0•0•Updated Apr 16, 2024Apr 16, 2024

    • scCUTseq

      Public
      Code and data used for scCUTseq manuscript
      HTML
      •
      MIT License
      •2•2•0•0•Updated Feb 17, 2024Feb 17, 2024

    • nextflow-scdnaseq

      Public
      Nextflow pipeline to process scDNAseq data
      R
      •3•0•0•0•Updated Jan 25, 2024Jan 25, 2024

    • scCircle-seq

      Public
      Python
      •1•4•0•0•Updated Jan 3, 2024Jan 3, 2024

    • FRET_FISH

      Public
      MATLAB
      •0•0•0•0•Updated Sep 29, 2022Sep 29, 2022

    • NatSciData_Neuro

      Public
      Code Repository for the BLISS Nature Scientific Data analyses
      MIT License
      •0•1•0•0•Updated May 12, 2022May 12, 2022

    • blissNP

      Public
      Step-by-step procedure for the analysis of BLISS and sBLISS datasets. For more information:
      genomic-data-analysisdouble-strand-breaks
      genomic-data-analysisdouble-strand-breaks
      Shell
      •
      MIT License
      •4•3•4•0•Updated Nov 19, 2021Nov 19, 2021

    • nucleAI

      Public
      Unsupervised machine learning of WSI
      Jupyter Notebook
      •
      MIT License
      •2•1•0•0•Updated Nov 26, 2020Nov 26, 2020

    • 3Dstructures2communities

      Public
      Find recurrent colocalized genomic loci in ensembles of 3D chromosome structures
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Nov 25, 2020Nov 25, 2020

    • blissNPanalysis

      Public
      Tutorial on Nature Protocols (s)BLISS downstream analysis
      MIT License
      •2•3•0•0•Updated Oct 7, 2020Oct 7, 2020

    • gpseqc

      Public archive
      Nuclear centrality estimation from GPSeq experiment.
      Python
      •
      MIT License
      •2•0•0•0•Updated Jul 15, 2020Jul 15, 2020

    • WSI-analysis

      Public
      Pipeline to analyze WSI
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jul 13, 2020Jul 13, 2020

    • GPSeq-source-data

      Public archive
      Source data for GPSeq manuscript.
      C
      •
      MIT License
      •1•0•0•0•Updated May 22, 2020May 22, 2020

    • gpseqc-snakemake

      Public archive
      Python
      •1•0•0•0•Updated Mar 25, 2020Mar 25, 2020

    • iFISH-singleLocus-analysis

      Public archive
      Pipeline for iFISH single locus data analysis
      R
      •
      MIT License
      •1•0•0•0•Updated Mar 25, 2020Mar 25, 2020

    • pygpseq

      Public archive
      Python3 package to analyse GPSeq images and manage TIFF files.
      Python
      •
      MIT License
      •1•0•0•0•Updated Dec 9, 2019Dec 9, 2019

    • gpseq_structures_SG

      Public
      My gpseq repo
      Jupyter Notebook
      •0•0•0•0•Updated Nov 19, 2019Nov 19, 2019

    • BLISS

      Public
      Repository for the BLISS pipeline.
      Shell
      •0•0•0•0•Updated Sep 26, 2019Sep 26, 2019

    • CUTseq

      Public
      CUTseq pipeline
      Jupyter Notebook
      •0•0•0•0•Updated Sep 26, 2019Sep 26, 2019

    • iFISH-probe-design

      Public archive
      iFISH Probe Design: a Python3 package to build iFISH probes.
      Python
      •
      MIT License
      •6•0•0•0•Updated Sep 11, 2019Sep 11, 2019

    • bed-fix-chrom-rearrangement

      Public archive
      Python
      •
      MIT License
      •1•0•0•0•Updated Aug 12, 2019Aug 12, 2019

    • ood-fish

      Public archive
      Orthogonal Oligo Design for Fluorescence In Situ Hybridization (a.k.a. OOD-FISH)
      R
      •
      MIT License
      •2•0•0•0•Updated Apr 29, 2019Apr 29, 2019

    • oligo-picker

      Public archive
      Pipeline for identification of FISHing location-specific oligonucleotide sequences.
      Perl
      •
      MIT License
      •1•0•0•0•Updated Feb 15, 2019Feb 15, 2019
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