Repositories list

• .github

  Public
  bicrolabs

  0•0•0•0•Updated Dec 13, 2024Dec 13, 2024

• nextflow-gpseqyfish

  Public
  Nextflow pipeline for the processing of GPSeq YFISH data

  Nextflow

  •1•0•0•0•Updated Dec 12, 2024Dec 12, 2024

• radiantkit

  Public
  Analysis of YFISH image for GPSeq

  Python

  •

  MIT License

  •0•0•1•0•Updated Nov 21, 2024Nov 21, 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-gpseq

  Public
  Nextflow pipeline for processing of GPSeq data

  R

  •2•0•0•0•Updated Feb 9, 2024Feb 9, 2024

• nextflow-scdnaseq

  Public
  Nextflow pipeline to process scDNAseq data

  R

  •2•0•0•0•Updated Jan 25, 2024Jan 25, 2024

• scCircle-seq

  Public
  Python

  •0•3•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

  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