Repositories list

• MERlin

  Public
  MERlin is an extensible analysis pipeline applied to decoding MERFISH data

  Python

  •

  MIT License

  •31•1•1•0•Updated Nov 12, 2024Nov 12, 2024

• new_merfish_pipeline

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Sep 20, 2024Sep 20, 2024

• Spateo-with-MERFISH-Data

  Public
  0•0•0•0•Updated Nov 21, 2023Nov 21, 2023

• bican

  Public
  Jupyter Notebook

  •1•0•0•0•Updated Nov 3, 2023Nov 3, 2023

• merfish_tools

  Public
  Functions and scripts for processing RNA MERFISH data

  Jupyter Notebook

  •1•2•0•0•Updated Jul 6, 2023Jul 6, 2023

• MERlin_Parameters

  Public
  Parameter files for MERlin

  0•0•0•0•Updated Feb 21, 2023Feb 21, 2023

• epigen_ucsd_django

  Public
  djangoillumina

  Python

  •1•1•140•0•Updated Jun 28, 2021Jun 28, 2021

• huang-natgen2021

  Public
  Jupyter Notebook

  •0•4•0•0•Updated Jun 27, 2021Jun 27, 2021

• utility_epigen

  Public
  Shell

  •1•1•0•0•Updated Mar 5, 2021Mar 5, 2021

• atac_seq_pipeline

  Public
  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•6•10•0•Updated Mar 5, 2021Mar 5, 2021

• HiC_scripts

  Public
  HiC processing scripts used in the center.

  pipelinehic

  Jupyter Notebook

  •4•3•0•0•Updated Dec 10, 2020Dec 10, 2020

• chipseq_pipeline

  Public
  pipelinechip-seqbds

  Java

  •

  BSD 3-Clause "New" or "Revised" License

  •0•1•11•0•Updated Nov 15, 2019Nov 15, 2019

• atacMotif

  Public
  Motif analysis of atac peaks

  HTML

  •1•0•1•0•Updated Oct 9, 2019Oct 9, 2019

• SNAP-CHIP_epicypher

  Public
  A tool for QC snap-chip from epicypher

  Shell

  •1•0•4•0•Updated Sep 5, 2018Sep 5, 2018

• washUeg_json

  Public
  A tool to generate json for http://epigenomegateway.wustl.edu/browser/

  Shell

  •0•0•1•0•Updated Aug 3, 2018Aug 3, 2018

• onboarding

  Public
  Getting started in epigen-UCSD

  Shell

  •

  GNU General Public License v2.0

  •2•0•4•0•Updated May 30, 2018May 30, 2018

• snATAC_index_designer

  Public
  A tool to design reliable index sets for scATAC

  primer-designscatac

  Python

  •1•0•2•0•Updated May 18, 2018May 18, 2018

• bcl2fastq_undetermined_parser

  Public
  Parse the result from bcl2fastq and get the undermined barcode info

  Python

  •1•1•0•0•Updated May 4, 2018May 4, 2018

• snATAC_preprocess

  Public
  Python

  •0•0•1•0•Updated Apr 9, 2018Apr 9, 2018

• docker-4dn-hic

  Public
  Docker for 4DN Hi-C processing pipeline

  HTML

  •

  MIT License

  •18•0•0•0•Updated Apr 5, 2018Apr 5, 2018

• snATAC_pipeline

  Public
  based on Roxing's pipeline

  Shell

  •1•0•2•0•Updated Jan 9, 2018Jan 9, 2018