Repositories list

• merfish_tools

  Public
  Functions and scripts for processing RNA MERFISH data

  Jupyter Notebook

  •11 fork•33 stars•00 issues•00 pull requests•Updated May 18, 2026May 18, 2026

• MERlin

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

  Python

  •

  MIT License

  •3434 forks•22 stars•11 issue•00 pull requests•Updated Mar 29, 2026Mar 29, 2026

• MERMAKE

  Public
  Python

  •

  GNU General Public License v3.0

  •22 forks•00 stars•00 issues•00 pull requests•Updated Mar 9, 2026Mar 9, 2026

• MERFISH_Plus_Paper

  Public
  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 16, 2026Jan 16, 2026

• bpToolbox

  Public
  scripts and functions for single cell genomic analysis

  processingannotationtransposable-elements+ 4

  processingannotationtransposable-elementspeak-callingdimesion-reductiondifferential-comparisonsgrns

  R

  •00 forks•11 star•00 issues•00 pull requests•Updated Jan 8, 2026Jan 8, 2026

• new_merfish_pipeline

  Public
  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 22, 2025Mar 22, 2025

• Spateo-with-MERFISH-Data

  Public
  00 forks•00 stars•11 issue•00 pull requests•Updated Nov 21, 2023Nov 21, 2023

• bican

  Public
  Jupyter Notebook

  •11 fork•00 stars•00 issues•00 pull requests•Updated Nov 3, 2023Nov 3, 2023

• MERlin_Parameters

  Public
  Parameter files for MERlin

  00 forks•00 stars•00 issues•00 pull requests•Updated Feb 21, 2023Feb 21, 2023

• epigen_ucsd_django

  Public
  djangoillumina

  djangoillumina

  Python

  •11 fork•11 star•140140 issues•00 pull requests•Updated Jun 28, 2021Jun 28, 2021

• huang-natgen2021

  Public
  Jupyter Notebook

  •00 forks•44 stars•00 issues•00 pull requests•Updated Jun 27, 2021Jun 27, 2021

• utility_epigen

  Public
  Shell

  •11 fork•11 star•00 issues•00 pull requests•Updated Mar 5, 2021Mar 5, 2021

• atac_seq_pipeline

  Public
  Python

  •

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

  •00 forks•66 stars•1010 issues•00 pull requests•Updated Mar 5, 2021Mar 5, 2021

• HiC_scripts

  Public
  HiC processing scripts used in the center.

  pipelinehic

  pipelinehic

  Jupyter Notebook

  •44 forks•33 stars•00 issues•00 pull requests•Updated Dec 10, 2020Dec 10, 2020

• chipseq_pipeline

  Public
  pipelinechip-seqbds

  pipelinechip-seqbds

  Java

  •

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

  •00 forks•11 star•1111 issues•00 pull requests•Updated Nov 15, 2019Nov 15, 2019

• atacMotif

  Public
  Motif analysis of atac peaks

  HTML

  •11 fork•00 stars•11 issue•00 pull requests•Updated Oct 9, 2019Oct 9, 2019

• SNAP-CHIP_epicypher

  Public
  A tool for QC snap-chip from epicypher

  Shell

  •11 fork•00 stars•44 issues•00 pull requests•Updated Sep 5, 2018Sep 5, 2018

• washUeg_json

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

  Shell

  •00 forks•00 stars•11 issue•00 pull requests•Updated Aug 3, 2018Aug 3, 2018

• onboarding

  Public
  Getting started in epigen-UCSD

  Shell

  •

  GNU General Public License v2.0

  •22 forks•00 stars•44 issues•00 pull requests•Updated May 30, 2018May 30, 2018

• snATAC_index_designer

  Public
  A tool to design reliable index sets for scATAC

  primer-designscatac

  primer-designscatac

  Python

  •11 fork•00 stars•22 issues•00 pull requests•Updated May 18, 2018May 18, 2018

• bcl2fastq_undetermined_parser

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

  Python

  •11 fork•11 star•00 issues•00 pull requests•Updated May 4, 2018May 4, 2018

• snATAC_preprocess

  Public
  Python

  •00 forks•00 stars•11 issue•00 pull requests•Updated Apr 9, 2018Apr 9, 2018

• docker-4dn-hic

  Public
  Docker for 4DN Hi-C processing pipeline

  HTML

  •

  MIT License

  •1616 forks•00 stars•00 issues•00 pull requests•Updated Apr 5, 2018Apr 5, 2018

• snATAC_pipeline

  Public
  based on Roxing's pipeline

  Shell

  •11 fork•00 stars•22 issues•00 pull requests•Updated Jan 9, 2018Jan 9, 2018