Skip to content
View e-south's full-sized avatar
5 followers · 21 following

Achievements

Achievement: Pull Shark

Achievements

Achievement: Pull Shark

Block or report e-south

Block user

Prevent this user from interacting with your repositories and sending you notifications. Learn more about blocking users.

You must be logged in to block users.

Maximum 250 characters. Please don't include any personal information such as legal names or email addresses. Markdown supported. This note will be visible to only you.
Report abuse

Contact GitHub support about this user’s behavior. Learn more about reporting abuse.

Report abuse
e-south/README.md

👋 Hi, I’m @e-south

PhD Candidate in the Dunlop Lab, Biological Design Center, Boston University.

Previously at Imperial College London and James Madison University.

Current works

dnadesign

A DNA sequence design workspace: a modular set of bioinformatics pipelines and utilities for designing, analyzing, and managing biological data.

  • Wraps packages like densearrays and Evo 2 to support workflows.
  • Provides a suite of command‑line entry points for many pipelines.

reader

  • Command-line workbench for experimental data.
  • Plugin‑extensible registry that ingests raw instrument exports, applies transformations and post‑processing, and outputs tidy data and plots for downstream pipelines.

Past works

densearrays

Method for designing sequences with densely packed DNA–protein binding motifs.

deg2tfbs

Links differential expression to transcription factors and their binding sites.

Get in touch

Pinned Loading

  1. dense-arrays dense-arrays Public

    We introduce a computational technique that efficiently assembles sets of DNA-protein binding sites into dense, contiguous stretches of double-stranded DNA.

    Python

  2. dnadesign dnadesign Public

    A collection of Python modules and data analysis pipelines, all related to DNA sequence design.

    Python

  3. reader reader Public

    Command-line workbench for experimental data.

    Python

  4. dnadesign-data dnadesign-data Public

    This repository contains datasets, such as RegulonDB, EcoCyc, primary literature data.

    Python

  5. deg2tfbs deg2tfbs Public

    Pipeline for differential expression analysis (DEGs), transcription factor mapping, and TFBS identification.

    Python

  6. CIDARLAB/ibis CIDARLAB/ibis Public

    Graph-based Datastructure Library for Genetic and Boolean Circuits.

    Python 1 2