Edmund Miller

For keeping all my Dotfiles update to date

My private module for Doom Emacs

A package to run jest inside emacs

Emacs major mode for Nextflow

Create interactive UpSet plots using Altair

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Most simple webapp to bulk follow bioinformatics accounts on Mastodon.

An opinionated pack of modern color-themes, from the doom-emacs community

A package and module for using GNU Guix on Nix(OS). Kinda more a code dump than for actual use.

ETHSF 2018

Herdr plugin for opening Hunk diffs in split panes or tabs

My personal site

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ZSH Completions for Guix

Notebook-native Nextflow: stay in marimo/Jupyter while still getting reproducible runs, typed outputs, and observable execution.

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Herdr plugin for previewing GitHub issues and pull requests in a side pane

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Public repository for Agent Skills

Neovim plugin for managing TaskNotes - task management with markdown files and YAML frontmatter

A Neovim plugin for reading Obsidian Bases files

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Haplotype VCF comparison tools

Assembly and intrahost/low-frequency variant calling for viral samples

A tool to map bisulfite converted sequence reads and determine cytosine methylation states

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`taskwarrior-tui`: A terminal user interface for taskwarrior

Parallel Party Parrots

A Model Context Protocol (MCP) server implementation for DuckDB, providing database interaction capabilities

Visidata Plugins for Bioinformatics file formats

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Examples showing how to configure Nextflow to run with Wave containers provisioning service

A Vale-compatible implementation of common Bioinformatics terms

Examples of using Rust with Nextflow

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A collection of Snippets for Solidity for Emacs

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A GitHub action for org to html documentation.

An Emacs configuration for the stubborn martian vimmer

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⌥ AI Coding agent for the terminal — hash-anchored edits, optimized tool harness, LSP, Python, browser, subagents, and more

Temporary Fusion Doctor PR image for Wave validation

Codex-style goal tracking and continuation for pi.

Herdr plugin for opening my dotfiles dev workspace layout

Test data for MultiQC.

A minimal Nextflow workflow for testing infrastructure.

The agent that grows with you

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Terminal-native conductor for parallel Pi workspaces

Local Twitter/X bookmark organizer with AI categorization and mindmap visualization

OpenCode plugin for WorkTrunk worktree management

OpenClaw plugin that turns Linear into a multi-agent workspace — autonomous issue resolution, delegation, progress tracking, and more.

TUI for reviewing git changes

Gmail CLI, manage emails & calendar from your terminal

Download VEP cache for annotation-cache

A DSL for data-driven computational pipelines

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OpenCode plugin enforcing JJ define-before-implement workflow

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OpenCode plugin for macOS notifications when child sessions complete

A non-AI automatic scheduler for taskwarrior (i.e. alternative to skedpal/timehero/flowsavvy/reclaim/trevor/motion)

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fresh directories for every vibe

A command-line interface for TaskNotes with an NLP task-creation mode, task filtering, and FZF integration

🥋 Drive Jujutsu (jj) VCS from Neovim like a pro

Official repository of Trino, the distributed SQL query engine for big data, formerly known as PrestoSQL (https://trino.io)

👻 Ghostty is a fast, feature-rich, and cross-platform terminal emulator that uses platform-native UI and GPU acceleration.

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Custom dev container features

An Emacs interface for jujutsu, inspired by magit and humbly not attempting to match it in scope.

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Detecting contamination in NGS data and multi-species analysis

An interactive and powerful Git interface for Neovim, inspired by Magit

Adds support for MDX to Vale.

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Nextflow pipeline for hyperparameter optimization of machine learning models

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AI coding agent, built for the terminal.

A todo.txt plugin for Neovim.

Manage multiple AI terminal agents like Claude Code, Aider, Codex, OpenCode, and Amp.

Nextflow plugins index repository

Command line tool for Wave containers provisioning service

Personal task-tracking library

Tasksh is a shell for Taskwarrior

The next version of bwa-mem

Taskwarrior iOS interface app

Homebrew formulae for taskagent - Interactive AI-powered task review interface for Taskwarrior

Pull github, bitbucket, and trac issues into taskwarrior

Simple test framework for Nextflow pipelines

ChIP-seq peak-calling, QC and differential analysis pipeline.

1Password helpers for direnv

Manage Motion tasks directly from Raycast with powerful commands for capturing, searching, and organizing your work

Everything you need to extend Raycast.

Schedule your day visually, using timeblocking technique inside Emacs

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Web application to collect and visualise data across multiple MultiQC runs.

Utility to query Canny API

code templates and training materials to perform downs-tream analysis from nf-core RNAseq pipelines

Classic hello world script in Nextflow language

reproducible benchmark of database-like ops

A GPU-accelerated cross-platform terminal emulator and multiplexer written by @wez and implemented in Rust

The browser extension for gitpod.io. Works with Chrome and Firefox.

Declarative visualization library for Python

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Jupyter Notebooks and other code for Altair-based Interactive UpSet Plots

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Seamless authentication for every tool in your terminal.

Python implementation and field-tool for automated pipeline launching through Tower CLI (beta)

Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq

A tool for creating resource prediction models for scientific workflows

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Hone computational biology skills by re-enacting Figure 1 of modern biology papers

Removes all files in the work directory.

Aggregate results from bioinformatics analyses across many samples into a single report.

Core registry for mason.nvim.

Emacs client/library for the Language Server Protocol

Nextflow language support for Visual Studio Editor

gReLU is a python library to train, interpret, and apply deep learning models to DNA sequences.

Org Mode babel support for DuckDB

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🌷 Run code formatter on buffer contents without moving point, using RCS patches and dynamic programming.

The uncompromising Snakemake code formatter

A small, featureful neovim template

Proof-of-concept Nextflow pipeline to interact with OpenAI Whisper

Analysis pipeline for the identification of viral integration events in genomes using a chimeric read approach.

💬 Personal AI application powered by GPT-4 and beyond, with AI personas, AGI functions, text-to-image, voice, response streaming, code highlighting and execution, PDF import, presets for developers, much more. Deploy and gift #big-AGI-energy! Using Next.js, React, Joy.

🦆 A curated list of awesome DuckDB resources

A Github Action to gather Github stats about an organization. Written by Harrison Hogg for Spotify Backstage and slightly adapted to nf-core.

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Get a free 1Password Teams membership for your open source project

Provide extra protocols to make like Fever, NewsBlur, Nextcloud/ownCloud News and Tiny Tiny RSS work with elfeed

Categorize, and add order numbers, to Amazon transactions in LunchMoney

GitHub’s official command line tool

Nextflow public web site

Python script to fix Framework fingerprint on a NixOS install

Nextflow and Clickhouse Examples

SQL support plugin for Nextflow

A collection of useful .gitignore templates

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This is the development home of the workflow management system Snakemake. For general information, see

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Homework from the course that changed my life.

Render any Markdown content in Astro, optionally integrating with any existing configuration.

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Save 30-50%+ of CI time without any effort or cost. Use Magic Nix Cache, a totally free and zero-configuration binary cache for Nix on GitHub Actions.

Outliner for taking notes and managing to-do lists

Emacs helper library (and minor mode) to work with pixi environments

BioJulia's Website

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A collection of data tranformers and plugins

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A template for NUR repositories: [maintainer=@fgaz]

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Repository for calss notes and lectures

Repo for Notes and Examples from ETHDenver

Website for decentrailized RPG Game

Rotohive Repo for CometHacks

Texas Weight and Wellness Website

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Did someone say... vim?

Trino website

Sandbox for testing out Astrojs for use as a replacement framework for Sylvan

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Conda recipes for the bioconda channel.

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UNDER CONSTRUCTION: Demultiplexing pipeline for Illumina sequencing data

Analysis of Chromosome Conformation Capture data (Hi-C)

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An opinionated pack of modern color-themes

A collection of NixOS modules covering hardware quirks.

Test data to be used for automated testing with the nf-core pipelines

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Template for creating a k3s cluster with k3sup backed by flux and sops

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Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

Testing building mulled containers for multi-requirement tools.

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a Jupyter kernel for Clojure

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The pytest framework makes it easy to write small tests, yet scales to support complex functional testing

Config files used to define parameters specific to compute environments at different Institutions

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