jdidion/hon

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1
Language
Python
License
MIT License
Created almost 6 years ago
Updated over 4 years ago

jdidion/hon

jdidion

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An opinionated Python project management tool (pre-alpha)

biotools

A list of useful bioinformatics resources

atropos

An NGS read trimming tool that is specific, sensitive, and speedy. (production)

pairwise-alignment

Catalogue of pairwise alignment algorithms and benchmarks

xphyle

Python library that facilitates opening, reading, and writing files (and file-like entities like URLs and streams) agnostic of compression format. (production)

Zooper

Zotero plugin for updating metadata and managing PDFs. (alpha)

autoclick

Create Click-based CLIs from python3 type annotations (beta)

pest-test

Testing framework for pest parser (similar to `tree-sitter test`)

feedme

A simple, flexible, and extensible RSS and Atom parser for Ruby. Based on the popular SimpleRSS library, but with many nice extra features. (retired)

OpenBioinformaticsWorkshops

Open courseware for workshops in applied bioinformatics

papers2

Python library for interacting with a Papers2 database, plus scripts to export into various formats. (beta)

genomics_scripts

Python scripts and functions for doing things with different types of genomic data. (unsupported)

wdl-rs

Rust parser for Workflow Description Language (WDL)

rna-quick

Differential gene, transcript, exon, and splice junction testing framework. (pre-alpha)

seqio

A library for high-performance reading and writing of common NGS formats. (pre-alpha)

driver

Generic base class for batch programs. (unsupported)

ngsindex

Parsers for common NGS index formats (production)

subby

Python subprocesses simplified.

ngstream

Simple reading/streaming of NGS reads from SRA. (alpha)

labels

This is a simple program to generate labels from a table (CSV file). (production)

tree-sitter-wdl

Tree-sitter grammar for WDL (Workflow Description Language)

knitrtools

Library of utilities for use in RMarkdown documents. (beta)

jwnl

Java library for accessing WordNet. (retired)

imetric-api

Project done during an NHGRI hackathon. (unsupported)

htsget-server

htsget server; pre-alpha, deprecated (see https://gitlab.com/genomicsengland/htsget/gel-htsget instead)

wdlkit

pest-wdl

Pest parser grammar for Workflow Description Language (WDL)

audiodrama

My audio drama feeds OPML

jdidion.github.io

dxcompiler-compile-action

A GitHub action to compile a WDL workflow using dxCompiler

docparse

Parse python docstrings (beta)

fancyplots

Some useful plots for genomic data, in base R. (beta)

DEUtils

Utilities for differential expression testing. (beta)

clasp

Cell Line Authentication by SNP Profiling (CLASP). (production)

pytest-datadir-nng

The *next* next generation of python-datadir