jdidion

John Didion's repositories

Zooper

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

Language:JavaScript13 50

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)

Language:Ruby8 40

OpenBioinformaticsWorkshops

Open courseware for workshops in applied bioinformatics

Language:HTMLCC0-1.08 60

papers2

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

Language:Python6 4 4

genomics_scripts

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

Language:Python500

driver

Generic base class for batch programs. (unsupported)

Language:Python400

rna-quick

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

Language:R4 4 1

labels

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

Language:Python200

clasp

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

Language:R1 40

DEUtils

Utilities for differential expression testing. (beta)

Language:R100

fancyplots

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

Language:R100

htsget-server

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

Language:PythonNOASSERTION100

imetric-api

Project done during an NHGRI hackathon. (unsupported)

Language:PythonGPL-3.0100

jwnl

Java library for accessing WordNet. (retired)

Language:JavaNOASSERTION100

knitrtools

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

Language:R100

atropos-multiqc

MultiQC plugin for Atropos. (beta)

Language:HTMLNOASSERTION000

blockmute

Use the twitter API to block muted IDs, and vice-versa

Language:PythonMIT000

clicktypes

Create Click CLIs with type annotations (Moved -> AutoClick)

Language:PythonMIT000

developments-in-next-generation-sequencing

Developments in next generation sequencing: instruments, read lengths, throughput. See

Language:Jupyter NotebookNOASSERTION000

geneticsFormats

R functions for working with different genetics formats. (beta)

Language:R000

intensities

Utilities for working with raw genotype array intensities. (unsupported)

Language:R000

LikeThis

R package that adds regular expression infix operators. (pre-alpha)

Language:R030

markey

Create slides and posters using Markdown. (pre-alpha)

Language:JavaScript000

media

Utiliies for working with different types of media files and apps. (unsupported)

Language:Python000

MeSS

Computing tissue specificity of methylation from WGBS data. (production)

Language:R000

miscUtils

Miscellaneous utility functions I use often. (beta)

Language:R000

pylabels

Python library to create PDFs for printing labels.

Language:PythonGPL-3.0030

pytest-wdl

WDL plugin for pytest

Apache-2.0000

Rre2

R package that wraps the re2 C++ regular expression library. (alpha)

Language:C++000

statTests

Implementations of statistical tests that I can't find in another R package. (beta)

Language:R000