jakelever

kindred

A Python biomedical relation extraction package that uses a supervised approach (i.e. needs training data).

pubrunner

A framework for keeping biomedical text mining result up-to-date

cancermine

Text-mined knowledgebase for drivers, oncogenes and tumor suppressors in cancer

pgxmine

Text mining for pharmacogenomic associations for PharmGKB

civicmine

Text mining cancer biomarkers for the CIVIC database

biowordlists

Biomedical wordlists (of drugs, genes, etc) for several text mining projects

biotext

Get a nicely-chunked local copy of the biomedical literature (to use for other projects)!

corona-ml

Machine learning to text-mine coronavirus research for CoronaCentral.ai

corona-web

Website for viewing database of Coronavirus research at CoronaCentral.ai

GNBR

Tools to work with Global Network of Biomedical Relationships data

docstringtest

Little package to test if docstrings are up-to-date in Python code

glasgowcs_labtest

Testing framework for online labs

pubtator

Running various NER tools on big corpora

text_classification_in_R

Demonstration of some text classification methods in R

textae

textasdata_bugbounty

Bug bounty programme for TextAsData course

2020-03-23-stanford

bigzenodo

Python tool for doing big uploads to Zenodo

bioc

Data structures and code to read/write BioC XML and Json.

bootstrap_lesson

Lesson materials for learning the bootstrap method

gputest

Basic test case for stressing a GPU

isub

Job submitter for OpenShift cluster

jakelever.github.io

Personal webpage

mesh_extract

Tool for extracting MeSH tags from PubMed documents

python-base

Dockerfile with some useful dependencies installed

rainstorm

Some Python experiments

shell-novice-adventure

An extension of the shell-novice SWC lesson with a story

spans_and_trees

swc-machine-learning-short

transpose

Command-line tool to transpose data