Jim's repositories
TIS_transformer_outdated
Transformer model for TIS annotation
TIS_transformer
Old repository for TIS_transformer
awesome-deepbio
A curated list of awesome deep learning applications in the field of computational biology
bio-attention
PyTorch implementation of 2D sliding window attention
boinq2
(in progress) JHipster based boinq edition
DS-python-data-analysis
Data manipulation, analysis and visualisation in Python - specialist course Doctoral schools of Ghent University
flasky
Companion code to my O'Reilly book "Flask Web Development".
gtfparse
Parsing tools for GTF (gene transfer format) files
h5torch
HDF data utilities for PyTorch
htsjdk
A Java API for high-throughput sequencing data (HTS) formats.
jannovar
Java library for annotating VCF files with gene/transcript-based annotations
jbrowse
A modern genome browser built with JavaScript and HTML5.
local-attention
An implementation of local windowed attention for language modeling
mQC
Ribosome profiling mapping quality control tool
neural_cake
cakes and neural networks
pandas
Flexible and powerful data analysis / manipulation library for Python, providing labeled data structures similar to R data.frame objects, statistical functions, and much more
pclab_CNN
pclab
plastid
Position-wise analysis of sequencing and genomics data
prompred_outdated
Promoter Predictor
PromPred_WebApp
Web application for PromPred
tis_streamlit
streamlit app for TIS transformer
ympd
Standalone MPD Web GUI written in C, utilizing Websockets and Bootstrap/JS