Jacob Hepkema's Projects
Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)
Annotate pictures given classes and keybindings
going to try to get this https://hub.docker.com/u/lzamparo to singularity img
Barcoding utilities (work in progress)
A skeleton of my previous personal website based on blogdown and Hugo. I no longer use it.
Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)
don't think, let computer think
CountESS
Dataloader for enformer
Flax is a neural network library for JAX that is designed for flexibility.
:books: Freely available programming books
Script to automatically create and run IGV snapshot batchscripts
Config files for my GitHub profile.
Source code for my Github Pages website
Artificial chemistry game
Modelling insertion efficiency for Prime Insertion Experiments
A DSL for data-driven computational pipelines
An introduction to Nextflow, focussed on files and channels
A collection (work in progress) of tools to help with visualisation of the non-coding genome.
Random bits and bobs
Tensors and Dynamic neural networks in Python with strong GPU acceleration
A singularity and docker container to run pytorch in a HPC environment
Singularity Container for PyTorch
TOMTOM docker/singularity container for scanem
R docker container for scanem
A not-too-orderly collection of scripts for preprocessing and dimensionality reduction of scATAC-seq data