jacobhepkema

scover

scover

annotpics

Annotate pictures given classes and keybindings

jacobhepkema.github.io

Source code for my Github Pages website

scoverplots

Reproduce plots for scover manuscript

basset_singularity_from_docker

going to try to get this https://hub.docker.com/u/lzamparo to singularity img

batch_bus_booker

bcutils

Barcoding utilities (work in progress)

cell2location

Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)

conv_shapes

don't think, let computer think

flax

Flax is a neural network library for JAX that is designed for flexibility.

CountESS

CountESS

enformer_loader

Dataloader for enformer

IGV-snapshot-automator

Script to automatically create and run IGV snapshot batchscripts

jacobhepkema

Config files for my GitHub profile.

MinsePIE

Modelling insertion efficiency for Prime Insertion Experiments

nextflow

A DSL for data-driven computational pipelines

noncoding_visualisations

A collection (work in progress) of tools to help with visualisation of the non-coding genome.

primeflag

pybiofun

Random bits and bobs

pytorch

Tensors and Dynamic neural networks in Python with strong GPU acceleration

RNA_deletions

scanem-motif

TOMTOM docker/singularity container for scanem

scanem-r

R docker container for scanem

scATAC_prep

A not-too-orderly collection of scripts for preprocessing and dimensionality reduction of scATAC-seq data

scfind

scover_docker

WORK IN PROGRESS - trying to create Docker repo for scover

scover_singularity_python

Singularity environment containing pytorch, plotting tools, etc

scvi-tools

Deep generative models for single-cell omics data

singularity_pytorch

uvadlc_notebooks

Repository of Jupyter notebook tutorials for teaching the Deep Learning Course at the University of Amsterdam (MSc AI), Fall 2020