Erik Storrs's repositories
deep-spatial-genomics
Pytorch implementations of deep learning methods for spatial genomic data. Intended to speed up spatial genomics method development.
DINO-extended
Reimplementation of DINO (Emerging Properties in Self-Supervised Vision Transformers) that is modified for non-RGB image data types - including n-dimensional multichannel images and multimodal data.
airlab
Image registration laboratory for 2D and 3D image data
beautiful-tensors
Turn tensor operations into aesthetic diagrams.
multiplex-imaging-pipeline
A pipeline for multiplex imaging analysis
paste2
Probabilistic Alignment of Spatial Transcriptomics Experiments v.2
pecgs-cnv
pecgs-cnv cwl wrapper
pecgs-fusion
cwl wrapper for dinglab fusion pipeline
pytorch-spatial-data
PyTorch datasets and dataloaders for various spatial genomics and imaging modalities.
skeleton-tool
A skeleton for creating Python tools. Includes build, documentation, and publishing steps.
spatial-genomics-autoencoders
Autoencoders for spatial genomics datasets.
SpiceMix
spatial transcriptome, single cell
summer-researchers
Notebooks/documentation for summer student researchers in the lab
TinDaisy
CWL somatic variant caller
vit-pytorch
Implementation of Vision Transformer, a simple way to achieve SOTA in vision classification with only a single transformer encoder, in Pytorch
wombat
A toolkit for using bsub and cromwell on compute1