The Jackson Laboratory's repositories
splicing-pipelines-nf
Repository for the Anczukow-Lab splicing pipeline
cnn_autoencoder
A deep learning model for histological image compression and decompression
diachromatic
Diachromatic is a Java application for preprocessing and quality control of Hi-C and CHi-C data.
long-read-workshop-2019
https://thejacksonlaboratory.github.io/long-read-workshop-2019/
omero-training-materials
Repo with materials for OMERO training and scripts to set up a training server.
DIY-Geropathology
This Repository will provide code to help you apply our geropathology tools to your datasets
drug-synergy
Drug synergy prediction tool
grails-console
A web-based Groovy console for interactive runtime application management and debugging
hne_image_utils
Utilies for H&E image post-processing
nf-core-atacseq
A modified version of the peer reviewed nf-core/atacseq analysis pipeline
unet-glomeruli
U-Net model for glomeruli segmentation in Whole Slide Images
intro-to-hpc
An introduction to HPC
cancer-cube-st-pilot-ffpe-ff
Pilot Visium 10X experiment comparing FFPE and fresh frozen protocols
deeplearning-image-analysis-workshop
Notebooks for the workshop Deep Learning for Image Analysis with PyTorch
ExperimentalModelSchema
Experimental Model Schema
gene_exp_psi
Gene expression and percent spliced in
intro-to-google-cloud
Introduction to Google Cloud Platform workshop
meta_mapper
Map fields in existing metadata documents to those in new, standardized templates.
metadata_mongo_ingester
Generic tool for ingesting metadata into a user-named mongoDB and document, with optional validation against a schema
mouse_demuxlet
Single cell genetic demultiplexing in the mouse
sns
Analysis pipelines for genomic sequencing data