Explore @TheJacksonLaboratory Open Source projects

The Jackson Laboratory (@TheJacksonLaboratory)

TheJacksonLaboratory

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Location 🇺🇸 United States
Country Total Rank 11,140
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Nextflow 6

Common Workflow Language 7

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SVE

Picky

Structural Variants Pipeline for Long Reads

ezomero

A module with convenience functions for writing Python code that interacts with OMERO.

JAXBD2K-ShortCourse

This repository contains course materials from JAX-BD2K workshop.

ChIA-PIPE

ChIA-PIPE: A fully automated pipeline for comprehensive ChIA-PET data analysis and visualization

loinc2hpoAnnotation

loinc2hpo Annotation Data

LIRICAL

LIkelihood Ratio Interpretation of Clinical AbnormaLities

pyBedGraph

A Python package for fast operations on 1-dimensional genomic signal tracks

zarrdataset

A dataset for loading zarr files to be used in machine learning training pipelines

Computational-Genome-Analysis

Website for Computational Exome and Genome Analysis

CloudNeo

CWL implementation of CloudNeo: A cloud pipeline for identifying patient-specific tumor neoantigens

Common Workflow Language

HPOworkbench

Human Phenotype Ontology Workbench

cs-nf-pipelines

The Jackson Laboratory Computational Sciences Nextflow based analysis pipelines

IntroToHPC

HPC and queue usage class syllabus

splicing-pipelines-nf

Repository for the Anczukow-Lab splicing pipeline

BRCA-LRseq-pipeline

Pipeline to analyze long-read mRNA isoforms and ORF products sequenced in breast cancer using PacBio Single-Molecule technology.

hpo-web

a web application to search and navigate the Human Phenotype Ontology (HPO)

basic-browser

STQ

Spatial Transcriptomics Quantification pipeline for 10x Visium and H&E-stained whole slide images

ATAC-seq

ATAC-seq Pipeline in conjunction with Duygu Ucar & Jacques Banchereau Laboratories

PDX-Analysis-Workflows

tcga_subtype_classification

Detecting cancer subtypes with machine learning.

Jupyter Notebook

dask_relabeling

A relabeling tool for tiled segmentation with Dask

singlecellglioma-verhaaklab

Jupyter Notebook

weinstock_full_length_16s

Code referenced in the manuscript 'The 16S rRNA gene for species and strain-level microbiome analysis'

Jupyter Notebook

HBA-DEALS

PhenopacketLab

An Angular/Springboot web application for the loading, editing, saving of data that follows the Phenopacket Schema

JAX-CNV

Official code repository for JAX-CNV

loinchpo

Python version of LOINC2HPO

cape

An R package for the combined analysis of Epistasis and Pleiotropy

ChIA-DropBox

add support to SRRxxx fastq.

nf-tenx

All 10x Genomics processing pipelines rolled into one containerized pipelines

phenix-service

scanpy_recipes

Generalized and aggregated analysis functions for working with Anndata and Scanpy

mia-sig

Multiplex chromatin interaction analysis by signal processing and statistical algorithms

Phenomiser

Phenotype-based Diagnosis Tool for Rare Diseases

jax-omeroutils

A module and scripts for working with OMERO

PhenopacketGenerator

Generate a phenopacket for use with LIRICAL or Exomiser

isopretGO

Isoform function prediction and interpretation

geneweaver-api

A system for the integration and analysis of heterogeneous functional genomics data.

CUP-AI-Dx

SAMPLER

SAMPLER: Unsupervised representations for rapid analysis of whole slide tissue images

endometriosis-scrnaseq

Code to reproduce analysis and figures for scRNA-seq analysis of endometriosis in Tan et al. 2021.

Jupyter Notebook

SCI-DNN

Basic_skimageJAX

Tutorials for using scikit-image, written for The Jackson Laboratory

jax-omero-transfer

Transfer OMERO datsets from the Research server to the Public server.

geneweaver-docs

Documentation site for the Geneweaver project.

sbas

CloudOS Digital Research Environment

Jupyter Notebook

syntenybrowser

An interactive web-based conserved synteny browser application

jax-single-cell

A curated space for the JAX Single Cell Community of Practice

omero_for_developers

material for the "OMERO for developers" workshop.

Jupyter Notebook

geneweaver-boolean-algebra

ChIA-view

haploqa

Tool to facilitate genetic quality assurance of mice using genotype data derived from genotyping platforms such as GigaMUGA and MegaMUGA

diachromatic

Diachromatic is a Java application for preprocessing and quality control of Hi-C and CHi-C data.

scbl-utils

A set of command-line utilities that facilitates data processing in the Single Cell Biology Lab at the Jackson Laboratory.

universal-nextflow-config

Configuration files to kickstart new Nextflow pipelines at JAX

ontology-service

A generic ontology term microservice

cnn_autoencoder

A deep learning model for histological image compression and decompression

hpcutils

geneweaver-testing

AMPAD_Submodules

Analysis of AMP-AD gene expression data to detect submodules and heterogeneity relevant for LOAD, published in Milind et al. 2020

HCS_visualization_tools

Tools to visualize HCS data stored in zarr files

Jupyter Notebook

epihet

marea

Filter PubMed articles for relevance

mbiome_containers

Docker and Singular container definition files, as used by the MbiomeCore at JAX-GM

rit-imageanalysis-containers

Making it easier for users to spin up a Singularity container with image analysis tools from a slurm-based cluster

ImageEchelon

Tool to quantify images where meaningful differences are discernible by eye, but difficult to quantify using traditional methods.

geneweaver-client

A client library for the integration and analysis of heterogeneous functional genomics data.

long-read-workshop

Long-Read Sequencing Workshop

Digital-Glomerular-identification

This will detail how to run ilastik headless and track jobs submissions etc.

geneweaver-tools

PDX-SOC

Drug response graphs for PDX tumors

geneweaver-core

The core library for GeneWeaver projects.

POET

A curation application for HPO and MAxO

preprocess_histoQC

Container for preprocessing slides using HistoQC

long-read-workshop-2019

https://thejacksonlaboratory.github.io/long-read-workshop-2019/

osdf_submit

Stanford/JAX-GM submission metadata to OSDF; boilerplate files.

ncells

Calculating the number of cells in single cell RNA-seq experiments

zarr_and_dask_demo

Demo use of dask with imaging data saved as OME-zarr

Jupyter Notebook

omero-training-materials

Repo with materials for OMERO training and scripts to set up a training server.

images-as-signals

code and data for 'Intermediate Image Analysis - Images as Signals' workshop

slurm-templates

Slurm templates and notes.

2023-02-01-the-bash-shell

https://thejacksonlaboratory.github.io/2023-02-01-the-bash-shell/

isopretEM

napari_omero_rois

Saving napari ROIs into OMERO

ontology-annotation-network

A rest-api to serve a neo4j database of supported ontology annotations.

geneweaver-db

The GeneWeaver database interaction code.

mergegtfs

For non-redundant merging of transcript records from GTF2.2 files

HUSHDataAnalysis

source code for data analysis of UNC HUSH+ dataset on asthma patients

quilt-nf

sumnerdocs

Sumner HPC Documentation - Beta and Unofficial!

GDCSlicing

Code and data for manuscript

jax-omerometrics

Repo for generating OMERO reports/dashboards

ClimbToLabguruExporter

Basic tools for exporting sample data from Climb into Labguru

GenomeMUSter

GenomeMUSter is available at https://muster.jax.org/

chIA-diff

wfm

Workflows for the Introduction to Scientific Workflow Manager workshop

imc-preprocessor

Simple python app to quickly pre-process Imaging Mass Cytometry data for visualization and segmentation.

2021-09-30-hpc