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The Jackson Laboratory (@TheJacksonLaboratory)

TheJacksonLaboratory

Stars
780
Global Org. Rank 17,877 (Top 6 %)
Registered about 8 years ago
Most used languages

Python
37.6 %

Java
11.3 %

HTML
10.5 %

Jupyter Notebook
9.0 %

R
9.0 %

Shell
6.8 %

Nextflow 3.0 %

JavaScript
2.3 %

Perl
1.5 %

Groovy
1.5 %

C++
1.5 %

TypeScript
1.5 %

Others 4.8 %
Location 🇺🇸 United States
Country Total Rank 11,140
Country Ranking

Common Workflow Language 7

Nextflow 7

ImageJ Macro 9

Perl
274

Groovy
471

R
868

Dockerfile
936

Shell
2,625

Jupyter Notebook
2,771

Java
2,985

Makefile 3,336

HTML
3,888

Python
4,080

C
4,814

MATLAB
8,656

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

pyBedGraph

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

LIRICAL

LIkelihood Ratio Interpretation of Clinical AbnormaLities

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

cs-nf-pipelines

The Jackson Laboratory Computational Sciences Nextflow based analysis pipelines

HPOworkbench

Human Phenotype Ontology Workbench

zarrdataset

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

basic-browser

PDX-Analysis-Workflows

ATAC-seq

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

hpo-web

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

STQ

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

tcga_subtype_classification

Detecting cancer subtypes with machine learning.

Jupyter Notebook

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

JAX-CNV

Official code repository for JAX-CNV

dask_relabeling

A relabeling tool for tiled segmentation with Dask

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

loinchpo

Python version of LOINC2HPO

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

PhenopacketLab

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

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

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

haploqa

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

ChIA-view

scbl-utils

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

diachromatic

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

hpcutils

jax-omero-transfer

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

cnn_autoencoder

A deep learning model for histological image compression and decompression

geneweaver-boolean-algebra

geneweaver-testing

universal-nextflow-config

Configuration files to kickstart new Nextflow pipelines at JAX

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

geneweaver-core

The core library for GeneWeaver projects.

PDX-SOC

Drug response graphs for PDX tumors

POET

A curation application for HPO and MAxO

long-read-workshop-2019

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

geneweaver-api

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

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

slurm-templates

Slurm templates and notes.

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

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

omero_for_developers

material for the "OMERO for developers" workshop.

Jupyter Notebook

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

microbiome-workshop-2019

https://thejacksonlaboratory.github.io/microbiome-workshop-2019/

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

wild_AD_mic_scRNA

scRNA-seq on microglia from wild-derived Alzheimer's mouse model

hne_image_utils

Utilies for H&E image post-processing