Discover TheJacksonLaboratory/marea Open Source project

Structural Variants Pipeline for Long Reads

Picky

Perl

ezomero

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

This repository contains course materials from JAX-BD2K workshop.

JAXBD2K-ShortCourse

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

ChIA-PIPE

loinc2hpoAnnotation

loinc2hpo Annotation Data

LIkelihood Ratio Interpretation of Clinical AbnormaLities

LIRICAL

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

pyBedGraph

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

zarrdataset

Website for Computational Exome and Genome Analysis

Computational-Genome-Analysis

Perl

CloudNeo

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

Common Workflow Language

HPOworkbench

Human Phenotype Ontology Workbench

The Jackson Laboratory Computational Sciences Nextflow based analysis pipelines

cs-nf-pipelines

Nextflow

IntroToHPC

HPC and queue usage class syllabus

splicing-pipelines-nf

Repository for the Anczukow-Lab splicing pipeline

Nextflow

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)

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

basic-browser

Dockerfile

STQ

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

ATAC-seq

PDX-Analysis-Workflows

Detecting cancer subtypes with machine learning.

tcga_subtype_classification

A relabeling tool for tiled segmentation with Dask

dask_relabeling

singlecellglioma-verhaaklab

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

weinstock_full_length_16s

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

HBA-DEALS

PhenopacketLab

TypeScript

JAX-CNV

Official code repository for JAX-CNV

C++

loinchpo

Python version of LOINC2HPO

An R package for the combined analysis of Epistasis and Pleiotropy

cape

ChIA-DropBox

add support to SRRxxx fastq.

All 10x Genomics processing pipelines rolled into one containerized pipelines

nf-tenx

Groovy

phenix-service

Generalized and aggregated analysis functions for working with Anndata and Scanpy

scanpy_recipes

Multiplex chromatin interaction analysis by signal processing and statistical algorithms

mia-sig

Phenotype-based Diagnosis Tool for Rare Diseases

Phenomiser

A module and scripts for working with OMERO

jax-omeroutils

Generate a phenopacket for use with LIRICAL or Exomiser

PhenopacketGenerator

Isoform function prediction and interpretation

isopretGO

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

geneweaver-api

CUP-AI-Dx

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

SAMPLER

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

endometriosis-scrnaseq

SCI-DNN

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

Basic_skimageJAX

jax-omero-transfer

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

Documentation site for the Geneweaver project.

geneweaver-docs

sbas

CloudOS Digital Research Environment

An interactive web-based conserved synteny browser application

syntenybrowser

JavaScript

jax-single-cell

A curated space for the JAX Single Cell Community of Practice

omero_for_developers

material for the "OMERO for developers" workshop.

geneweaver-boolean-algebra

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

ChIA-view

20191127

haploqa

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

diachromatic

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

scbl-utils

Configuration files to kickstart new Nextflow pipelines at JAX

universal-nextflow-config

Groovy

ontology-service

A generic ontology term microservice

A deep learning model for histological image compression and decompression

cnn_autoencoder

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

Tools to visualize HCS data stored in zarr files

HCS_visualization_tools

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

epihet

EpiHet

mbiome_containers

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

rit-imageanalysis-containers

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

ImageEchelon

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

geneweaver-client

Long-Read Sequencing Workshop

long-read-workshop

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

Digital-Glomerular-identification

ImageJ Macro

geneweaver-tools

Drug response graphs for PDX tumors

PDX-SOC

JavaScript

geneweaver-core

The core library for GeneWeaver projects.

A curation application for HPO and MAxO

POET

Container for preprocessing slides using HistoQC

preprocess_histoQC

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

long-read-workshop-2019

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

osdf_submit

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

ncells

zarr_and_dask_demo

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

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

omero-training-materials

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

images-as-signals

Slurm templates and notes.

slurm-templates

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

2023-02-01-the-bash-shell

Saving napari ROIs into OMERO

isopretEM

napari_omero_rois

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

ontology-annotation-network

The GeneWeaver database interaction code.

geneweaver-db

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

mergegtfs

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

HUSHDataAnalysis

Sumner HPC Documentation - Beta and Unofficial!

quilt-nf

sumnerdocs

Code and data for manuscript

GDCSlicing

Repo for generating OMERO reports/dashboards

jax-omerometrics

Basic tools for exporting sample data from Climb into Labguru

ClimbToLabguruExporter

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

GenomeMUSter

chIA-diff

Workflows for the Introduction to Scientific Workflow Manager workshop

wfm

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

imc-preprocessor

2021-09-30-hpc

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

100

wild_AD_mic_scRNA