Discover TheJacksonLaboratory/STQ 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

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

pyBedGraph

LIkelihood Ratio Interpretation of Clinical AbnormaLities

LIRICAL

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

cs-nf-pipelines

The Jackson Laboratory Computational Sciences Nextflow based analysis pipelines

Nextflow

HPOworkbench

Human Phenotype Ontology Workbench

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

zarrdataset

HPC and queue usage class syllabus

IntroToHPC

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.

basic-browser

Dockerfile

PDX-Analysis-Workflows

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

ATAC-seq

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

hpo-web

Detecting cancer subtypes with machine learning.

tcga_subtype_classification

singlecellglioma-verhaaklab

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

weinstock_full_length_16s

Official code repository for JAX-CNV

HBA-DEALS

JAX-CNV

C++

dask_relabeling

A relabeling tool for tiled segmentation with Dask

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

Python version of LOINC2HPO

loinchpo

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

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

PhenopacketLab

TypeScript

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

geneweaver-docs

Documentation site for the Geneweaver project.

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

haploqa

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

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

ChIA-view

20191127

scbl-utils

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

diachromatic

hpcutils

HPC Utilities

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

jax-omero-transfer

A deep learning model for histological image compression and decompression

cnn_autoencoder

geneweaver-boolean-algebra

geneweaver-testing

Configuration files to kickstart new Nextflow pipelines at JAX

universal-nextflow-config

Groovy

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

Filter PubMed articles for relevance

epihet

EpiHet

marea

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

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

The core library for GeneWeaver projects.

geneweaver-core

Drug response graphs for PDX tumors

PDX-SOC

JavaScript

POET

A curation application for HPO and MAxO

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

long-read-workshop-2019

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

geneweaver-api

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

Slurm templates and notes.

slurm-templates

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

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

material for the "OMERO for developers" workshop.

omero_for_developers

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

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

microbiome-workshop-2019

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

wild_AD_mic_scRNA

Utilies for H&E image post-processing

hne_image_utils

A generic ontology term microservice

100

ontology-service