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SVE
Picky
Structural Variants Pipeline for Long Readsezomero
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 visualizationloinc2hpoAnnotation
loinc2hpo Annotation DataLIRICAL
LIkelihood Ratio Interpretation of Clinical AbnormaLitiespyBedGraph
A Python package for fast operations on 1-dimensional genomic signal trackszarrdataset
A dataset for loading zarr files to be used in machine learning training pipelinesComputational-Genome-Analysis
Website for Computational Exome and Genome AnalysisCloudNeo
CWL implementation of CloudNeo: A cloud pipeline for identifying patient-specific tumor neoantigensHPOworkbench
Human Phenotype Ontology Workbenchcs-nf-pipelines
The Jackson Laboratory Computational Sciences Nextflow based analysis pipelinesIntroToHPC
HPC and queue usage class syllabussplicing-pipelines-nf
Repository for the Anczukow-Lab splicing pipelineBRCA-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 imagesATAC-seq
ATAC-seq Pipeline in conjunction with Duygu Ucar & Jacques Banchereau LaboratoriesPDX-Analysis-Workflows
tcga_subtype_classification
Detecting cancer subtypes with machine learning.dask_relabeling
A relabeling tool for tiled segmentation with Dasksinglecellglioma-verhaaklab
weinstock_full_length_16s
Code referenced in the manuscript 'The 16S rRNA gene for species and strain-level microbiome analysis'HBA-DEALS
HBA-DEALSPhenopacketLab
An Angular/Springboot web application for the loading, editing, saving of data that follows the Phenopacket SchemaJAX-CNV
Official code repository for JAX-CNVloinchpo
Python version of LOINC2HPOcape
An R package for the combined analysis of Epistasis and PleiotropyChIA-DropBox
add support to SRRxxx fastq.nf-tenx
All 10x Genomics processing pipelines rolled into one containerized pipelinesphenix-service
scanpy_recipes
Generalized and aggregated analysis functions for working with Anndata and Scanpymia-sig
Multiplex chromatin interaction analysis by signal processing and statistical algorithmsPhenomiser
Phenotype-based Diagnosis Tool for Rare Diseasesjax-omeroutils
A module and scripts for working with OMEROPhenopacketGenerator
Generate a phenopacket for use with LIRICAL or ExomiserisopretGO
Isoform function prediction and interpretationgeneweaver-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 imagesendometriosis-scrnaseq
Code to reproduce analysis and figures for scRNA-seq analysis of endometriosis in Tan et al. 2021.SCI-DNN
Basic_skimageJAX
Tutorials for using scikit-image, written for The Jackson Laboratoryjax-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 Environmentsyntenybrowser
An interactive web-based conserved synteny browser applicationjax-single-cell
A curated space for the JAX Single Cell Community of Practiceomero_for_developers
material for the "OMERO for developers" workshop.geneweaver-boolean-algebra
ChIA-view
20191127haploqa
Tool to facilitate genetic quality assurance of mice using genotype data derived from genotyping platforms such as GigaMUGA and MegaMUGAdiachromatic
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 JAXontology-service
A generic ontology term microservicecnn_autoencoder
A deep learning model for histological image compression and decompressionhpcutils
HPC Utilitiesgeneweaver-testing
AMPAD_Submodules
Analysis of AMP-AD gene expression data to detect submodules and heterogeneity relevant for LOAD, published in Milind et al. 2020HCS_visualization_tools
Tools to visualize HCS data stored in zarr filesepihet
EpiHetmarea
Filter PubMed articles for relevancembiome_containers
Docker and Singular container definition files, as used by the MbiomeCore at JAX-GMrit-imageanalysis-containers
Making it easier for users to spin up a Singularity container with image analysis tools from a slurm-based clusterImageEchelon
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 WorkshopDigital-Glomerular-identification
This will detail how to run ilastik headless and track jobs submissions etc.geneweaver-tools
PDX-SOC
Drug response graphs for PDX tumorsgeneweaver-core
The core library for GeneWeaver projects.POET
A curation application for HPO and MAxOpreprocess_histoQC
Container for preprocessing slides using HistoQClong-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 experimentszarr_and_dask_demo
Demo use of dask with imaging data saved as OME-zarromero-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' workshopslurm-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 OMEROontology-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 filesHUSHDataAnalysis
source code for data analysis of UNC HUSH+ dataset on asthma patientsquilt-nf
sumnerdocs
Sumner HPC Documentation - Beta and Unofficial!GDCSlicing
Code and data for manuscriptjax-omerometrics
Repo for generating OMERO reports/dashboardsClimbToLabguruExporter
Basic tools for exporting sample data from Climb into LabguruchIA-diff
wfm
Workflows for the Introduction to Scientific Workflow Manager workshopimc-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 modelLove Open Source and this site? Check out how you can help us