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Oncoscape
a web application to apply/develop analysis tools for Molecular and Clinical datamotuz
Motuz - A web based infrastructure for large scale data movements between on-premise and cloudSEACR
SEACR: Sparse Enrichment Analysis for CUT&RUNproxmox-tools
prox command line interface for proxmox and other tools and customizationswiki
SciWiki: Collective KnowledgeBase for Scientific Data and Useslurm-examples
examples of using slurm in life sciences workflows using posix file systems and object storageGaleano-Nino-Bullman-Intratumoral-Microbiota_2022
Analysis code used in Galeano Nino et al., Impact of Intratumoral Microbiota on Spatial and Cellular Heterogeneity in human cancer. 2022easybuild-life-sciences
Howto and implementation documentationmaxquant-pipeline
MaxQuant Automated Pipelinestlite-template
Template for stlite single-page appFAMLI
Functional Analysis of Metagenomes by Likelihood Inferenceworkflow-template-nextflow
Template for building a small workflow in Nextflownf-anvio-pangenome
Analyze a set of genomes with the anvi'o pangenome pipelineswift-commander
swift commander is a wrapper for various command line openstack swift clients to provide a simplified user interfacereproducible-workflows
Reproducible Workflows, curated at the Fred Hutchdns-shield
CoreDNS server with blacklist to block ads, tracking and malwareoctapus
Bacterial Operon Finder for Functional Organizationgig-map
Build a map of genes present across a set of microbial genomesEChO
Enhanced Chromatin Occupancy (EChO)R_Package_Validation_Tutorial
Bookdown Tutorial for R Package Validation Frameworkmicrobial-rnaseq
Analysis of RNAseq data from (host-associated) microbial mixturesFHBig
FHBig project page: https://fredhutch.github.io/FHBig/chromium-zfs-beegfs
Full configuration of FredHutch Scratch File System using commodity disks, Ubuntu ZFS and BeeGFSbioDS-bootcamp
A repo for new interns learning the basics of biomedical data sciencemap_viruses
Align short reads against viral genomes in protein spacebash-workbench
BASH Workbenchnextflow-aws-batch-squared
Run Nextflow on AWS Batch (Squared)VISCfunctions
batch_pipeline
Example workflows for a multi-step array job on AWS Batchaws-batch-helpers
Helper scripts to run and monitor jobs on AWS Batchfind-cags
Find Co-Abundant Groups of Genestfcb_2022
Course website for MCB 536 Tools for Computational BiologyEBcb
EasyBuild container build - A docker container for building software with EasyBuildtfcb_2021
Tool for Computational Biology MCB 536crispr-screen-nf
Nextflow workflow for analyzing CRISPR screen NGS dataRedcapDotNetDETs
Data entry triggers for REDCap written using .NET Web APIshiny-app-template
Template for creating Shiny web applicationss3uploader
simple program that can upload to s3 using a named pipe (useful for AWS Batch)DB4SCI
Containerized Database Service (DBaaS)batchman
Batchman - Nextflow on Fargate x AWS Batchsra-pipeline
download sra files from SRA, pipe through fastq_dump and bowtie2 to S3, in a containerstorage-crawler
parallel file system crawler that manages file metadata in a postgres databaser-shiny-base
Base Docker container for R Shiny appssci-pkg
a loose collection of functions used in Scientific Computing put into a python packagefs-cleaner
delete or archive files based on last access timedocker-diamond
Docker image running DIAMONDinteractiveVolcano
A shiny app that creates interactive volcano plots.coop
Blog for the Fred Hutch Bioinformatics and Data Science Cooperativeseatrac-hackday-2023
Public repo organized for the SEATRAC TB Hackday on 13-Dec-2023diy-cromwell-server
A repo containing instructions for running a Cromwell server on Gizmo at the Fred Hutch. (Contact Amy Paguirigan for questions)ad2openldap
Replicate user, group, nis information from a Microsoft Active Directory server into an OpenLDAP servercellprofiler-batch-nf
Batch execution of CellProfiler analyses using NextflowVISCtemplates
Tools for writing reproducible reports at VISCtfcb_2023
Course website for MCB 536 Tools for Computational Biologyejotl
Extend JOb Time Limit - extend a slurm job's time limitHDC-DataEngineering-SQLSync
Table synchronization utility for MS-SQLunicycler-nf
De novo assembly with UniCycler, within a Nextflow workflowsc-benchmark
Scientific Computing benchmarks (HPC, storage, genomics)metaphlan-nf
Quantify microbial abundance from whole-genome shotgun sequencing datatfcb_2024
Course website for MCB 536 Tools for Computational Biology Fall 2024freddie
A community R packagewiki-code-templates
docker-humann2
Docker image running HUMANN2SDGenotypingAnalysis
Public repo containing all of the required analysis tools to generate SD Genotyping datadata-science-examples
A repository of tested, documented example code for use with Fred Hutch computing resources.pgMAP_pipeline
A Snakemake pipeline to enable guide RNA read mapping from dual-targeting CRISPR screenss3tagcrawler
search s3 based on tagswho-is-who
A repo to create a who's who website for the Fred Hutch data communityAWE
Wrapper for Cromwell workflow engine, adding auth, multiuser, github integration & morePGAP-nf
Nextflow tool running the NCBI Prokaryotic Genome Annotation Pipelinedv-pipelines
Pipelines for Analysis And Visualizationloqui
Shiny app for Creating Automated Videosfast-file-zfs-beegfs
Architecture and configurations for Fred Hutch "Fast File" service, our HPC posix file systemls2_relion
RELION container for dockerdocker-eggnog-mapper
Docker image for eggNOG mapperAMGMA
Annotation of Microbial Genomes by Microbiome Associationnf-anvio-metagenomics
Nextflow implementation of Anvio metagenomic workflowinvadeseq
Analysis of combined 10X human and microbial dataRedactO
a collection of scripts to convert images, OCR, and redactFlaskPHI_ID
A Flask PHI for identifying Protected Health Information (PHI)KInhibition-Public
Public repository for KInhibition source code and data filestgR
Convenience R package for the Translational Genomics RepositoryCutAndRun-Seq
Analysis tools and gh-pages for CutAndRun-Seq technologytarget-data-viz
Shiny app for visualizing TARGET pediatric AML datahadland-etal-2022
Repo for the computational code used in Hadland et al. 2022, Nat Comm manuscript.fh.wdlR
A repo containing a basic R package for using Cromwell with WDL workflows at Fred Hutch. (Contact Amy Paguirigan for help).VMAA
Nextflow tools for viral metagenomicsMeningiomaLandscape-HollandLab
This repository contains R scripts for the latest paper from the Holland Lab on Meningiomaprokka-nf
Nextflow workflow running prokka for bacterial genome annotationanvio-pangenome-launcher
Small application to launch the anvi'o pangenome browserintegrate-metagenomic-assemblies
Combine a set of metagenomic assemblies into a common set of referencesdocker-metaspades
Docker image running metaSPAdesswiftclient-gui
SwiftClientGUI is a simple wrapper for the Python Swift client that allows users to upload and download files to/from a swift object store by right clicking folders in Windows Explorerworkflow-patterns
Repository to keep track of commonly used elements of computational workflows, e.g. Nextflow and Cromwellcbioportal-data-formatting
A repository with easy-to-follow instructions on how to prepare you study data files for upload into cBioportalshiny-cromwell
Shiny app for interacting with the Fred Hutch instances of Cromwell. Contact Taylor Firman.dvc-pipelines
coopMetrics
Functions to easily pull metrics for the coop blog and wiki from github and google analyticsstrelka-docker
strelka in dockerCOVID_modeling_sensitivity
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