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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 HUMANN2cromwell-on-slurm
Info related to running a Cromwell server on a SLURM clusterSDGenotypingAnalysis
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.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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