Discover FredHutch/motuz Open Source project

prox command line interface for proxmox and other tools and customizations

proxmox-tools

SciWiki: Collective KnowledgeBase for Scientific Data and Use

wiki

examples of using slurm in life sciences workflows using posix file systems and object storage

slurm-examples

Analysis code used in Galeano Nino et al., Impact of Intratumoral Microbiota on Spatial and Cellular Heterogeneity in human cancer. 2022

Galeano-Nino-Bullman-Intratumoral-Microbiota_2022

MaxQuant Automated Pipeline

maxquant-pipeline

Howto and implementation documentation

easybuild-life-sciences

C++

stlite-template

Template for stlite single-page app

Functional Analysis of Metagenomes by Likelihood Inference

FAMLI

Template for building a small workflow in Nextflow

workflow-template-nextflow

Analyze a set of genomes with the anvi'o pangenome pipeline

nf-anvio-pangenome

swift commander is a wrapper for various command line openstack swift clients to provide a simplified user interface

swift-commander

Reproducible Workflows, curated at the Fred Hutch

reproducible-workflows

WDL

dns-shield

CoreDNS server with blacklist to block ads, tracking and malware

Bacterial Operon Finder for Functional Organization

octapus

Build a map of genes present across a set of microbial genomes

gig-map

Enhanced Chromatin Occupancy (EChO)

EChO

R_Package_Validation_Tutorial

Bookdown Tutorial for R Package Validation Framework

microbial-rnaseq

Analysis of RNAseq data from (host-associated) microbial mixtures

FHBig project page: https://fredhutch.github.io/FHBig/

FHBig

Full configuration of FredHutch Scratch File System using commodity disks, Ubuntu ZFS and BeeGFS

chromium-zfs-beegfs

A repo for new interns learning the basics of biomedical data science

bioDS-bootcamp

Align short reads against viral genomes in protein space

map_viruses

bash-workbench

BASH Workbench

Run Nextflow on AWS Batch (Squared)

nextflow-aws-batch-squared

Example workflows for a multi-step array job on AWS Batch

VISCfunctions

batch_pipeline

Helper scripts to run and monitor jobs on AWS Batch

aws-batch-helpers

Find Co-Abundant Groups of Genes

find-cags

EasyBuild container build - A docker container for building software with EasyBuild

EBcb

Tool for Computational Biology MCB 536

tfcb_2021

Nextflow workflow for analyzing CRISPR screen NGS data

crispr-screen-nf

RedcapDotNetDETs

Data entry triggers for REDCap written using .NET Web API

shiny-app-template

Template for creating Shiny web applications

Course website for MCB 536 Tools for Computational Biology

tfcb_2022

Containerized Database Service (DBaaS)

DB4SCI

Batchman - Nextflow on Fargate x AWS Batch

batchman

JavaScript

sra-pipeline

download sra files from SRA, pipe through fastq_dump and bowtie2 to S3, in a container

parallel file system crawler that manages file metadata in a postgres database

storage-crawler

simple program that can upload to s3 using a named pipe (useful for AWS Batch)

s3uploader

r-shiny-base

Base Docker container for R Shiny apps

sci-pkg

a loose collection of functions used in Scientific Computing put into a python package

delete or archive files based on last access time

fs-cleaner

Docker image running DIAMOND

docker-diamond

A shiny app that creates interactive volcano plots.

interactiveVolcano

coop

Blog for the Fred Hutch Bioinformatics and Data Science Cooperative

Public repo organized for the SEATRAC TB Hackday on 13-Dec-2023

seatrac-hackday-2023

A repo containing instructions for running a Cromwell server on Gizmo at the Fred Hutch. (Contact Amy Paguirigan for questions)

diy-cromwell-server

Replicate user, group, nis information from a Microsoft Active Directory server into an OpenLDAP server

ad2openldap

Batch execution of CellProfiler analyses using Nextflow

cellprofiler-batch-nf

Tools for writing reproducible reports at VISC

VISCtemplates

TeX

tfcb_2023

Course website for MCB 536 Tools for Computational Biology

Extend JOb Time Limit - extend a slurm job's time limit

ejotl

Table synchronization utility for MS-SQL

HDC-DataEngineering-SQLSync

PLpgSQL

unicycler-nf

De novo assembly with UniCycler, within a Nextflow workflow

Scientific Computing benchmarks (HPC, storage, genomics)

sc-benchmark

Quantify microbial abundance from whole-genome shotgun sequencing data

metaphlan-nf

freddie

A community R package

wiki-code-templates

Docker image running HUMANN2

docker-humann2

cromwell-on-slurm

Public repo containing all of the required analysis tools to generate SD Genotyping data

SDGenotypingAnalysis

data-science-examples

A repository of tested, documented example code for use with Fred Hutch computing resources.

A Snakemake pipeline to enable guide RNA read mapping from dual-targeting CRISPR screens

pgMAP_pipeline

A repo to create a who's who website for the Fred Hutch data community

s3tagcrawler

search s3 based on tags

who-is-who

SCSS

AWE

Wrapper for Cromwell workflow engine, adding auth, multiuser, github integration & more

WDL

PGAP-nf

Nextflow tool running the NCBI Prokaryotic Genome Annotation Pipeline

Pipelines for Analysis And Visualization

dv-pipelines

Shiny app for Creating Automated Videos

loqui

fast-file-zfs-beegfs

Architecture and configurations for Fred Hutch "Fast File" service, our HPC posix file system

RELION container for docker

ls2_relion

Docker image for eggNOG mapper

docker-eggnog-mapper

Annotation of Microbial Genomes by Microbiome Association

AMGMA

Nextflow implementation of Anvio metagenomic workflow

nf-anvio-metagenomics

Analysis of combined 10X human and microbial data

invadeseq

a collection of scripts to convert images, OCR, and redact

RedactO

A Flask PHI for identifying Protected Health Information (PHI)

FlaskPHI_ID

Public repository for KInhibition source code and data files

KInhibition-Public

tgR

Convenience R package for the Translational Genomics Repository

CutAndRun-Seq

Analysis tools and gh-pages for CutAndRun-Seq technology

target-data-viz

Shiny app for visualizing TARGET pediatric AML data

Repo for the computational code used in Hadland et al. 2022, Nat Comm manuscript.

hadland-etal-2022

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 metagenomics

Nextflow workflow running prokka for bacterial genome annotation

prokka-nf

Small application to launch the anvi'o pangenome browser

anvio-pangenome-launcher

Combine a set of metagenomic assemblies into a common set of references

integrate-metagenomic-assemblies

Docker image running metaSPAdes

docker-metaspades

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 Explorer

swiftclient-gui

Repository to keep track of commonly used elements of computational workflows, e.g. Nextflow and Cromwell

workflow-patterns

shiny-cromwell

Shiny app for interacting with the Fred Hutch instances of Cromwell. Contact Taylor Firman.

dvc-pipelines

Functions to easily pull metrics for the coop blog and wiki from github and google analytics

coopMetrics

strelka-docker

strelka in docker

Dockerfile

COVID_modeling_sensitivity

index-genomes-nf

Generate a comprehensive set of indexes for a single reference genome