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elements-of-style-workflow-creation-maintenance

eos

eos

examplevolcanoplotnotebook

extractfromcram

Matthew Galbraith's method for reads extraction from a cram file.

fastqc-docker

a container for the bioconda command fastqc

fastqc-multiqc-nf

The nextflow workflow using fastqc and multiqc containers in my personal CAVATICA Docker Registry

federated-analysis

Melissa Clines Docker Image

fhir-cat-june22

Technical interop pilot using RNASeq data

gene-median-splitter-docker

gene-median-splitter-docker

georgetown

georgetown

google-sheet-to-github-website

This is a working project for publishing data to Github Pages using Google Spreadsheet as the data source.

guppy-gpu-docker

hello-world-docker-action

Testing, creating a Dockerfile and having it built and tested with GitHub actions

hisat2_index-docker

hisat2_index-docker

human-testdata

testdata

ibi-nf

Individualized Bayesian Inference Nextflow Workflow

ideas

Tracking of thoughts and ideas for projects, science advancing and what will get us to solving the problems we want to be solving

include_examples

Example R scripts for analysis of INCLUDE data in CAVATICA

isoseqneoantigen-nf

The scripts to go from PacBio ISOSeq reads to NeoAntigen with HLA-typing for patient specific neo-antigen discovery

iterative-cluster-analysis-using-multi-omics-modalities

jax-tutorial

Tutorial for Jackson Labs intro to Nextflow, containers, FlowCraft and Deploit

kids-first-elements-of-style-workflow-creation-maintenance

kids-first-include-elements-of-style-workflow-creation-maintenance

Elements of Style for Workflow Creation and Maintenance, users learn the know-how to ask scientific questions with these data using workflows agnostic to platform (laptop, on-premise HPC or cloud)

long-read-proteogenomics

A workflow for enhanced protein isoform detection through integration of long-read RNA-seq and mass spectrometry-based proteomics.

macterminalwindowsetup

Here in lies a description of steps to set up your terminal window to facilitate common workflow and jupyter lab analysis work in GitHub and Platform Agnostic ways

metamorpheus

Proteomics search software with integrated calibration, PTM discovery, bottom-up, top-down and LFQ capabilities

methylseq

Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel

methylseq-nf

Minimum methylseq workflow with Bismark

methylseqcaptureseq

Megan Barefoot's PhD thesis project

mkdocs

Project documentation with Markdown.