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2018-11-01-teachercarpentryexample

2022bioitworldhackathon_kidsfirst_include

This is the 2022 BioIT - World Hackathon GitHub repository for the NICHD Iterative Cluster Analysis working with Kids First and INCLUDE Open and Registered Tier Data

adeslatt.github.io

alevin-docker

Alevin is released within Salmon - so this is Salmon v1.4.0

alternativesplicing-nf

Alternative Splicing NextFlow Workflow - initially using rMATS

atacseq

ATAC-seq peak-calling, QC and differential analysis pipeline

bcftools-docker

a container for bcftools https://github.com/samtools/bcftools#readme

bioeditmultisequencealignment

Resurrecting multiple sequence alignment method used to analyze long read RNAsequencing data from PacBIo on Healthy Human Bone Marrow -- it begins with calling the open reading frames to translate the DNA to Protein sequence and ends with at time manual editing to align the sample specific sequence data.

bioithackathons-fairassessment2018jaxteam

bioitworld2019fairapplications

biojupies

Automated generation of tailored bioinformatics Jupyter Notebooks via a user interface.

bismark

A tool to map bisulfite converted sequence reads and determine cytosine methylation states

bismark-docker

bonemarrow

Code for reading in PacBio ToFU output and printing gene models

bonemarrowcomparsions

utilities to do analysis and comparisons between groups

brca-lrseq-pipeline

Pipeline to analyze long-read mRNA isoforms and ORF products sequenced in breast cancer using PacBio Single-Molecule technology.

building-a-cwl-script

Building-A-CWL-Script

building-a-nextflow-script

Building-A-Nextflow-Script

cdna-cupcake-docker

This is the repository for the Dockerfile made to containerize and make the package available for the tools in https://github.com/Magdoll/cDNA_Cupcake. The package is automatically built and pushed upon any push to the repository using GitHub actions.

cdna_cupcake

Miscellaneous collection of Python and R scripts for processing Iso-Seq data

combine-matrices-docker

combine-matrices-docker

computational-skills-for-the-researcher

Collection of classes offered - providing instruction surrounding community based workflows, such as nextflow as well as offering insights in using JupyterLab notebooks to perform analyses and generate publication ready figures.

covid

Workflows to be run for Diagnostics on new and existing data

curl-docker

container for curl

demo-from-template

deseq2-docker

deseq2-docker

docker-bio

Dockerfile repository for Bioinformatics

dockerfile_template

Use this template for Dockerfile creation

drop

Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders

dry-bench-skills-for-researchers

Resources for the Pilot Online Course "Dry bench skills for Researchers"