Discover NCBI-Codeathons/ASAP Open Source project by @NCBI-Codeathons

Using-PubMed-MEDLINE-Metadata-to-Generate-Knowledge

ToxPipe: Semi-autonomous AI integration of diverse toxicological data streams

ncbi-codeathons.github.io

NCBI Codeathons Website

CSS

mlxai-2024-team-saddler

Patient 'omics data in OMOP format

OMOPOmics

mlxai-2024-team-bhushan

vcf-4-population-genomics-team-abdennur

super-minityper

Long Read SVs

Dockerfile

mlxai-2024-team-beaumont

Variation Analysis and Visualization of SARS-CoV-2 sequences in GenBank

SARS2-Variation-Viewer

pubmed-codeathon-team1

Identifying-bulk-RNA-seq-derived-biomarkers-of-cancer-risk-within-single-cell-populations

automated-sc-RNA-seq-analysis-in-the-cloud

vcf-4-population-genomics-team-park

SeqMoid

vcf-4-population-genomics-team-hearn

mlxai-2024-team-gwadz-yang

mlxai-2024-team-smith

A QC suite for large VCF files

Clouseau

Understanding how Phages Affect Microbial Disease

Host_Phage_Interactions

bothie

Making Representative Genome Graphs from Eukaryotic Viruses and Phages

Virus_Graphs

Rich Text Format

vcf-4-population-genomics-team-agustinho

Understand-cancer-evolution-through-single-cell-expression-dynamics

Classify your health/medical/life sciences search terms

Use-UMLS-and-Python-to-classify-website-visitor-queries-into-measurable-categories

This repository contains tools and resources developed by Team Prasad Feldgarden during the "Resistance is Futile: A Codeathon to Combat Antimicrobial Resistance" (September 2024), hosted by NCBI and NIAID.

amr-2024-team-prasad-feldgarden

mlxai-2024-team-landrum-song

vcf-4-population-genomics-team-warren

A pipeline for calling de novo structural variants from a trio with Nanopore long read data

DeNovoSV

pubmed-codeathon-team2

NCGAS-cloud-workshop

NCGAS Cloud Workshop

psss-datasets

beyond-phylogenies-team6

vcf-4-population-genomics-team-phan

mlxai-2024-team-chen

beyond-phylogenies-team3

mlxai-2024-team-hall

MASCARA

A-DEEP-CONVOLUTIONAL-NEURAL-NETWORK-FOR-IDENTIFYING-THYROID-CANCER

RNAseq Reporting Designed for Clinical Deliverability

ViraVate

pubmed-codeathon-team4

Build a marker gene reference set

asm-ngs-workshop

ASM NGS Workshop

Perl

Marker-Gene-Validator

mlxai-2024-team-connor-gunti

XXX is a all-inclusive pipeline we developed for multi-omics data analysis. XXX can take genomics, RNA-seq, proteomics and metabolomics data (for yeast) and integrate with Canonical Correlation Analysis and analyze by OPLS-DA for variables driving the differences between samples. Difference driving pathways then can then be visualized through visNetwork. Lastly, follow-up experiment guidance and be yielded through COBRA simulations with Yeast 8 database.

Integrating-multi-omics-data-in-yeast

mlxai-2024-team-xu

A Federated Index of Virus Metadata and Hyperdata in Public Repositories

vcf-4-population-genomics-team-elder

The_Virus_Index

Quality control tool for metagenomic assemblies

Diversifying-the-pipeline-for-identifying-bulk-RNA-seq-derived-biomarkers-of-cancer-risk-within-sing

MASQ

Genomic Responses to Infectious Disease

GWAusage

Characterization of SARS-CoV-2 host genes

lung-rna-seq

Nextflow

beyond-phylogenies-team4

PureBasic

SARS-CoV-2-host-genes

vcf-4-population-genomics-team-nguyen

Automated-Figure-extraction-and-Tagging

airbending_isoseq

Taxonomy-specific-RPS-BLAST-part-I

Identify antiphage defense systems in the bacterial pangenome

Genes-in-the-Hood

single-cell-comparison

psss-team4

Protein-Variant-Impact-Score

C++

nds1-team-2-design-package

USING-MACHINE-LEARNING-TO-IMPROVE-POST-ACUTE-REHABILITATION-PROCESS-FLOW

This repository contains tools and resources developed by Team Sridharan during the "Resistance is Futile: A Codeathon to Combat Antimicrobial Resistance" (September 2024), hosted by NCBI and NIAID.

OPTICAL-COHERENCE-TOMOGRAPHY-ANGIOGRAPHY-IN-GLAUCOMA

amr-2024-team-sridharan

This repository contains tools and resources developed by Team Dave during the "Resistance is Futile: A Codeathon to Combat Antimicrobial Resistance" (September 2024), hosted by NCBI and NIAID.

amr-2024-team-dave

This repository contains curricular materials developed by Team Finlay during NCBI's BioEd Summit (August 2024).

bioed-2024-team-finlay

SLEuth

Assessment-of-log-transformation-and-z-scores-for-scRNA-seq-data-analysis

Refining Domain Boundaries and Performing Large Scale Parsing

Domain_HMM_Boundaries

NOVEL-CLINICAL-PREDICTION-APPROACHES-TO-MANAGING-CARE-FOR-ACUTE-PULMONARY-EMBOLISM-PATIENTS

DEFINITION-OF-CELL-CYCLE-STATE-IN-LABEL-FREE-IMAGES

Solidifying the VirusGraphs Infrastructure for Deployment

VirusGraphs3

codeathon-info

beyond-phylogenies-team2

glaucoma-oct-scans

MONITORING-POST-OPERATIVE-HEAD-NECK-CANCER-PATIENTS-VIA-SELF-POWERED-SMART-INSOLES

HOPDARM

REAL-TIME-CARDIAC-ASSESSMENT-OF-CATHETERIZATION-DERIVED-FICK-AND-CMR-DERIVED-FLOW

Automating-tools-to-search-and-analyze-large-genome-sequence-repositories

beyond-phylogenies-team1

pubmed-codeathon-team3

beyond-phylogenies-team5

A workspace for the BOSC 2021 CoFest virtual codeathon to explore the functionality of Elastic Blast at Scale and to improve documentation.

ElasticBLAST-CoFest-BOSC-2021

Taxonomy_Domain_Integration

Making a Domain Map Across Approximate Metagenomic Taxonomy.

Creating an awesome tool to perform CNV QC on WES data independent of callers/platform that focuses on confidence and reportability of CNV calls, particularly in clinical data.

SCANCNV

This repository contains curricular materials developed by Team * during NCBI's BioEd Summit (August 2024).

bioed-2024-team-mcclintock

amr-2024-team-nassar

This repository contains tools and resources developed by Team Nassar during the "Resistance is Futile: A Codeathon to Combat Antimicrobial Resistance" (September 2024), hosted by NCBI and NIAID.