NCBI-Codeathons/amr-2024-team-dave

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NCBI-Codeathons/amr-2024-team-dave

NCBI-Codeathons

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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.

SWIGG

A pipeline for making SWIft Genomes in a Graph (SWIGG) using k-mers

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

Jupyter Notebook

ncbi-codeathons.github.io

NCBI Codeathons Website

mlxai-2024-team-saddler

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

OMOPOmics

Patient 'omics data in OMOP format

mlxai-2024-team-bhushan

Jupyter Notebook

vcf-4-population-genomics-team-abdennur

Jupyter Notebook

super-minityper

mlxai-2024-team-beaumont

Jupyter Notebook

SARS2-Variation-Viewer

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

pubmed-codeathon-team1

Jupyter Notebook

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

Jupyter Notebook

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

vcf-4-population-genomics-team-park

SeqMoid

Jupyter Notebook

vcf-4-population-genomics-team-hearn

mlxai-2024-team-gwadz-yang

Jupyter Notebook

mlxai-2024-team-smith

Jupyter Notebook

Clouseau

A QC suite for large VCF files

Host_Phage_Interactions

Understanding how Phages Affect Microbial Disease

bothie

Virus_Graphs

Making Representative Genome Graphs from Eukaryotic Viruses and Phages

Rich Text Format

vcf-4-population-genomics-team-agustinho

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

Jupyter Notebook

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

Classify your health/medical/life sciences search terms

Jupyter Notebook

amr-2024-team-prasad-feldgarden

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.

mlxai-2024-team-landrum-song

vcf-4-population-genomics-team-warren

Jupyter Notebook

DeNovoSV

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

pubmed-codeathon-team2

Jupyter Notebook

NCGAS-cloud-workshop

NCGAS Cloud Workshop

psss-datasets

beyond-phylogenies-team6

vcf-4-population-genomics-team-phan

Jupyter Notebook

mlxai-2024-team-chen

beyond-phylogenies-team3

mlxai-2024-team-hall

Jupyter Notebook

MASCARA

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

Jupyter Notebook

ViraVate

RNAseq Reporting Designed for Clinical Deliverability

pubmed-codeathon-team4

Jupyter Notebook

asm-ngs-workshop

ASM NGS Workshop

Marker-Gene-Validator

Build a marker gene reference set

Jupyter Notebook

mlxai-2024-team-connor-gunti

Jupyter Notebook

Integrating-multi-omics-data-in-yeast

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.

Jupyter Notebook

mlxai-2024-team-xu

Jupyter Notebook

vcf-4-population-genomics-team-elder

The_Virus_Index

A Federated Index of Virus Metadata and Hyperdata in Public Repositories

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

MASQ

Quality control tool for metagenomic assemblies

GWAusage

Genomic Responses to Infectious Disease

lung-rna-seq

beyond-phylogenies-team4

SARS-CoV-2-host-genes

Characterization of SARS-CoV-2 host genes

vcf-4-population-genomics-team-nguyen

Automated-Figure-extraction-and-Tagging

Jupyter Notebook

airbending_isoseq

Taxonomy-specific-RPS-BLAST-part-I

Genes-in-the-Hood

Identify antiphage defense systems in the bacterial pangenome

single-cell-comparison

psss-team4

Protein-Variant-Impact-Score

nds1-team-2-design-package

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

Jupyter Notebook

OPTICAL-COHERENCE-TOMOGRAPHY-ANGIOGRAPHY-IN-GLAUCOMA

amr-2024-team-sridharan

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.

bioed-2024-team-finlay

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

SLEuth

Jupyter Notebook

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

Domain_HMM_Boundaries

Refining Domain Boundaries and Performing Large Scale Parsing

Jupyter Notebook

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

Jupyter Notebook

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

Jupyter Notebook

VirusGraphs3

Solidifying the VirusGraphs Infrastructure for Deployment

Jupyter Notebook

codeathon-info

beyond-phylogenies-team2

glaucoma-oct-scans

Jupyter Notebook

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

ASAP

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

beyond-phylogenies-team1

Jupyter Notebook

pubmed-codeathon-team3

Jupyter Notebook

beyond-phylogenies-team5

ElasticBLAST-CoFest-BOSC-2021

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

Taxonomy_Domain_Integration

Making a Domain Map Across Approximate Metagenomic Taxonomy.

SCANCNV

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.

bioed-2024-team-mcclintock

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

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.

Jupyter Notebook

curriculathon-team-template

team-chang-test

codeathon-team-template

bioed-2024-team-uchida

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

vcf-4-population-genomics-team-aribi-fattouch