NCBI Hackathon Products
Biollante: A Tool to Identify Contamination in Plant Genomic Datasets
VirusFriends: discover viral sequences in the NCBI Sequence Read Archive!
A simple method for finding antimicrobial resistance genes in metagenomic datasets
Gene Expression in Aging
Modular toolkit for RNAseq viewers and viewing
A database of adapter sequences found in public databases
A Robotic Encapsulation of a variant calling robot that can return deidentified results
A dockerized database and flask template for presentation of RNAseq results!
Products Generated in the SVAI NF2 Hackathon
Calculates clone-specific mutational burden and evaluates whether there is any evidence counterindicating immunotherapy
Estimating Association of Genetic Features with Survival
Protein Correlation with Shiny
A Shiny App to Support Proteomic Correlation
BarcSeek: A Flexible Barcode Partitioning Tool for Demultiplexing Genomic Sequencing Data
Simulation of Tumor Genomes.
A system for evaluating difficult to assess regions that uses SV calls and mappability to generate a genome-wide score.
Master gff3 parser
SeqIDMapper provides naming consistency in these input files by converting the sequence feature IDs in the entire file to the desired ID format using a single command.
ga4gh ncbi api
Making NCBI data available using GA4GH methods.
Motivate the transition to graph genomes, we developed a simple graph-based genome browser that is accessible at http://graphymcbrowserface.umbc.in.
Virus Detection SRA
Sidearm searches the SRA database for viruses using the NCBI magicBLAST tool.
Generate CNV calls from raw SNP array data using the command line.
A CWL Pipeline and Docker Image for Performing Standard Single-Cell DNA Methylation Analyses.
PhenVar is designed to take one or more rsids and generate a list of PubMed IDs to query and generate novel associations between publications.
Text-driven identification and ranking of associated gene pairs in PubMed.
Visualizing MeSH Term Interaction Over Time
A tool to visually browse co-occurrence of MeSH terms in PubMeb.
Framework for running text mining tools on latest publications.
Comparison and estimation of breakpoints for SVs across different technologies and resources.
Structural Variant Comparison
Tools to compare structural variants to those in public databases!.
Structural Variants CSHL
10x genomics read simulator, topsorter and danger track.
An R package for using the SRA toolki.
Ultrafast Mapping CSHL
Finding expressed variants while streaming data.
A self-guided hands-on RNAseq tutorial designed to run for free on cloud services.
An ideogram-based viewer for whole transcriptome RNAseq experiments.
Code in PubMed Abstracts
This tool searches for code cited in PubMed abstracts by searching for popular repositories such as GitHub and Bitbucket.
MetaNetVar is a pipeline for applying network analysis tools for genomic variant analysis.
Network Stats Acc Interop
SNP FSA is a pipeline for applying statistical analysis tools to identify interactions between SNPs and their effects on phenotypic expression.
3D 2D Rep Structure
Tool to create 2D diagrams from 3D protein structures and render them side by side.
Ultrafast transfer of protein structure information from pdb to the NCBI iCN3D viewer.
Mapping PDB structures to gene-level in genome browsers, and visualizing SNPs.
A crowdsourcing/expert curation platform for metadata categorization.
The repository contains scripts to automatically fetch related dbGaP studies and subsequently the specific sequence files for given TCGA data.
Machine Learning Immunogenicity
A pipeline to learn about the immunogenicity of peptides based on prior data using TensorFlow.
Cancer Epitopes CSHL
A pipeline to approximate the immunogenicity of peptides resulting from cancer mutations based on structure and other factors.