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  • Common Workflow Language dependency manager

    Developed at GCC-BOSC 2018 Hackathon

  • SeqAcademy

    Self-guided educational workshop for ChIP-Seq and RNA-Seq https://seqacademy.org

  • Retrospotter

    A computational pipeline for measuring the expression of Human Endogenous Retroviruses using publicly available RNA Seq Data.

  • Gerber

    Generalized Easy Reproducible Bioinformatics Environment wRapper

  • SpoonFedNanopore

    The world's simplest open-source nanopore alignment and assembly algorithm

  • HapPyNet

    Haplotype Block Based Dimensionality Reduction for Complex Variant-Disease Associations

  • ClusterDuck (alpha)

    Disease Clustering from Literature Based on Minimal Training Data

  • EgreTT (alpha)

    a merezoite Egress Tracking Tool for light microscopy studies

  • viSRAtoo (beta)

    Viewing genome expression on the gene and genome level

  • PubCode (concept)

    An app platform for CLI Apps that engage NCBI/NLM Data and Services

  • MASSIF-BLAST (concept)

    A toolkit of pipelines to assess and repair badly assembled genomes

  • drugdisco (beta)

    A high throughput automated drug discovery pipeline

  • MR_BACOn (beta)

    Mendelian Randomization with Biomarker Associations for Causality with Outcomes

  • Biollante

    Biollante: A Tool to Identify Contamination in Plant Genomic Datasets

  • VirusFriends

    VirusFriends: discover viral sequences in the NCBI Sequence Read Archive!

  • NastyBugs

    A simple method for finding antimicrobial resistance genes in metagenomic datasets

  • Gene Expression in Aging

    Modular toolkit for RNAseq viewers and viewing

  • Adapter Database

    A database of adapter sequences found in public databases

  • Genomic Robots

    A Robotic Encapsulation of a variant calling robot that can return deidentified results

  • arvos

    A dockerized database and flask template for presentation of RNAseq results!

  • Products Generated in the SVAI NF2 Hackathon

  • Mutation_burden

    Calculates clone-specific mutational burden and evaluates whether there is any evidence counterindicating immunotherapy

  • SuMu

    Estimating Association of Genetic Features with Survival

  • Protein Correlation with Shiny

    A Shiny App to Support Proteomic Correlation

  • BarcSeek

    BarcSeek: A Flexible Barcode Partitioning Tool for Demultiplexing Genomic Sequencing Data

  • Tumor_sim

    Simulation of Tumor Genomes.

  • DangerTrack

    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.

  • Graph Extraction

    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.

  • Scan2CNV

    Generate CNV calls from raw SNP array data using the command line.

  • Epigenomics CWL

    A CWL Pipeline and Docker Image for Performing Standard Single-Cell DNA Methylation Analyses.

  • PhenVar

    PhenVar is designed to take one or more rsids and generate a list of PubMed IDs to query and generate novel associations between publications.

  • PubMed2GenePairs

    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.

  • PubRunner

    Framework for running text mining tools on latest publications.

  • svcompare

    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.

  • SRA2R

    An R package for using the SRA toolki.

  • Ultrafast Mapping CSHL

    Finding expressed variants while streaming data.

  • RNA mapping

    A self-guided hands-on RNAseq tutorial designed to run for free on cloud services.

  • rnaseqview

    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.

  • Network SNPs

    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.

  • iCN3D MMTF

    Ultrafast transfer of protein structure information from pdb to the NCBI iCN3D viewer.

  • PDB2Genome

    Mapping PDB structures to gene-level in genome browsers, and visualizing SNPs.

  • Metadata categorization

    A crowdsourcing/expert curation platform for metadata categorization.

  • TCGA dbGaP

    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.