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ConsensusML
Machine Learning to Detect Cancer Biomarkers from RNAseq Data
The-Broad-Institute-Single-Cell-RNA-Seq-Data-Set
Visualize cancer genomes with FAIR single-cell RNA-seq data
TheHumanPangenome
A Strategy for Building and Using a Human Reference Pangenome
personalgenomics
Empowering individuals to analyze their personal genomics data using publicly available tools
RNA-Seq-in-the-Cloud
An Easy to Use Analysis System for All Human Public bulk RNAseq Data!
UPWARD
UPWARD: Uniting People Working Against Rare Diseases
VirusDiscoveryProject
Software, architecture, and data index design for the 2018/2019 Virus Discovery Project
BioSyntax
Syntax Highlighting for Computational Biology (hackseq '17)
phenotypeXpression
Subclassification of disease states based on the intersection of literature and expression
PrIMP
A python toolkit for the predictive analysis of infection-prone microbiome pathways
FlowBio
https://github.com/NCBI-Hackathons/FlowBio
ScrubSV
A QC pipeline for SVs calls based on coverage and SNP calls
Bugs and Drugs
A Versatile Antibiotic Resistance Pipeline
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.