Discover

NovoGraph: building whole genome graphs from long-read-based de novo assemblies

Community_Software_Tools_for_NGS

NovoGraph

Perl

rnaseqview

RNA-seq Viewer Team at the NCBI-assisted Boston Genomics Hackathon

Machine Learning to Detect Cancer Biomarkers from RNAseq Data

ConsensusML

Software, architecture, and data index design for the 2018/2019 Virus Discovery Project

VirusDiscoveryProject

A high throughput automated drug discovery pipeline.

drugdisco

Jupyter notebooks to more effectively leverage computational resources at NCBI.

Pharmacogenomics_Prediction_Pipeline_P3

NCBIComputationalCookbook

A pipeline for viral identification from metagenomic samples

ViruSpy

Automatic Packaging and Distribution of Bioinformatics Pipelines

SPeW

Mendelian Randomization with Biomarker Associations for Causality with Outcomes

MR_BACOn

Machine_Learning_Immunogenicity

This is a repo for the Machine Learning Immunogenicity Team in the August 2016 NCBI Hackathon

Framework for Creating Pipeline Software

LabPype

NastyBugs: a simple method for extracting antimicrobial resistance information from metagenomes

MetagenomicAntibioticResistance

Use machine learning to find patterns of similar eligibility protocol criteria for clinical trials

CTEligible

PowerShell

RNA-Seq-in-the-Cloud

An Easy to Use Analysis System for All Human Public bulk RNAseq Data!

Develop a function to be incorporated into the R package 'icd' that will convert International Classification of Diseases codes from Ninth to Tenth revisions

Design-of-ICD-9-to-10-conversion-function-for-the-R-package-icd

RNA_mapping

A framework for network analysis and display of SNPs

Network_SNPs

Find hot data sets in your area (of research)!

SRA_Tinder

Tutorial content for NCBI cloud data and computing

ncbi-cloud-tutorials

Convert sequence IDs between ucsc/refseq/genbank

Master_gff3_parser

A Template for Clear and Simple Documentation of Bioinformatics Code

GoodDoc

seqacademy

Self-guided educational workshop for ChIP-Seq and RNA-Seq

An ATAC-seq pipeline wrapped in NextFlow that can be run by Jupyter

ATACFlow

svcompare

Structural_Variant_Comparison

Classify web visitor queries so you can chart, and respond to, trends in information seeking

Semantic-search-log-analysis-pipeline

Framework for running text mining tools on latest publications. Main page at:

PubRunner

A virtual reality environment for physically assembling deep learning models to solve data science problems.

deVoReaNN

seqr

Java

HLAClustRView

R package specialized in HLA typing clustering and visualization based on specific similarity metrics

phenotypeXpression

Subclassification of disease states based on the intersection of literature and expression

Metagenomics Pipeline Repository for January, 2015 NCBI/ADDS Hackathon at NIH

hackathon_v001_metagenomics

A fast, easy way to present complex bioinformatics pipelines to biologists

FlowBio

Gene expression viewer template

GeneExpressionAging

Visualize cancer genomes with FAIR single-cell RNA-seq data

The-Broad-Institute-Single-Cell-RNA-Seq-Data-Set

TCGA_dbGaP

Search public databases for given genotypic information

Virus_Detection_SRA

Perl

PrecisionMedicineToolkit

We aim to make it easier for biomedical researchers to access and customize synthetic sequence data for the purpose of sharing and testing analysis methods as well as training and collaboration

Bringing-the-Power-of-Synthetic-Data-Generation-to-the-Masses

Programs to quantify expression of transcripts from public datasets

SimpleGeneExpression

Metabolomics-Data-Portal

R shiny application for the visualization and analysis of untargeted metabolomics datasets.

deSRA

An automated protocol to extract variation or expression from public NGS datasets

A detection algorithm for expression features that correspond to previous viral infection

chervil

Structural_Variants_CSHL

Perl

Kipoi-GWAS

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

VirusFriends

Retreive and visualize plasmid sequences from SRA and Next Generation Sequencing data.

Got_Plasmid

Mutation_burden

Building a pipeline to assess effects of mutation burden

Epigenomics_CWL

SCREW: A Reproducible Workflow for Single-Cell Epigenomics

PhenVar

Disease Clustering from Literature Based on Minimal Training Data

ClusterDuck

AssesSV

Code_in_PubMed_Abstracts

An Automated Pipeline to Classify Gene Families based on Protein Domain Organization using Auxin Response Factors in Legumes as an Example

GeneHummus

Clustering-autism-phenotypes-by-automated-text-analysis

A versatile tool to classify diseases using cluster analysis of published phenotypic data

A pipeline for inferring gender for acknowledged individuals in scientific literature on a massive scale

Hidden-Figures

A pipeline to approximate the immunogenicity of peptides resulting from cancer mutations based on structure and other factors.

Cancer_Epitopes_CSHL

HASSL_Homogeneous_Analysis_of_SRA_rnaSequencing_Libraries

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

PubCode

Virulence Factor Characterization in Metagenomes

Virulence_Factor_Characterization

Linking publicly deposited data to sequencing adapters.

OnlineAdapterDatabase

Capsule Networks for improving protein secondary structure prediction accuracy

CapNetProtStruct

A variety of NCBI Computational Tools Distributed as Jupyter Notebooks

NCBI_Jupyter

Polygenic SNP Search Tool

PSST

Discovery of Novel Endogenous Viruses

EndoVir

UPWARD: Uniting People Working Against Rare Diseases

UPWARD

PHP

clint

Linking clinical questions with fMRI research literature

Simulation of Tumor Genomes -- Initiated at the 2017 NYGC-NCBI Hackathon

Tumor_sim

RNAseq Pipeline Repository for January, 2015 NCBI/ADDS Hackathon at NIH

hackathon_v001_rnaseq

Collaborative Computational Development, or, How to Run an NCBI-Style Hackathon

Run_an_NCBI-style_hackathon

SRA2R

SRA2R, a package to import SRA data directly into R

A python tool that uses Machine Learning to identify cancer targeting T-Cells

TCRecePy

A semi-curated list of enhancer and promoter databases. If you know of others, please put them in issues!

Awesome_enhancer_promoter_dbs

CakeCell

Segmenting cells (and other objects!) in microscopy images via neural networks.

Gerber: Generalized Easy Reproducible Bioinformatics Environment wRapper

ContainerInception

A crowdsourcing/expert curation platform for metadata categorization.

Metadata_categorization

Web Ontology Language

DiseaseCluster

Disease prediction based on transcriptomics clustering

Pubmed Research Search String Extraction (PuRSSE)

PuRSSE

Mapping complex genotypes to phenotypic subclusters

Complex_Phenogeno

The goal of this project is use natural language processing to extract exclusion and inclusion criteria from free form text fields to match patients with clinical trials.

TriFECTA

A computational pipeline to find Human Endogenous Retroviruses in RNA Seq Data

RetroSpotter

A machine learning approach to detect micropeptides from noncoding RNAs

LNCPEP

A tool to visually browse co-occurrence of MeSH terms in PubMeb

Visualizing_MeSH_Term_Interaction_Over_Time

The fastest gigascale image annotation system in the world!

HistoloMaps

A QC pipeline for SVs calls based on coverage and SNP calls

ScrubSV

Ultrafast_Mapping_CSHL

TraIN

Graph_Extraction

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

BarcSeek

NCBI_August_Hackathon_Push_Button_Genomics_Solution

Push button solution for setting up an NCBI-style Hackathon

HAQmap

Consolidation of tools in the MutPred Suite to work with VCF files

MutPredMerge

Jupyter Notebooks to analyze T-cell Receptor Sequencing

PyClonal

Viral VDAP: a viral alignment, variant discovery, and annotation pipeline launched at the NCBI-Hackathon 2019

Viral-VDAP

Implements NCBI Contamination Screen Publicly in CWL

ContamFilter

Text-driven identification and ranking of associated gene pairs in PubMed

100

PubMed2GenePairs