Discover ncbi/NetREX Open Source project

NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases.

370

datasets

NCBI Prokaryotic Genome Annotation Pipeline

347

pgap

AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.

300

amr

A new way to view journal articles

262

PubReader

JavaScript

193

icn3d

web-based protein structure viewer and analysis tool interactively or in batch mode

JavaScript

151

TPMCalculator

TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files

Code for MedCPT, a model for zero-shot biomedical information retrieval.

124

MedCPT

dbsnp

ngs

NGS Language Bindings

SKESA

blast_plus_docs

ngs-tools

vadr

Viral Annotation DefineR: classification and annotation of viral sequences based on RefSeq annotation

Foreign Contamination Screening caller scripts and documentation

fcs

ncbi-vdb

gprobe

client app for the gRPC health-checking protocol

robotframework-pageobjects

Implementation of the Page Object pattern with Robot Framework and selenium. Also facilitates page object pattern independent of Robot Framework

SSDraw

BAMscale is a one-step tool for either 1) quantifying and normalizing the coverage of peaks or 2) generated scaled BigWig files for easy visualization of commonly used DNA-seq capture based methods.

BAMscale

clinvar

ClinVar aggregates information about genomic variation and its relationship to human health. Contact us at '[email protected]' with any questions or comments.

HTML

rapt

Read Assembly and Annotation Pipeline Tool

ncbi-cxx-toolkit-public

NCBI C++ Toolkit package sources

An SRA tool that takes as input local fastq file from a clinical infection sample, identifies and removes any significant human read, and outputs the edited (cleaned) fastq file that can safely be used for SRA submission.

JATSPreviewStylesheets

JATS Preview Stylesheets

XSLT

docker

Dockerfile

sra-human-scrubber

Shell

elastic-blast

ElasticBLAST is a cloud-based tool to perform your BLAST searches faster and make you more effective

BioConceptVec

dbvar

AIONER

magicblast

JUDI

This repository contains the source code of JUDI, a workflow management system for developing complex bioinformatics software with many parameter settings. Bioinformatics pipeline: Just Do It!

SRAToolkit has been REPLACED - see README

sratoolkit

bert_gt

Eukaryotic Genome Annotation Pipeline-External caller scripts and documentation

egapx

Nextflow

osiris

OSIRIS is a public domain quality assurance software package that facilitates the assessment of multiplex short tandem repeat (STR) DNA profiles based on laboratory-specific protocols. OSIRIS evaluates the raw electrophoresis data contained in .fsa or .hid files using an independently derived mathematically-based sizing algorithm. OSIRIS currently supports ABI capillary analytical platforms and numerous commercially available marker kits including all CODIS-compliant kits as well as those favored by biomedical laboratories.

Project Manager for NGS data analysis

pm4ngs

BioREx

A set of CWL tools and workflows used by NCBI Computational Biology Branch for NGS data analysis

cwl-ngs-workflows-cbb

Service announcer for Consul (https://www.consul.io/).

consul-announcer

A python tool to do comparative analysis of mulitple single cell datasets.

scPopCorn

workshop-ncbi-data-with-python

This repository contains the source code of the R package for EvoGeneX, a software to infer the mode of evolution from the gene expression data.

BioRED

cxx-toolkit

HTML

EvoGeneX

tree-tool

Incremental building of phylogenetic distance trees

GNorm2

Java

pipelines

Genetic Relationship And Fingerprinting

tmVar3

Java

graf

ribovore

biomedical-citation-selector

dbGaP data validation tool repo

PMCXMLConverters

PMC XML Converters

XSLT

gaptools

Shell

AF2_benchmark

The NCBI SARS-CoV-2 Variant Calling (SC2VC) Pipeline allows calling high-confidence variants from SARS-CoV-2 NGS data in a standardized format

sars2variantcalling

ICITY

Foreign Contamination Screening - GX source code

fcs-gx

Documentation for NCBI BLAST AMI

blast-cloud

CSS

RepairSig

Service discovery for Finagle cluster with Consul.

finagle-consul

python-libpq-dev

Shell

packit

Python packaging in declarative way (wrapping pbr to make it flexible)

Pre-conference workshop for ASM NGS 2022

workshop-asm-ngs-2022

elastic-blast-demos

ElasticBLAST demos

Petabyte Scale Sequence Search Initiative

PSSS-Bytes2Biology

Python package for analyzing hydroxyl-radical footprinting experiments of DNA-protein complexes

HYDROID

ncbi-drs

GA4GH DRS Service

Log monitoring and gathering infrastructure to feed analytics

ncbi-logging

CWL demonstration pipelines

cwl-demos

SpeciesAssignment

niso-jats

dual_fold_coevolution

NLM Medical Text Indexer (MTI)

mti

DbGaP-FHIR-API-Docs

The documentation repository for the dbGaP FHIR API.

ML based NLM Medical Text Indexer

mtix

Not the official ITSx repository, please visit https://microbiology.se/software/itsx/

ITSx

deeplensnet

gtax

Biomedical Citation Selector Trainer

biomedical-citation-selector-trainer

SuPER

This repository contains the source code of Co-SELECT, a computational tool to analyze the results of in vitro HT-SELEX experiments for TF-DNA binding to show the role of DNA shape in TF-DNA binding by using a novel method of deconvoluting the contributions of DNA sequence and DNA shape on the binding.

Co-SELECT

Assembly

AceView

Acedb object oriented database engine and AceView/MAGIC RNA_seq pipeline, NCBI/NLM/NIH

stxtyper

StxTyper uses a standardized algorithm to accurately type both known and unknown Shiga toxin operons from assembled genomic sequence.

NCBI’s fork of “xmlwrapp” -- a C++ wrapper for libxml2/libxslt libraries

ncbi-xmlwrapp

NCBI C++ Toolkit package recipe

ncbi-cxx-toolkit-conan

Evaluation scripts of the Biocreative LitCovid track

biocreative_litcovid

A computational tool to identify mutated subnetworks that are associated with a continuous cancer phenotype

NETPHIX

SRPRISM

deflake.py Helps debug a non determinate test (or any flaky program) by running it until it exits with a non-zero exit code.

deflake

Assorted plugins for Solr

ncbi_doc_template

CSS

Solr-Plugins

ncbi_css_standards

datadicer

GeneSigNet

nlm-dtd

CoV-Dist

cloud-transcriptome-annotation

Time and cost comparison on GCP and AWS for transcriptome annotation