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sra-tools
SRA ToolsGeneGPT
Code and data for GeneGPT.datasets
NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases.pgap
NCBI Prokaryotic Genome Annotation Pipelineamr
AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.PubReader
A new way to view journal articlesicn3d
web-based protein structure viewer and analysis tool interactively or in batch modeTPMCalculator
TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM filesMedCPT
Code for MedCPT, a model for zero-shot biomedical information retrieval.dbsnp
dbSNPngs
NGS Language BindingsSKESA
SKESA assemblerblast_plus_docs
ngs-tools
vadr
Viral Annotation DefineR: classification and annotation of viral sequences based on RefSeq annotationfcs
Foreign Contamination Screening caller scripts and documentationncbi-vdb
ncbi-vdbgprobe
client app for the gRPC health-checking protocolrobotframework-pageobjects
Implementation of the Page Object pattern with Robot Framework and selenium. Also facilitates page object pattern independent of Robot FrameworkSSDraw
BAMscale
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.clinvar
ClinVar aggregates information about genomic variation and its relationship to human health. Contact us at '[email protected]' with any questions or comments.rapt
Read Assembly and Annotation Pipeline Toolncbi-cxx-toolkit-public
NCBI C++ Toolkit package sourcesJATSPreviewStylesheets
JATS Preview Stylesheetsdocker
sra-human-scrubber
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.elastic-blast
ElasticBLAST is a cloud-based tool to perform your BLAST searches faster and make you more effectiveBioConceptVec
dbvar
dbVarAIONER
AIONERmagicblast
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
SRAToolkit has been REPLACED - see READMEbert_gt
egapx
Eukaryotic Genome Annotation Pipeline-External caller scripts and documentationosiris
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.pm4ngs
Project Manager for NGS data analysisBioREx
cwl-ngs-workflows-cbb
A set of CWL tools and workflows used by NCBI Computational Biology Branch for NGS data analysisconsul-announcer
Service announcer for Consul (https://www.consul.io/).scPopCorn
A python tool to do comparative analysis of mulitple single cell datasets.workshop-ncbi-data-with-python
BioRED
cxx-toolkit
EvoGeneX
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.tree-tool
Incremental building of phylogenetic distance treesGNorm2
pipelines
tmVar3
graf
Genetic Relationship And Fingerprintingribovore
biomedical-citation-selector
PMCXMLConverters
PMC XML Convertersgaptools
dbGaP data validation tool repoAF2_benchmark
sars2variantcalling
The NCBI SARS-CoV-2 Variant Calling (SC2VC) Pipeline allows calling high-confidence variants from SARS-CoV-2 NGS data in a standardized formatICITY
fcs-gx
Foreign Contamination Screening - GX source codeblast-cloud
Documentation for NCBI BLAST AMIRepairSig
finagle-consul
Service discovery for Finagle cluster with Consul.NetREX
python-libpq-dev
packit
Python packaging in declarative way (wrapping pbr to make it flexible)workshop-asm-ngs-2022
Pre-conference workshop for ASM NGS 2022elastic-blast-demos
ElasticBLAST demosPSSS-Bytes2Biology
Petabyte Scale Sequence Search InitiativeHYDROID
Python package for analyzing hydroxyl-radical footprinting experiments of DNA-protein complexesncbi-drs
GA4GH DRS Servicencbi-logging
Log monitoring and gathering infrastructure to feed analyticscwl-demos
CWL demonstration pipelinesSpeciesAssignment
SpeciesAssignmentniso-jats
dual_fold_coevolution
mti
NLM Medical Text Indexer (MTI)DbGaP-FHIR-API-Docs
The documentation repository for the dbGaP FHIR API.mtix
ML based NLM Medical Text IndexerITSx
Not the official ITSx repository, please visit https://microbiology.se/software/itsx/deeplensnet
gtax
biomedical-citation-selector-trainer
Biomedical Citation Selector TrainerSuPER
Co-SELECT
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.AceView
Acedb object oriented database engine and AceView/MAGIC RNA_seq pipeline, NCBI/NLM/NIHstxtyper
StxTyper uses a standardized algorithm to accurately type both known and unknown Shiga toxin operons from assembled genomic sequence.ncbi-xmlwrapp
NCBIβs fork of βxmlwrappβ -- a C++ wrapper for libxml2/libxslt librariesncbi-cxx-toolkit-conan
NCBI C++ Toolkit package recipebiocreative_litcovid
Evaluation scripts of the Biocreative LitCovid trackNETPHIX
A computational tool to identify mutated subnetworks that are associated with a continuous cancer phenotypeSRPRISM
deflake
deflake.py Helps debug a non determinate test (or any flaky program) by running it until it exits with a non-zero exit code.ncbi_doc_template
Solr-Plugins
Assorted plugins for Solrncbi_css_standards
NCBI CSSdatadicer
GeneSigNet
nlm-dtd
CoV-Dist
elastic-blast-docs
ElasticBLAST documentationLove Open Source and this site? Check out how you can help us