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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
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
cloud-transcriptome-annotation
Time and cost comparison on GCP and AWS for transcriptome annotationelastic-blast-docs
ElasticBLAST documentationLove Open Source and this site? Check out how you can help us