Projects in Awesome Lists by ncbi
A curated list of projects in awesome lists by ncbi .
https://github.com/ncbi/datasets
NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases.
Last synced: 03 Mar 2026
https://github.com/ncbi/amr
AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.
antibiotic-resistance bioinformatics genomics pathogen
Last synced: 10 Oct 2025
https://github.com/ncbi/medcpt
Code for MedCPT, a model for zero-shot biomedical information retrieval.
Last synced: 04 Jul 2025
https://github.com/ncbi/egapx
Eukaryotic Genome Annotation Pipeline-External caller scripts and documentation
Last synced: 28 Jan 2026
https://github.com/ncbi/icn3d
web-based protein structure viewer and analysis tool interactively or in batch mode
3d-structure 3d-viewer ar chemical delphi icn3d jupyter-notebook molecular-viewer nodejs nucleotide protein protein-viewer snp structure-viewer vr webgl
Last synced: 16 May 2025
https://github.com/ncbi/dbsnp
dbSNP
bioinformatics database genomics ncbi variations
Last synced: 05 Mar 2026
https://github.com/ncbi/tpmcalculator
TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files
Last synced: 04 Jul 2025
https://github.com/ncbi/fcs
Foreign Contamination Screening caller scripts and documentation
Last synced: 04 Jul 2025
https://github.com/ncbi/vadr
Viral Annotation DefineR: classification and annotation of viral sequences based on RefSeq annotation
Last synced: 03 Oct 2025
https://github.com/ncbi/gprobe
client app for the gRPC health-checking protocol
Last synced: 04 Jul 2025
https://github.com/ncbi/ncbi-cxx-toolkit-public
NCBI C++ Toolkit package sources
Last synced: 03 Mar 2026
https://github.com/ncbi/robotframework-pageobjects
Implementation of the Page Object pattern with Robot Framework and selenium. Also facilitates page object pattern independent of Robot Framework
Last synced: 19 Oct 2025
https://github.com/ncbi/clinvar
ClinVar aggregates information about genomic variation and its relationship to human health. Contact us at 'clinvar@ncbi.nlm.nih.gov' with any questions or comments.
Last synced: 27 Oct 2025
https://github.com/ncbi/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.
Last synced: 04 Jul 2025
https://github.com/ncbi/elastic-blast
ElasticBLAST is a cloud-based tool to perform your BLAST searches faster and make you more effective
Last synced: 04 Jul 2025
https://github.com/ncbi/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.
Last synced: 04 Jul 2025
https://github.com/ncbi/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!
Last synced: 04 Jul 2025
https://github.com/ncbi/pm4ngs
Project Manager for NGS data analysis
bioinformatics chipexo chipseq cwl-workflow next-generation-sequencing ngs-analysis ngs-pipeline rnaseq
Last synced: 04 Jul 2025
https://github.com/ncbi/tree-tool
Incremental building of phylogenetic distance trees
bioinformatics bioinformatics-tool data-analysis distance-measures evolution phylogenetic-trees
Last synced: 31 Jan 2026
https://github.com/ncbi/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.
Last synced: 04 Jul 2025
https://github.com/ncbi/consul-announcer
Service announcer for Consul (https://www.consul.io/).
Last synced: 04 Jul 2025
https://github.com/ncbi/cwl-ngs-workflows-cbb
A set of CWL tools and workflows used by NCBI Computational Biology Branch for NGS data analysis
cwl-workflow ngs ngs-analysis ngs-pipeline
Last synced: 31 Jul 2025
https://github.com/ncbi/scpopcorn
A python tool to do comparative analysis of mulitple single cell datasets.
Last synced: 04 Jul 2025
https://github.com/ncbi/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.
Last synced: 20 Jun 2025
https://github.com/ncbi/fcs-gx
Foreign Contamination Screening - GX source code
Last synced: 20 Jun 2025
https://github.com/ncbi/stxtyper
StxTyper uses a standardized algorithm to accurately type both known and unknown Shiga toxin operons from assembled genomic sequence.
bioinformatics bioinformatics-tool escherichia-coli genomics pathogen virulence-genes
Last synced: 24 Oct 2025
https://github.com/ncbi/pubchem-align3d
This is a generic C++ library that can be used to rapidly align two small molecules in 3D space, with shape - and optionally color - Tanimoto scoring. Included is a sample RDKit application whereby any two SDF-format chemicals are read in and aligned.
Last synced: 04 Jul 2025
https://github.com/ncbi/finagle-consul
Service discovery for Finagle cluster with Consul.
Last synced: 02 Feb 2026
https://github.com/ncbi/hydroid
Python package for analyzing hydroxyl-radical footprinting experiments of DNA-protein complexes
bioinformatics structural-biology
Last synced: 04 Jul 2025
https://github.com/ncbi/packit
Python packaging in declarative way (wrapping pbr to make it flexible)
Last synced: 27 Feb 2026
https://github.com/ncbi/ncbi-cxx-toolkit-conan
NCBI C++ Toolkit package recipe
Last synced: 22 Feb 2026
https://github.com/ncbi/workshop-asm-ngs-2022
Pre-conference workshop for ASM NGS 2022
Last synced: 04 Jul 2025
https://github.com/ncbi/ncbi-logging
Log monitoring and gathering infrastructure to feed analytics
Last synced: 05 Oct 2025
https://github.com/ncbi/psss-bytes2biology
Petabyte Scale Sequence Search Initiative
Last synced: 10 Oct 2025
https://github.com/ncbi/workshop-asm-ngs-2024
Pre-conference workshop for ASM NGS 2024
Last synced: 17 Oct 2025
https://github.com/ncbi/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.
Last synced: 04 Jul 2025
https://github.com/ncbi/ncbi-xmlwrapp
NCBI’s fork of “xmlwrapp” -- a C++ wrapper for libxml2/libxslt libraries
Last synced: 04 Jul 2025
https://github.com/ncbi/aceview
Acedb object oriented database engine and AceView/MAGIC RNA_seq pipeline, NCBI/NLM/NIH
Last synced: 07 Oct 2025
https://github.com/ncbi/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.
Last synced: 03 Oct 2025
https://github.com/ncbi/biocreative_litcovid
Evaluation scripts of the Biocreative LitCovid track
biocreative biomedical-text-mining deep-learning machine-learning natural-language-processing
Last synced: 22 Aug 2025
https://github.com/ncbi/gtr
The Genetic Testing Registry (GTR®) provides a central location for voluntary submission of genetic test information by providers. The scope includes the test's purpose, methodology, validity, evidence of the test's usefulness, and laboratory contacts and credentials. The overarching goal of the GTR is to advance the public health and research into the genetic basis of health and disease.
Last synced: 20 Jan 2026
https://github.com/ncbi/cloud-transcriptome-annotation
Time and cost comparison on GCP and AWS for transcriptome annotation
aws gcp jupyter-notebook transcriptome-annotation
Last synced: 07 Oct 2025
https://github.com/ncbi/netphix
A computational tool to identify mutated subnetworks that are associated with a continuous cancer phenotype
Last synced: 04 Jul 2025