ncbi-database

FlexTaxD (Flexible Taxonomy Databases) - Create, add, merge different taxonomy sources (QIIME, GTDB, NCBI and more) and create metagenomic databases (kraken2, ganon and more )

Deep learning methods for feature selection in gene expression autism data.

Assign taxonomy with blast, can be used for qiime

🌱 ➡️ 🌳 Add new taxa or taxonomic groups to the NCBI Taxdump files

Microarray Analysis Pipeline in Python

An AI-driven genomic intelligence system delivering structured ClinVar interpretation and high-precision exon, intron, and gene queries using the Model Context Protocol (MCP).

Julia package to handle the NCBI Taxonomy database.

Analysis of the viral genomes of SARS-CoV2 using MAFFT and igtree

A tool for manipulating fasta files and obtaining new sequence data from NCBI in fasta format

Bio Python Project using getopt library in python and engaging with the command line prompt.

An R code to convert NCBI data files into CSV

Find and retrieve biological data and its metadata from NCBI

Genome Metadata Visualizer is a series of scripts written to process and visualise genome metadata after it is pulled from NCBI using the dataset and dataformat command line tools.

Downloads plasmids from refseq ftp

How to download genomes using the accession number

PubMatrixR is an R package that performs systematic literature searches on PubMed and PMC databases using pairwise combinations of search terms. It creates co-occurrence matrices showing the number of publications that mention both terms from two different sets, enabling researchers to explore relationships between genes, diseases, pathways.

A list of publicly available Microarray Gene Expression datasets with proper attribution and associated toolkits.

Python class project in collab with @heloint and @AniValle. Using Entrez, Seq.io, regex, pandas

Crawling NCBI Pubmed Data using HTML and jQuery

This Python script retrieve all children organism under an ancestor in NCBI taxonomy.