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

• UpdatedMar 12, 2025
• Python

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

• UpdatedJun 21, 2022
• Jupyter Notebook

Assign taxonomy with blast, can be used for qiime

• UpdatedAug 18, 2023
• Python

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

• UpdatedMar 9, 2020
• Perl

Microarray Analysis Pipeline in Python

• UpdatedAug 1, 2019
• Jupyter Notebook

Julia package to handle the NCBI Taxonomy database.

• UpdatedMar 11, 2025
• Julia

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

• UpdatedAug 14, 2020
• Python

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

• UpdatedOct 23, 2018
• Go

An R code to convert NCBI data files into CSV

• UpdatedOct 8, 2019
• R

Explore bioinformatics tasks with Python! This collection offers scripts using Biopython for NCBI database access, sequence parsing, DNA transcription, translation, GC content calculation, and sequence analysis. Perfect for beginners learning bioinformatics in Python.

• UpdatedNov 15, 2023
• Python

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

• UpdatedJan 30, 2023
• Python

Identifying viruses as an anomaly

• UpdatedJan 14, 2023
• Python

Find and retrieve biological data and its metadata from NCBI

• UpdatedMar 20, 2025
• Rust

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.

• UpdatedApr 18, 2024
• HTML

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

• UpdatedJul 28, 2020
• Python

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

• UpdatedFeb 17, 2023
• Python

NCBI Datasets is an experimental resource for finding and building datasets

• UpdatedNov 27, 2020

Crawling NCBI Pubmed Data using HTML and jQuery

• UpdatedApr 20, 2017
• HTML

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

• UpdatedFeb 19, 2025
• Python

How to download genomes using the accession number

• UpdatedApr 20, 2023
• Shell