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biocommons
eutils

simplified searching, fetching, and parsing records from NCBI using their E-utilities interface

53K 64 29
pachterlab
gget

🧬 gget enables efficient querying of genomic reference databases

38K 1K 85
vanheeringen-lab
genomepy

genes and genomes at your fingertips

21K 412 41
u9401066
pubmed-search-mcp

🔬 Professional MCP server for biomedical literature research — 40 tools, multi-source search (PubMed, Europe PMC, CORE, OpenAlex), full-text access, citation networks, PICO analysis, and more

6K 9 7
kblin
ncbi-genome-download

Scripts to download genomes from the NCBI FTP servers

3K 1K 178
dvklopfenstein
pmidcite

Get citation counts for a PubMed paper from the command line

2K 34 7
pirovc
multitax

A Python package for obtaining, parsing and exploring biological taxonomies (GTDB, NCBI, Silva, Greengenes, OTT)

1K 50 4
suqingdong
pypubmed

Toolkits for NCBI Pubmed

1K 29 8
HadrienG
taxadb

:hatching_chick: locally query the ncbi taxonomy

953 39 15
crosenth
medirect

Multithreaded ncbi edirect and ftract

832 6 3
andgineer
http-stream-xml

Parse HTTP response as stream, by chunks. Example for NCBI (PubMed) Entrez.

815 1 0
CVUA-RRW
taxidtools

A Python Toolkit for Taxonomy

635 3 2
bihealth
clinvar-this

ClinVar Submission API Made Easy

609 11 2
ncbi
elastic-blast

ElasticBLAST is a cloud-based tool to perform your BLAST searches faster and make you more effective

605 69 22
linzhi2013
taxonomy-ranks

To get taxonomy ranks information with ETE3 Python3 module (http://etetoolkit.org/)

487 9 4
enviro-lab
ncbi-submit

A tool to prepare files and run/monitor programmatic submissions to NCBI

432 4 0
zyxue
ncbitax2lin

A tool that converts NCBI taxonomy dump into lineages

404 153 31
suqingdong
pubmed2

search pubmeds quickly

373 6 5
dhimmel
pubmedpy

Utilities for interacting with NCBI EUtilities relating to PubMed

340 11 2
MuteJester
pyncbi

A Python API library for exploration and data retrieval from NCBI

292 3 3
hunglin59638
makura

NCBI Genome downloader

251 0 0
Edinburgh-Genome-Foundry
genome-collector

:stars: Easily download genomes and build BLAST/Bowtie indexes in Python

217 22 0
AiAgentKarl
bioinformatics-mcp-server

MCP server for bioinformatics data — genes, proteins, PubMed, ClinVar and sequences via NCBI & UniProt (free, no API key)

174 0 0
datasnakes
orthoevol

An easy to use and comprehensive python package which aids in the analysis and visualization of orthologous genes. 🐵

147 28 5
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