PyRank

Ncbi Python Packages

Python packages with the GitHub topic ncbi. Sorted by monthly downloads, with stars and forks.
biocommons
eutils

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

161K 63 29
pachterlab
gget

🧬 gget enables efficient querying of genomic reference databases

46K 1K 98
musharna
data-aggregator-mcp

Unified research-data acquisition MCP — search & fetch datasets across Zenodo, DataCite, NCBI omics (GEO/SRA/BioProject), and literature (PubMed/OpenAIRE) behind one normalized model.

32K 4 0
vanheeringen-lab
genomepy

genes and genomes at your fingertips

30K 410 41
u9401066
pubmed-search-mcp

MCP SDK v2 server for PubMed and multi-source biomedical research, with resilient search, full text, citations, and tenant-safe deployment.

5K 28 9
kblin
ncbi-genome-download

Scripts to download genomes from the NCBI FTP servers

3K 1K 178
bihealth
clinvar-this

ClinVar Submission API Made Easy

875 11 2
dvklopfenstein
pmidcite

Get citation counts for a PubMed paper from the command line

849 33 7
pirovc
multitax

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

606 53 5
HadrienG
taxadb

:hatching_chick: locally query the ncbi taxonomy

557 39 15
datasnakes
orthoevol

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

538 28 5
crosenth
medirect

multiprocessed ncbi edirect

495 6 3
suqingdong
pypubmed

Toolkits for NCBI Pubmed

461 30 8
Edinburgh-Genome-Foundry
genome-collector

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

441 23 0
qgeng1465
biomcp-server

🧬 BioMCP — bioinformatics MCP server: 83 tools · 43 databases · PubMed/NCBI/BLAST/PDB/UniProt/enrichment · `pip install biomcp-server` · 生信 MCP 服务器

436 13 0
PFreda-Lab
okf-loremaster

Multi-agentic biomedical literature evidence extraction, curation, and summarization from PubMed/PMC in Open Knowledge Format (OKF) for downstream machine learning, feature selection, and agentic applications.

414 2 0
ncbi
elastic-blast

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

402 72 24
CVUA-RRW
taxidtools

Python library to deal with taxonomic IDs and lineages from the NCBI's Taxdump files

376 3 2
AiAgentKarl
bioinformatics-mcp-server

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

296 1 0
andgineer
http-stream-xml

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

263 1 0
zyxue
ncbitax2lin

🐞 Convert NCBI taxonomy dump into lineages

239 154 32
enviro-lab
ncbi-submit

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

174 4 1
linzhi2013
taxonomy-ranks

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

167 9 4
MuteJester
pyncbi

A Python API library for exploration and data retrieval from NCBI

163 3 3