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Ncbi Python Packages

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

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

66K 64 29
pachterlab
gget

🧬 gget enables efficient querying of genomic reference databases

37K 1K 85
vanheeringen-lab
genomepy

genes and genomes at your fingertips

18K 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 12 9
kblin
ncbi-genome-download

Scripts to download genomes from the NCBI FTP servers

3K 1K 178
suqingdong
pypubmed

Toolkits for NCBI Pubmed

1K 29 8
dvklopfenstein
pmidcite

Turbocharge a PubMed literature search using citation data from the NIH

1K 34 7
andgineer
http-stream-xml

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

1K 1 0
bihealth
clinvar-this

ClinVar Submission API Made Easy

1K 11 2
pirovc
multitax

Python package to obtain, parse and explore biological and custom taxonomies.

974 50 4
HadrienG
taxadb

:hatching_chick: locally query the ncbi taxonomy

951 39 15
crosenth
medirect

Multithreaded ncbi edirect and ftract

713 6 3
dhimmel
pubmedpy

Utilities for interacting with NCBI EUtilities relating to PubMed

639 11 2
suqingdong
pubmed2

search pubmeds quickly

615 6 5
ncbi
elastic-blast

ElasticBLAST runs BLAST searches faster by distributing its work to multiple cloud instances. This allows larger numbers of queries to be searched in less time compared to BLAST+ on a single host. Use of the cloud facilitates collaboration, sharing of results, datasets and pipelines on a common platform. The National Center for Biotechnology Information ([NCBI](https://www.ncbi.nlm.nih.gov)), part of the National Library of Medicine at the NIH, developed and maintains ElasticBLAST.

507 69 22
CVUA-RRW
taxidtools

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

497 3 2
zyxue
ncbitax2lin

A tool that converts NCBI taxonomy dump into lineages

399 153 31
MuteJester
pyncbi

A Python API library for exploration and data retrieval from NCBI

380 3 3
enviro-lab
ncbi-submit

A tool for submitting to NCBI (SRA, BioSample, & GenBank).

374 4 0
linzhi2013
taxonomy-ranks

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

210 9 4
Edinburgh-Genome-Foundry
genome-collector

Easily download and store taxID genomes from NCBI

204 22 0
datasnakes
datasnakes

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

202 28 5
delveopers
enigmadatabase

NCBI DNA Database Builder and Dataset Loader for ML pipelines (Enigma2).

192 0 0
AiAgentKarl
bioinformatics-mcp-server

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

189 1 0
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