Awesome Open Source

Programming Languages

Search results for python ncbi

27 search results found

Ncbi Genome Download ⭐ 784

Scripts to download genomes from the NCBI FTP servers

Genomepy ⭐ 355

genes and genomes at your fingertips

Ncbitax2lin ⭐ 96

🐞 Convert NCBI taxonomy dump into lineages

ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refseq/genbank), taxonomic profiling (ncbi/gtdb), binning and hierarchical classification, customized reporting and more

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

Elastic Blast ⭐ 35

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

🐣 locally query the ncbi taxonomy

PLSDB pipeline to collect bacterial plasmids from NCBI

Multisub ⭐ 28

Prepares a SARS-CoV-2 submission for GISAID, NCBI or ENA. Can read GISAID or NCBI files, or plain fasta+tsv/csv/xls. Finds files in input directory and merges everything into a single output directory. Auto-detects input file formats. Can submit the results to multiple repositories from the command line.

Orthoevolution ⭐ 28

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

VAPiD: Viral Annotation and Identification Pipeline

Pmidcite ⭐ 24

Turbocharge a PubMed literature search using citation counts and data from the NIH

Multitax ⭐ 23

Python package to obtain, parse and explore biological taxonomies (GTDB, NCBI, Silva, Greengenes, OTT)

Pypubmed ⭐ 20

Toolkits for NCBI Pubmed

Pipetaxon ⭐ 18

PipeTaxon exposes the ncbi taxonomy database as a REST API.

Genome_collector ⭐ 17

🌠 Easily download genomes and build BLAST/Bowtie indexes in Python

Set of tools for viral metagenomics.

Phenotypexpression ⭐ 11

Subclassification of disease states based on the intersection of literature and expression

Tostadas ⭐ 10

🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission

Sequence Database Curator ⭐ 10

This program dereplicates and/or filter nucleotide and/or protein database from a list of names or sequences (by exact match).

Pubmedsoso ⭐ 7

一个批量下载pubmed免费文献的python小工具

Taxonomy_ranks ⭐ 6

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

Fasta_utilities ⭐ 6

Utilities for downloading and managing protein FASTA files.

UPWARD: Uniting People Working Against Rare Diseases

Clusterduck ⭐ 5

Disease Clustering from Literature Based on Minimal Training Data

Genbankpy ⭐ 5

Tools to download, parse and filter GenBank files

A Python API library for exploration and data retrieval from NCBI

Related Searches

Python Django (28,897)

Python Script (17,070)

Python Docker (14,113)

Python Machine Learning (14,099)

Python Command Line (13,351)

Python Jupyter Notebook (12,976)

Python Html (10,924)

Python Database (9,985)

Python Plugin (9,231)

Python Paper (6,580)

1-27 of 27 search results

Privacy | About | Terms | Follow Us On Twitter

Copyright 2018-2024 Awesome Open Source. All rights reserved.