Awesome Open Source
Search
Programming Languages
Languages
All Categories
Categories
About
Search results for ncbi
ncbi
x
40 search results found
Ncbi Genome Download
⭐
784
Scripts to download genomes from the NCBI FTP servers
Genomepy
⭐
355
genes and genomes at your fingertips
Datasets
⭐
259
NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases.
Genome_updater
⭐
123
Bash script to download/update snapshots of files from NCBI genomes repository (refseq/genbank) with track of changes and without redundancy
Ncbitax2lin
⭐
96
🐞 Convert NCBI taxonomy dump into lineages
Ganon
⭐
73
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
Eutils
⭐
53
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
Taxadb
⭐
32
🐣 locally query the ncbi taxonomy
Plsdb
⭐
29
PLSDB pipeline to collect bacterial plasmids from NCBI
Orthoevolution
⭐
28
An easy to use and comprehensive python package which aids in the analysis and visualization of orthologous genes. 🐵
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.
Vapid
⭐
27
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)
Primerminer
⭐
22
R mased batch sequence downloader, with primer development and in silico evaluation capabilities
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
Virmet
⭐
13
Set of tools for viral metagenomics.
Entrez Rs
⭐
12
A Rust wrapper around the Entrez API. Helps you access the Entrez API using idiomatic Rust. It also provides tools to parse the XML results from Entrez.
Ncbi_acc2gtdb_acc
⭐
12
Mapping NCBI Genbank accession to GTDB accession
Fastax
⭐
12
Make phylogenetic trees and lineages from the NCBI Taxonomy database
Phenotypexpression
⭐
11
Subclassification of disease states based on the intersection of literature and expression
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).
Tostadas
⭐
10
🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission
Atacflow
⭐
10
An ATAC-seq pipeline wrapped in NextFlow that can be run by Jupyter
Virus_detection_sra
⭐
10
Taxonomy.jl
⭐
10
Julia package to handle the NCBI Taxonomy database.
Flowbio
⭐
9
A fast, easy way to present complex bioinformatics pipelines to biologists
Taxonomy Tools
⭐
9
C++ tools for NCBI taxonomy tasks
Pubmedsoso
⭐
7
一个批量下载pubmed免费文献的python小工具
Ncbitaxonomy.jl
⭐
7
Wrapper around the NCBI taxonomy files
Cent
⭐
6
Prediction Analysis of COVID-19 Genome Beyond Omicron Variant on Cloud
Fasta_utilities
⭐
6
Utilities for downloading and managing protein FASTA files.
Taxonomy_ranks
⭐
6
To get taxonomy ranks information with ETE3 Python3 module (http://etetoolkit.org/)
Upward
⭐
5
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
Pyncbi
⭐
5
A Python API library for exploration and data retrieval from NCBI
1-40 of 40 search results
Privacy
|
About
|
Terms
|
Follow Us On Twitter
Copyright 2018-2024 Awesome Open Source. All rights reserved.