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Projects in Awesome Lists tagged with ncbi

A curated list of projects in awesome lists tagged with ncbi .

https://github.com/pachterlab/gget

🧬 gget enables efficient querying of genomic reference databases

alphafold alphafold2 archs4 blast databases enrichment-analysis enrichr ensembl gget ncbi reference uniprot

Last synced: 17 Dec 2024

https://github.com/kblin/ncbi-genome-download

Scripts to download genomes from the NCBI FTP servers

bioinformatics biology command-line download-genomes genbank genomics ncbi python

Last synced: 01 Nov 2024

https://github.com/vanheeringen-lab/genomepy

genes and genomes at your fingertips

bioconda ensembl genome ncbi python ucsc

Last synced: 20 Dec 2024

https://github.com/zyxue/ncbitax2lin

🐞 Convert NCBI taxonomy dump into lineages

lineage ncbi ncbi-taxonomy pandas python taxdump taxonomy

Last synced: 17 Dec 2024

https://github.com/pirovc/genome_updater

Bash script to download/update snapshots of files from NCBI genomes repository (refseq/genbank) with track of changes and without redundancy

bash bioinformatics database download genbank genome genomes genomics ncbi refseq sequence

Last synced: 07 Nov 2024

https://github.com/dvklopfenstein/pmidcite

Turbocharge a PubMed literature rather than clicking and clicking and clicking on Google Scholar

citation-analysis citation-counts citation-downloader citedby command-line-tool library literature-review literature-search ncbi nih-citation-data pmid pubmed snowballing

Last synced: 20 Dec 2024

https://github.com/datasnakes/orthoevolution

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

bash bioinformatics biology biosql blast data-science ftp genetics ncbi orthologs orthologues orthology orthology-inference pbs phylogenetics python qsub sequence-alignment sge shell

Last synced: 16 Nov 2024

https://github.com/cdcgov/tostadas

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

azure bioinformatics conda docker genbank genetics liftoff metadata mpox ncbi nextflow nf-tower pipeline python rna-seq scicomp sequencing singularity sra vadr

Last synced: 16 Nov 2024

https://github.com/edinburgh-genome-foundry/genome_collector

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

bioinformatics blast bowtie ncbi python synbio synthetic-biology taxid

Last synced: 23 Nov 2024

https://github.com/dhimmel/pubmedpy

Utilities for interacting with NCBI EUtilities relating to PubMed

bibliometrics eutilities ncbi pubmed python

Last synced: 14 Oct 2024

https://github.com/pwilmart/fasta_utilities

Utilities for downloading and managing protein FASTA files.

ensembl fasta ncbi protein-databases python3 uniprot

Last synced: 11 Oct 2024

https://github.com/j-i-l/genbankparser

Parser (unofficial) for ncbi GenBank data

genbank ncbi parser python2 python3

Last synced: 20 Dec 2024

https://github.com/robaina/genbankpy

Tools to download, parse and filter GenBank files

bioinformatics computational-biology genbank genomics ncbi python sequencing

Last synced: 27 Oct 2024

https://github.com/audy/ncbi-taxonomy-bot

Bot that toots when NCBI updates their taxonomy database

bioinformatics bots ncbi taxonomy

Last synced: 21 Oct 2024

https://github.com/blinard-bioinfo/ncbitaxonomy

Tools to build a copy of the NCBI Taxonomy database in a local SQL schema and query it via a Java package.

blast blast-searches ncbi species-lists taxid taxonomy

Last synced: 02 Dec 2024

https://github.com/widdowquinn/ncfp

Program and package that retrieves nucleotide coding sequences from NCBI that correspond to a set of input protein sequences.

backtranslation bioinformatics ncbi protein-to-nucleotide sequence-to-sequence uniprot

Last synced: 27 Oct 2024

https://github.com/abdelhak-zaaim/bioblastautomation

bioBlastAutomation is a Python-based project designed to automate the process of performing BLAST search .

automation biology biopython blast django ncbi

Last synced: 01 Dec 2024

https://github.com/eggzilla/biobasehttptools

Tools for querying bioinformatics web resources

bioinformatics ensembl ncbi

Last synced: 21 Dec 2024

https://github.com/vaibhavvikas/fasta-sequence-retrieval

Python Project to extract the amino acid sequences using the nucleotides accession numbers retrieved from the NCBI.

fasta ncbi

Last synced: 11 Nov 2024

https://github.com/tracywong117/ncbi-get-all-children-organism-under-ancestor

This Python script retrieve all children organism under an ancestor in NCBI taxonomy.

bio-data bio-dataset dataset ncbi ncbi-database ncbi-sra ncbi-taxonomy taxonomy-database

Last synced: 18 Nov 2024

https://github.com/bcgsc/rsempipeline

A pipeline for running rsem analysis on thousands of samples

geo ncbi python rsem sra transcript-quantification

Last synced: 09 Nov 2024

https://github.com/iamsushantk/ncbi-explorer

A simple Vue based application that presents a simple interface to read Pubmed documents.

cordova ncbi pubmed

Last synced: 06 Dec 2024

https://github.com/tracywong117/autosuggest-words

With Tkinter GUI. Provides autocomplete suggestions for organism names from a SQLite database, using Levenshtein distance for string matching.

autocomplete autocomplete-search ncbi ncbi-taxonomy sqlite3 tkinter-gui

Last synced: 18 Nov 2024

https://github.com/emvivas/sarscov2origin

Analysis of the origin of SARS-COV 2, how could this pandemic have started?

analytics coronavirus covid19 dna genome levenshtein ncbi needleman-wunsch r rna sarscov2 virus

Last synced: 11 Nov 2024

https://github.com/iamsushantk/ncbi-api

A very simple back end service that calls NCBI api to fetch documents from Entrez database (Pubmed)

ncbi pubmed rest-api

Last synced: 01 Dec 2024

https://github.com/sethcg/ncbi-gene-finder

This is a desktop app. It takes protein accession numbers from a spreadsheet and gets the related NCBI gene information.

genes ncbi proteins rust svelte tauri typescript

Last synced: 12 Oct 2024

https://github.com/midnighter/sratools-settings-poc

Proof of concept showing a different way to handle the NCBI settings.

ncbi nextflow nf-core

Last synced: 09 Nov 2024

https://github.com/gabrielramirezv/biopython

Repository for BioPython class, belonging to the Undergraduate Program in Genomic Sciences, UNAM.

biopython entrez ncbi

Last synced: 12 Dec 2024

https://github.com/asbdaryaee/ncbi-blast-assistant

This tiny piece of program helps you transferring NCBI Blast result to spreadsheet. You just need to download the Blast result in a single JSON file.

data-science ncbi ncbi-blast

Last synced: 20 Dec 2024