GEOfetch: a command-line tool for downloading data and standardized metadata from GEO and SRA
Sign Up to like & getrecommendations! Published in 2023 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btad069
Abstract: Abstract Motivation The Gene Expression Omnibus has become an important source of biological data for secondary analysis. However, there is no simple, programmatic way to download data and metadata from Gene Expression Omnibus (GEO) in… read more here.
Keywords: line tool; command line; geofetch command; geo sra ... See more keywords
Primerdiffer: a python command-line module for large-scale primer design in haplotype genotyping
Sign Up to like & getrecommendations! Published in 2023 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btad188
Abstract: Abstract Motivation Primer design is a routine practice for modern molecular biology labs. Bioinformatics tools like primer3 and primer-blast have standardized the primer design for a specific region. However, large-scale primer design, especially for genome-wide… read more here.
Keywords: primer design; command line; large scale; primer ... See more keywords
Preserving Command Line Workflow for a Package Management System Using ASCII DAG Visualization
Sign Up to like & getrecommendations! Published in 2019 at "IEEE Transactions on Visualization and Computer Graphics"
DOI: 10.1109/tvcg.2018.2859974
Abstract: Package managers provide ease of access to applications by removing the time-consuming and sometimes completely prohibitive barrier of successfully building, installing, and maintaining the software for a system. A package dependency contains dependencies between all… read more here.
Keywords: command line; system; visualization; package ... See more keywords
Waggawagga-CLI: A command-line tool for predicting stable single α-helices (SAH-domains), and the SAH-domain distribution across eukaryotes
Sign Up to like & getrecommendations! Published in 2018 at "PLoS ONE"
DOI: 10.1371/journal.pone.0191924
Abstract: Stable single-alpha helices (SAH-domains) function as rigid connectors and constant force springs between structural domains, and can provide contact surfaces for protein-protein and protein-RNA interactions. SAH-domains mainly consist of charged amino acids and are monomeric… read more here.
Keywords: stable single; cli command; helices sah; sah domains ... See more keywords
Development of a Command Line Interface for the Analysis of Result Sets from Automated Queries to Literature Databases.
Sign Up to like & getrecommendations! Published in 2023 at "Studies in health technology and informatics"
DOI: 10.3233/shti230095
Abstract: The first step of a systematic review is the identification of publications related to a research question in different literature databases. The quality of the final review is mainly influenced by finding the best search… read more here.
Keywords: line interface; result sets; literature databases; command line ... See more keywords
From command-line bioinformatics to bioGUI
Sign Up to like & getrecommendations! Published in 2019 at "PeerJ"
DOI: 10.7717/peerj.8111
Abstract: Bioinformatics is a highly interdisciplinary field providing (bioinformatics) applications for scientists from many disciplines. Installing and starting applications on the command-line (CL) is inconvenient and/or inefficient for many scientists. Nonetheless, most methods are implemented with… read more here.
Keywords: line; line bioinformatics; bioinformatics applications; command line ... See more keywords