LAUSR

About LAUSR
Donate
Contact Us

Follow us:

You are not signed in:

Sign Up!


   Articles with "command line" as a keyword



GEOfetch: a command-line tool for downloading data and standardized metadata from GEO and SRA

Sign Up to like & get
recommendations! 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 & get
recommendations! 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

GRIEVOUS: your command-line general for resolving cross-dataset genotype inconsistencies

Sign Up to like & get
recommendations! Published in 2024 at "Bioinformatics"

DOI: 10.1093/bioinformatics/btae489

Abstract: Abstract Summary Harmonizing variant indexing and allele assignments across datasets is crucial for data integrity in cross-dataset studies such as multi-cohort genome-wide association studies, meta-analyses, and the development, validation, and application of polygenic risk scores.… read more here.

Keywords: grievous command; cross; cross dataset; command line ... See more keywords

Bakta Web – rapid and standardized genome annotation on scalable infrastructures

Sign Up to like & get
recommendations! Published in 2025 at "Nucleic Acids Research"

DOI: 10.1093/nar/gkaf335

Abstract: Abstract The Bakta command line application is widely used and one of the most established tools for bacterial genome annotation. It balances comprehensive annotation with computational efficiency via alignment-free sequence identifications. However, the usage of… read more here.

Keywords: command line; genome annotation; bakta web; web rapid ... See more keywords

Preserving Command Line Workflow for a Package Management System Using ASCII DAG Visualization

Sign Up to like & get
recommendations! 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 & get
recommendations! 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 & get
recommendations! 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 & get
recommendations! 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