ArticleBioinformatics (Oxford, England)2013
Nestly--a framework for running software with nested parameter choices and aggregating results.
Article in Bioinformatics (Oxford, England), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
4 citing papers in PubMed.
- Article
- Algorithms and design strategies towards automated glycoproteomics analysis.Mass spectrometry reviews · 2017Review
- SUSHI: an exquisite recipe for fully documented, reproducible and reusable NGS data analysis.BMC bioinformatics · 2016Article
- NGSANE: a lightweight production informatics framework for high-throughput data analysis.Bioinformatics (Oxford, England) · 2014Article
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4 authors.
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Abstract
unlabelledThe execution of a software application or pipeline using various combinations of parameters and inputs is a common task in bioinformatics. In the absence of a specialized tool to organize, streamline and formalize this process, scientists must write frequently complex scripts to perform these tasks. We present nestly, a Python package to facilitate running tools with nested combinations of parameters and inputs. nestly provides three components. First, a module to build nested directory structures corresponding to choices of parameters. Second, the nestrun script to run a given command using each set of parameter choices. Third, the nestagg script to aggregate results of the individual runs into a CSV file, as well as support for more complex aggregation. We also include a module for easily specifying nested dependencies for the SCons build tool, enabling incremental builds. AVAILABILITY: Source, documentation and tutorial examples are available at http://github.com/fhcrc/nestly. nestly can be installed from the Python Package Index via pip; it is open source (MIT license).
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.