Biology subjects

Dalton, J. E.

Publications and source records attributed to Dalton, J. E..

2 recordsLinked to original sources

bioRxiv2020

SimText: A text mining framework for interactive analysis and visualization of similarities among biomedical entities

Literature exploration in PubMed on a large number of biomedical entities (e.g., genes, diseases, experiments) can be time consuming and challenging comparing many entities to one other. Here, we describe SimText, a user-friendly toolset that provides customizable and systematic workflows for the analysis of similarities among a set of entities based on words from abstracts and/or other text. SimText can be used for (i) data generation: text collection from PubMed and extraction of words with different text mining approaches, and (ii) interactive analysis of data using unsupervised learning techniques and visualization in a Shiny web application.Availability and Implementation We developed SimText as an open-source R software and integrated it into Galaxy, an online data analysis platform. A command line version of the toolset is available for download from GitHub at https://github.com/mgramm1/simtext.Competing Interest StatementThe authors have declared no competing interest.View Full Text

bioinformatics↗

bioRxiv2019

Facilitating Replication and Reproducibility in Team Science: the 'projects' R Package

The contemporary scientific community places a growing emphasis on the reproducibility of research. The projects R package is a free, open-source endeavor created in the interest of facilitating reproducible research workflows. It adds to existing software tools for reproducible research and introduces several practical features that are helpful for scientists and their collaborative research teams. For each individual project, it supplies an intuitive framework for storing raw and cleaned study data sets, and provides script templates for protocol creation, data cleaning, data analysis and manuscript development. Internal databases of project and author information are generated and displayed, and manuscript title pages containing author lists and their affiliations are automatically generated from the internal database. File management tools allow teams to organize multiple projects. When used on a shared file system, multiple researchers can harmoniously contribute to the same project in a less punctuated manner, reducing the frequency of misunderstandings and the need for status updates.

scientific communication and education↗