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F1000Research, Volume 7
Volume 7, 2018
- Jonathan Ronen
, Altuna Akalin
netSmooth: Network-smoothing based imputation for single cell RNA-seq. 8 - Benjamin M. Delory
archiDART v3.0: A new data analysis pipeline allowing the topological analysis of plant root systems. 22 - Inge Alexander Raknes, Lars Ailo Bongo
META-pipe Authorization service. 32 - Agnes Norbury
Response heterogeneity: Challenges for personalised medicine and big data approaches in psychiatry and chronic pain. 55 - Anisa Rowhani-Farid
Badges for sharing data and code at Biostatistics: an observational study. 90 - Anis Fuad
UTAUT for HSS: initial framework to study health IT adoption in the developing countries. 101 - Elizama de Gregorio
Nutritional status, survival and mortality in Alzheimer patients - a cross-sectional study. 137 - Christian Ohmann
Classification of processes involved in sharing individual participant data from clinical trials. 138 - John Q. Wong, Nel Jason Haw
Reflections on the use of the World Health Organization's (WHO) OneHealth Tool: Implications for health planning in low and middle income countries (LMICs). 157 - Ewy A. Mathé, Ben Busby, Helen Piontkivska
Matchmaking in Bioinformatics. 171 - Patrice Godard
BED: a Biological Entity Dictionary based on a graph data model. 195 - Steven A. Frank
A biochemical logarithmic sensor with broad dynamic range. 200 - Richard G. Jackson
Knowledge discovery for Deep Phenotyping serious mental illness from Electronic Mental Health records. 210 - Bhakti Dwivedi
shinySISPA: A web tool for defining sample groups using gene sets from multiple-omics data. 213 - John Ksander
Breathe Easy EDA: A MATLAB toolbox for psychophysiology data management, cleaning, and analysis. 216 - Jonathan Z. L. Zhao, Eliseos J. Mucaki, Peter K. Rogan
Predicting ionizing radiation exposure using biochemically-inspired genomic machine learning. 233 - Kenneth W. Witwer
Alternative miRNAs? Human sequences misidentified as plant miRNAs in plant studies and in human plasma. 244 - Laura Downey
Identification of publicly available data sources to inform the conduct of Health Technology Assessment in India. 245 - Alejandra Duque-Torres
A new environmental monitoring system for silkworm incubators. 248 - Wolfram Höps, Matt Jeffryes
Gene Unprediction with Spurio: A tool to identify spurious protein sequences. 261 - Zachary S. L. Foster, Scott Chamberlain, Niklaus J. Grünwald
Taxa: An R package implementing data standards and methods for taxonomic data. 272 - Bo Gao
segment_liftover : a Python tool to convert segments between genome assemblies. 319 - Ihab B. Abdalrahman, Mohammed Elsanousi Huzaifa Mohammed, Abdelmohaymin A Abdalla, Sulaf Ibrahim Abdelaziz, Aboaagla Abdalbagi Ali, Dina Nader Mutwakel Osman, Ahmed Abdelmoniem Ahmed, Hagir Emad Elwasila, Romaisa Hashim Mokhtar Mohammed, Mohamed Dafaalla
Improving paper-based discharge process; a continuous full-cycle quality improvement project in low resource setting. 324 - Raghvendra Mall
An unsupervised disease module identification technique in biological networks using novel quality metric based on connectivity, conductance and modularity. 378 - Trung Huynh
Gene Annotation Easy Viewer (GAEV): Integrating KEGG's Gene Function Annotations and Associated Molecular Pathways. 416 - Mike L. Smith
Authoring Bioconductor workflows with BiocWorkflowTools. 431 - Tiago Chedraoui Silva, Antonio Colaprico
TCGAbiolinksGUI: A graphical user interface to analyze cancer molecular and clinical data. 439 - Robert R. Butler III
Clinotator: analyzing ClinVar variation reports to prioritize reclassification efforts. 462 - Andy R. Eugene
Predicting lithium treatment response in bipolar patients using gender-specific gene expression biomarkers and machine learning. 474 - Eric T. Leung
ShinyDiversity - Understanding Alpha and Beta Diversity through Interactive Visualizations. 479 - Hiroyuki Akama
Individual typological differences in a neurally distributed semantic processing system: Revisiting the Science article by Mitchell et al. on computational neurolinguistics. 487 - Lenin Javier Ramirez-Cando
Verhulst-Pearl growth model versus Malthusian growth model for in vitro evaluation of lead removal in wastewater by Photobacterium sp. 491 - Philipp Spohr, Kasper Dinkla, Gunnar W. Klau
eXamine: Visualizing annotated networks in Cytoscape. 519 - Fred Loney, Guanming Wu
Automation of ReactomeFIViz via CyREST API. 531 - Ehsan Abdekhodaie
WordCommentsAnalyzer: A windows software tool for qualitative research. 536 - Guillaume Brysbaert
Comparing protein structures with RINspector automation in Cytoscape. 563 - V. P. Nagraj
epicontacts: Handling, visualisation and analysis of epidemiological contacts. 566 - John Muschelli
freesurfer: Connecting the Freesurfer software with R. 599 - Parashkev Nachev
Lost in translation. 620 - Duc-Hau Le
autoHGPEC: Automated prediction of novel disease-gene and disease-disease associations and evidence collection based on a random walk on heterogeneous network. 658 - Zhe Hui Hoo
Using different methods to process forced expiratory volume in one second (FEV1) data can impact on the interpretation of FEV1 as an outcome measure to understand the performance of an adult cystic fibrosis centre: A retrospective chart review. 691 - Pedro Morell Miranda
Investigation of gut microbiome association with inflammatory bowel disease and depression: a machine learning approach. 702 - Nya Mehnwolo Boayue
Head models of healthy and depressed adults for simulating the effects of non-invasive brain stimulation. 704 - Adam Treister
Identifier Mapping in Cytoscape: idmapper. 725 - Li Jun Huang, Jeffrey N. Law
Automating the PathLinker app for Cytoscape. 727 - Kevin C. Rue-Albrecht
iSEE: Interactive SummarizedExperiment Explorer. 741 - Björn A. Grüning, Olivier Sallou, Pablo A. Moreno, Felipe da Veiga Leprevost, Hervé Ménager, Dan Søndergaard, Hannes L. Röst, Timo Sachsenberg, Brian O'Connor, Fábio Madeira, Victoria Dominguez Del Angel, Michael R. Crusoe, Susheel Varma, Daniel J. Blankenberg, Rafael C. Jiménez, Daniel Blankenberg, Yasset Pérez-Riverol:
Recommendations for the packaging and containerizing of bioinformatics software. 742 - Martina Kutmon
CyTargetLinker app update: A flexible solution for network extension in Cytoscape. 743 - Ruby Gupta, Samir Cayenne, Madhu Dyavaiah, Pragnya Srinivas, David Otohinoyi
Oncoyeasti: a web-based application to translate data obtained from Saccharomyces cerevisiae high-throughput drug screens into cancer therapeutics. 757 - Barry Demchak
The Cytoscape Automation app article collection. 800 - Brett Settle
Copycat Layout: Network layout alignment via Cytoscape Automation. 822 - Brett Settle
aMatReader: Importing adjacency matrices via Cytoscape Automation. 823 - Musatafa Khosa, Ahmed Waqas
Bibliometrics of the 100 most-cited articles on refugee populations. 878 - Jamie Kirkham
Who and why do researchers opt to publish in post-publication peer review platforms? - findings from a review and survey of F1000 Research. 920 - Michael I. Love
Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification. 952 - Kidane M. Tekle, Sveinung Gundersen
Norwegian e-Infrastructure for Life Sciences (NeLS). 968 - J. Jesús Naveja
Analysis of a large food chemical database: chemical space, diversity, and complexity. 993 - Gilles Didier
Identifying communities from multiplex biological networks by randomized optimization of modularity. 1042 - Sophie Graham, Laura McDonald, Radek Wasiak, Michael Lees, Sreeram V. Ramagopalan
Time to really share real-world data? 1054 - Sara Rodgers
A nested randomised controlled trial of a newsletter and Post-it® note did not increase postal questionnaire response rates in a falls prevention trial. 1083 - Jayaram Kancherla
Epiviz Web Components: reusable and extensible component library to visualize functional genomic datasets. 1096 - Paul Brennan
drawProteins: a Bioconductor/R package for reproducible and programmatic generation of protein schematics. 1105 - Angelo Duò
A systematic performance evaluation of clustering methods for single-cell RNA-seq data. 1141 - Samir A. Farooq, Samuel J. Weisenthal, Melissa Trayhan, Robert J. White
Revealing HIV viral load patterns using unsupervised machine learning and cluster summarization. 1144 - Pedro L. Varela, Camila V. Ramos, Pedro T. Monteiro
EpiLog: A software for the logical modelling of epithelial dynamics. 1145 - Suyan Tian
To select relevant features for longitudinal gene expression data by extending a pathway analysis method. 1166 - Sunil Munakomi
A pilot study on assessing the role of intra-operative Flow 800 vascular map model in predicting onset of vasospasm following micro vascular clipping of ruptured intracranial aneurysms. 1188 - Mikael Linden
Common ELIXIR Service for Researcher Authentication and Authorisation. 1199 - Juan Rincon-Patino
Exploring machine learning: A bibliometric general approach using SciMAT. 1210 - Kamil Erguler
sPop: Age-structured discrete-time population dynamics model in C, Python, and R. 1220 - Juan Rincon-Patino
Exploring machine learning: A bibliometric general approach using Citespace. 1240 - Gabriele Scheler
Neuromodulation influences synchronization and intrinsic read-out. 1277 - Thomas P. Quinn
Visualizing balances of compositional data: A new alternative to balance dendrograms. 1278 - Dimitri Perrin
Recursive module extraction using Louvain and PageRank. 1286 - Saskia Freytag
Comparison of clustering tools in R for medium-sized 10x Genomics single-cell RNA-sequencing data. 1297 - Clarence K. Mah
An accessible, interactive GenePattern Notebook for analysis and exploration of single-cell transcriptomic data. 1306 - Nomi L. Harris
The 2018 Bioinformatics Open Source Conference (GCCBOSC 2018). 1309 - Stefan Mitrasinovic
Silicon Valley new focus on brain computer interface: hype or hope for new applications? 1327 - Steven W. Wingett
FastQ Screen: A tool for multi-genome mapping and quality control. 1338 - Robert V. Baron, Justin R. Stickel, Daniel E. Weeks
The Mega2R package: R tools for accessing and processing genetic data in common formats. 1352 - Vivek Navale
Long-term preservation of biomedical research data. 1353 - Tyler Weirick
DRETools: A tool-suite for differential RNA editing detection. 1366 - Paula Moraga
epiflows: an R package for risk assessment of travel-related spread of disease. 1374 - Friederike Ehrhart
Providing gene-to-variant and variant-to-gene database identifier mappings to use with BridgeDb mapping services. 1390 - Evan Biederstedt, Jeffrey C. Oliver, Nancy F. Hansen, Aarti Jajoo, Nathan A. Dunn
NovoGraph: Genome graph construction from multiple long-read de novo assemblies. 1391 - Adam R. Rivers
ITSxpress: Software to rapidly trim internally transcribed spacer sequences with quality scores for marker gene analysis. 1418 - Nima S. Hejazi
methyvim: Targeted, robust, and model-free differential methylation analysis in R. 1424 - Erik Fasterius
seqCAT: a Bioconductor R-package for variant analysis of high throughput sequencing data. 1466 - Tyler Weirick
Increasing workflow development speed and reproducibility with Vectools. 1499 - Michail Tsagris
Feature selection with the R package MXM. 1505 - Brendan T. Innes
scClustViz - Single-cell RNAseq cluster assessment and visualization. 1522 - David Crane, Harveen Kaur Ubhi, Jamie Brown, Robert West
Relative effectiveness of a full versus reduced version of the 'Smoke Free' mobile application for smoking cessation: a randomised controlled trial. 1524 - Jesper L. V. Maag
gganatogram: An R package for modular visualisation of anatograms and tissues based on ggplot2. 1576 - Linhua Wang
Large-scale protein function prediction using heterogeneous ensembles. 1577 - Shoaib Sufi, Caroline Jay
Raising the status of software in research: A survey-based evaluation of the Software Sustainability Institute Fellowship Programme. 1599 - Fatemeh Behjati-Ardakani
Predicting transcription factor binding using ensemble random forest models. 1603 - James E. Johnson, Praveen Kumar, Caleb Easterly
Improve your Galaxy text life: The Query Tabular Tool. 1604 - Ajit Singh
KnetMaps: a BioJS component to visualize biological knowledge networks. 1651 - Sean Davis
Orchestrating a community-developed computational workshop and accompanying training materials. 1656 - Matt Buranosky
FDTool: a Python application to mine for functional dependencies and candidate keys in tabular data. 1667 - Eric Feng
DataViz: visualization of high-dimensional data in virtual reality. 1687 - Eugene Tseytlin, Faina Linkov
DomainBuilder: the knowledge authoring system for SlideTutor Intelligent Tutoring system. 1721 - Gaurav S. Kandlikar
ranacapa: An R package and Shiny web app to explore environmental DNA data with exploratory statistics and interactive visualizations. 1734 - Tallulah S. Andrews
False signals induced by single-cell imputation. 1740 - Dominik Sidler
Density artefacts at interfaces caused by multiple time-step effects in molecular dynamics simulations. 1745 - Andrew D. Oxman
Key Concepts for assessing claims about treatment effects and making well-informed treatment choices. 1784 - Daria Komkova
The InterMine Android app: Cross-organism genomic data in your pocket. 1837 - Marlon Burbano-Fernandez, Gustavo Ramírez-González
Wearable technology and health: A bibliometric analysis using SciMAT. 1893 - Fahrul Agus
ESforRPD2: Expert System for Rice Plant Disease Diagnosis. 1902 - Daniel S. Katz
The principles of tomorrow's university. 1926 - Ruipeng Lu, Peter K. Rogan
Transcription factor binding site clusters identify target genes with similar tissue-wide expression and buffer against mutations. 1933 - Yuan Liu
Carrying out streamlined routine data analyses with reports for observational studies: introduction to a series of generic SAS® macros. 1955 - João P. G. L. M. Rodrigues, João M. C. Teixeira
pdb-tools: a swiss army knife for molecular structures. 1961 - Bruno M. Grande
Hackathon-driven tutorial development. 1974 - Pamela H. Russell
Radtools: R utilities for smooth navigation of medical image data. 1976
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