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Page 1
SigTools: exploratory visualization for genomic signals.
Masoumi S, Libbrecht MW, Wiese KC. Masoumi S, et al. Bioinformatics. 2022 Jan 27;38(4):1126-1128. doi: 10.1093/bioinformatics/btab742. Bioinformatics. 2022. PMID: 34718413
To understand and evaluate the results of such studies, one needs to understand and analyze the characteristics of the input data. RESULTS: SigTools is an R-based genomic signals visualization package developed with two objectives: (i) to facilitate genomic signals explora …
To understand and evaluate the results of such studies, one needs to understand and analyze the characteristics of the input data. RESULTS: …
SUBSTRA: Supervised Bayesian Patient Stratification.
Khakabimamaghani S, Kelkar YD, Grande BM, Morin RD, Ester M, Ziemek D. Khakabimamaghani S, et al. Bioinformatics. 2019 Sep 15;35(18):3263-3272. doi: 10.1093/bioinformatics/btz112. Bioinformatics. 2019. PMID: 30768166
Moreover, SUBSTRA achieves predictive performance competitive with the supervised benchmark methods and provides interpretable transcriptional features in diverse biological settings, such as drug response prediction, cancer diagnosis, or kidney transplant rejection. AVAILABILITY …
Moreover, SUBSTRA achieves predictive performance competitive with the supervised benchmark methods and provides interpretable transcription …
flowCL: ontology-based cell population labelling in flow cytometry.
Courtot M, Meskas J, Diehl AD, Droumeva R, Gottardo R, Jalali A, Taghiyar MJ, Maecker HT, McCoy JP, Ruttenberg A, Scheuermann RH, Brinkman RR. Courtot M, et al. Bioinformatics. 2015 Apr 15;31(8):1337-9. doi: 10.1093/bioinformatics/btu807. Epub 2014 Dec 6. Bioinformatics. 2015. PMID: 25481008 Free PMC article.
CONCLUSION: By providing automated labelling of cell populations based on their immunophenotype, flowCL allows for unambiguous and reproducible identification of standardized cell types. AVAILABILITY AND IMPLEMENTATION: Code, R script and documentation are available …
CONCLUSION: By providing automated labelling of cell populations based on their immunophenotype, flowCL allows for unambiguous and reproduci …
How do fluctuating ecological dynamics impact the evolution of hosts and parasites?
Best A, Ashby B. Best A, et al. Philos Trans R Soc Lond B Biol Sci. 2023 Mar 27;378(1873):20220006. doi: 10.1098/rstb.2022.0006. Epub 2023 Feb 6. Philos Trans R Soc Lond B Biol Sci. 2023. PMID: 36744565 Free PMC article. Review.
We provide an in-depth guide to one of the methods by applying it to two worked examples of host evolution that have not previously been studied in the literature: when cycles occur owing to seasonal forcing in competition, and when the presence of a free-living parasite causes c …
We provide an in-depth guide to one of the methods by applying it to two worked examples of host evolution that have not previously been stu …
Designing cultural multilevel selection research for sustainability science.
Kline MA, Waring TM, Salerno J. Kline MA, et al. Sustain Sci. 2018;13(1):9-19. doi: 10.1007/s11625-017-0509-2. Epub 2017 Nov 21. Sustain Sci. 2018. PMID: 30147767 Free PMC article.
The electronic supplement provides a tutorial and simple computer code in the R environment to lead users from theory to data to an illustration of an empirical test for group-level adaptations in sustainability research....
The electronic supplement provides a tutorial and simple computer code in the R environment to lead users from theory to data …
Beyond ANOVA and MANOVA for repeated measures: Advantages of generalized estimated equations and generalized linear mixed models and its use in neuroscience research.
de Melo MB, Daldegan-Bueno D, Menezes Oliveira MG, de Souza AL. de Melo MB, et al. Eur J Neurosci. 2022 Dec;56(12):6089-6098. doi: 10.1111/ejn.15858. Epub 2022 Nov 14. Eur J Neurosci. 2022. PMID: 36342498
We illustrate these advantages by showing a comparison between rmANOVA and GEE in a real example and providing the data and a tutorial code to reproduce these analyses in R. We conclude that GEE and GLMM may provide more reliable results when compared to rmANOVA and …
We illustrate these advantages by showing a comparison between rmANOVA and GEE in a real example and providing the data and a tutorial co …
Factors influencing practice choices of early-career family physicians in Canada: a qualitative interview study.
Grudniewicz A, Randall E, Lavergne MR, Marshall EG, Jones L, Rudoler D, Horrey K, Mathews M, McKay M, Mitra G, Scott I, Snadden D, Wong ST, Goldsmith LJ. Grudniewicz A, et al. Hum Resour Health. 2023 Oct 26;21(1):84. doi: 10.1186/s12960-023-00867-9. Hum Resour Health. 2023. PMID: 37884968 Free PMC article.
Interview data were coded inductively and then charted onto a matrix in which each participant's data were summarized by code. RESULTS: Of the 63 participants that were interviewed, 24 worked solely in community-based practice, 7 worked solely in focused practice, and 32 w …
Interview data were coded inductively and then charted onto a matrix in which each participant's data were summarized by code. RESULT …
Simulating pedigrees ascertained for multiple disease-affected relatives.
Nieuwoudt C, Jones SJ, Brooks-Wilson A, Graham J. Nieuwoudt C, et al. Source Code Biol Med. 2018 Oct 15;13:2. doi: 10.1186/s13029-018-0069-6. eCollection 2018. Source Code Biol Med. 2018. PMID: 30356812 Free PMC article.
BACKGROUND: Studies that ascertain families containing multiple relatives affected by disease can be useful for identification of causal, rare variants from next-generation sequencing data. RESULTS: We present the R package SimRVPedigree, which allows researchers to simula …
BACKGROUND: Studies that ascertain families containing multiple relatives affected by disease can be useful for identification of causal, ra …
The Canadian Bikeway Comfort and Safety metrics (Can-BICS): National measures of the bicycling environment for use in research and policy.
Winters M, Beairsto J, Ferster C, Labaree K, Manaugh K, Nelson T. Winters M, et al. Health Rep. 2022 Oct 19;33(10):3-13. doi: 10.25318/82-003-x202201000001-eng. Health Rep. 2022. PMID: 36287574 Free article.
The Can-BICS continuous metric had low correlation with bike-to-work rates (R = 0.29) and was more strongly correlated with sustainable-transportation-to-work rates (R = 0.56) and the Can-ALE metrics (R=0.62). ...The metrics complement existing measures of wa …
The Can-BICS continuous metric had low correlation with bike-to-work rates (R = 0.29) and was more strongly correlated with sustainab …
21 results