scholarly journals Easyreporting simplifies the implementation of Reproducible Research layers in R software

PLoS ONE ◽  
2021 ◽  
Vol 16 (5) ◽  
pp. e0244122
Author(s):  
Dario Righelli ◽  
Claudia Angelini
Keyword(s):  
Data Analysis ◽  
Public Access ◽  
Reproducible Research ◽  
Language Documentation ◽  
Rna Seq ◽  
R Software ◽  
R Packages ◽  
Computational Procedures ◽  
R Functions

During last years “irreproducibility” became a general problem in omics data analysis due to the use of sophisticated and poorly described computational procedures. For avoiding misleading results, it is necessary to inspect and reproduce the entire data analysis as a unified product. Reproducible Research (RR) provides general guidelines for public access to the analytic data and related analysis code combined with natural language documentation, allowing third-parties to reproduce the findings. We developed easyreporting, a novel R/Bioconductor package, to facilitate the implementation of an RR layer inside reports/tools. We describe the main functionalities and illustrate the organization of an analysis report using a typical case study concerning the analysis of RNA-seq data. Then, we show how to use easyreporting in other projects to trace R functions automatically. This latter feature helps developers to implement procedures that automatically keep track of the analysis steps. Easyreporting can be useful in supporting the reproducibility of any data analysis project and shows great advantages for the implementation of R packages and GUIs. It turns out to be very helpful in bioinformatics, where the complexity of the analyses makes it extremely difficult to trace all the steps and parameters used in the study.

scholarly journals Easyreporting simplifies the implementation of Reproducible Research Layers in R software

2020 ◽  
Author(s):  
Dario Righelli ◽  
Claudia Angelini
Keyword(s):  
Data Analysis ◽  
User Interfaces ◽  
Public Access ◽  
Reproducible Research ◽  
Language Documentation ◽  
Rna Seq ◽  
R Software ◽  
Computational Procedures ◽  
R Functions

AbstractDuring last years “irreproducibility” became a general problem in omics data analysis due to the use of sophisticated and poorly described computational procedures. For avoiding misleading results, it is necessary to inspect and reproduce the entire data analysis as a unified product. Reproducible Research (RR) provides general guidelines for public access to the analytic data and related analysis code combined with natural language documentation, allowing third-parties to reproduce the findings. We developed easyreporting, a novel R/Bioconductor package, to facilitate the implementation of an RR layer inside reports/tools without requiring any knowledge of the R Markdown language. We describe the main functionalities and illustrate how to create an analysis report using a typical case study concerning the analysis of RNA-seq data. Then, we also show how to trace R functions automatically. Thanks to this latter feature, easyreporting results beneficial for developers to implement procedures that automatically keep track of the analysis steps within Graphical User Interfaces (GUIs). Easyreporting can be useful in supporting the reproducibility of any data analysis project and the implementation of GUIs. It turns out to be very helpful in bioinformatics, where the complexity of the analyses makes it extremely difficult to trace all the steps and parameters used in the study.

scholarly journals Operationalizing the Replication Standard

2018 ◽  
Vol 13 (1) ◽  
pp. 114-124 ◽  
Author(s):  
Thu-Mai Lewis Christian ◽  
Sophia Lafferty-Hess ◽  
William G Jacoby ◽  
Thomas Carsey
Keyword(s):  
Lessons Learned ◽  
Public Access ◽  
Data Curation ◽  
Reproducible Research ◽  
Data Archive ◽  
Data Repositories ◽  
Data Archives ◽  
Research Transparency ◽  
Manuscript Publication

In response to widespread concerns about the integrity of research published in scholarly journals, several initiatives have emerged that are promoting research transparency through access to data underlying published scientific findings. Journal editors, in particular, have made a commitment to research transparency by issuing data policies that require authors to submit their data, code, and documentation to data repositories to allow for public access to the data. In the case of the American Journal of Political Science (AJPS) Data Replication Policy, the data also must undergo an independent verification process in which materials are reviewed for quality as a condition of final manuscript publication and acceptance. Aware of the specialized expertise of the data archives, AJPS called upon the Odum Institute Data Archive to provide a data review service that performs data curation and verification of replication datasets. This article presents a case study of the collaboration between AJPS and the Odum Institute Data Archive to develop a workflow that bridges manuscript publication and data review processes. The case study describes the challenges and the successes of the workflow integration, and offers lessons learned that may be applied by other data archives that are considering expanding their services to include data curation and verification services to support reproducible research.

Development of Applications for Interactive and Reproducible Research: a Case Study

2016 ◽  
Vol 3 (1) ◽  
pp. 39 ◽  
Author(s):  
Federico Marini ◽  
Harald Binder
Keyword(s):  
Computational Analysis ◽  
Regulation Of Gene Expression ◽  
Scientific Workflow ◽  
Reproducible Research ◽  
Rna Seq ◽  
Internal Validation ◽  
Proper Understanding ◽  
Interactive Analysis ◽  
Exploratory Data

For a proper understanding of the organization and regulation of gene expression, the computational analysis is an essential component of the scientific workflow, and this is particularly true in the fields of biostatistics and bioinformatics. Interactivity and reproducibility are two highly relevant features to consider when adopting or designing a tool, and often they can not be provided simultaneously.In this work, we address the issue of developing a framework that can provide interactive analysis, in order to allow experimentalists to fully exploit advanced software tools, as well as reproducibility as an internal validation of the analysis steps, by providing the underlying code and data in such a way that enables the re-creation of the results, and also constitutes a didactic tool for the life scientist.We illustrate this paradigm with the help of the R/Bioconductor package pcaExplorer, designed as a practical companion for interactive and reproducible exploratory data analysis for high dimensional data (e.g. RNA-seq), and highlight some of the features that are provided in the software.

Teaching Computer Based Historical Data Analysis

1994 ◽  
Vol 6 (1) ◽  
pp. 52-58 ◽  
Author(s):  
Charles Anderson ◽  
Robert J. Morris
Keyword(s):  
Data Analysis ◽  
Social History ◽  
Historical Data ◽  
Good Practice ◽  
Computer Assisted ◽  
Historical Data Analysis ◽  
University Of Edinburgh ◽  
Computer Based ◽  
The University

A case study ofa third year course in the Department of Economic and Social History in the University of Edinburgh isusedto considerandhighlightaspects of good practice in the teaching of computer-assisted historical data analysis.

KAJIAN PENYELENGGARAAN PAUD DI KOTA BANJARMASIN DITINJAU DARI ASPEK PERENCANAAN

2018 ◽  
Vol 2 (2) ◽  
pp. 159
Author(s):  
Lisna Sulinar Sari
Keyword(s):  
Early Childhood ◽  
Data Analysis ◽  
Early Childhood Education ◽  
Educational Needs ◽  
Needs Analysis ◽  
Case Study Approach ◽  
Childhood Education ◽  
Study Approach ◽  
Early Childhood Institutions

Abstrak: Permasalahan dalam penelitian ini yaitu dari jumlah lembaga PAUD yang ada diKota Banjarmasin belum semuanya memiliki perencanaan khususnya pada analisispeningkatan legalitas kelembagaan PAUD dan analisis kebutuhan pendidikan untuk anak usiadini (AUD). Penelitian ini menggunakan pendekatan studi kasus dengan analisis data deskrtifkuantitatif dan kualitataif. Hasil studi menunjukkan bahwa: i) Disdik Kota Banjarmasin danLembaga PAUD sampel tidak melakukan perencanaan yang baik untuk pendataan analisiskebutuhan pendidikan AUD; ii) Belum semua lembaga PAUD sampel memiliki izinoperasional dikarenakan adanya persyaratan yang belum dapat dipenuhi karena memerlukanbiaya yang cukup besar seperti, pembuatan akta notaris; iii) Belum semua lembaga PAUDmemiliki sarpras sesuai dengan pedoman sarana dan prasarana dari pusat; iv) untuk membantuketersediaan sarpras, Disdik Kota Banjarmasin sudah mengalokasikan dana APBD II berupabantuan RKB, rehab kelas rusak ringan dan berat, serta bantuan APE Dalam dan Luar berupabarang. Abstract: The problem in this study is from the number of early childhood institutions in thecity of Banjarmasin not all have plans in particular to the analysis of institutional legalityincrease early childhood education and educational needs analysis for early childhood (AUD).This study uses a case study approach to data analysis of quantitative and qualitative deskrtif.The study shows that: i) Disdik Banjarmasin and Institutions ECD sample is not doing betterplanning for data analysis AUD educational needs; ii) Not all the samples of early childhoodinstitutions have an operating permit because of the requirements can not be met because itrequires significant costs such as notary deed; iii) Not all early childhood institutions haveinfrastructure accordance with the guidelines of the central infrastructure; iv) to assist theavailability infrastructure, Disdik Banjarmasin already allocated budget II in the form ofclassroom assistance, rehabilitation of damaged light and heavy classes, as well as the In andOut APE assistance in the form of goods.

scholarly journals Advancing clinical genomics and precision medicine with GVViZ: FAIR bioinformatics platform for variable gene-disease annotation, visualization, and expression analysis

2021 ◽  
Vol 15 (1) ◽  
Author(s):  
Zeeshan Ahmed ◽  
Eduard Gibert Renart ◽  
Saman Zeeshan ◽  
XinQi Dong
Keyword(s):  
Data Analysis ◽  
Patient Care ◽  
Expression Analysis ◽  
High Throughput ◽  
Gene Annotation ◽  
Next Generation Sequencing Data ◽  
Rna Seq ◽  
Sequencing Data ◽  
Complex Disorders ◽  
Transcriptomics Data

Abstract Background Genetic disposition is considered critical for identifying subjects at high risk for disease development. Investigating disease-causing and high and low expressed genes can support finding the root causes of uncertainties in patient care. However, independent and timely high-throughput next-generation sequencing data analysis is still a challenge for non-computational biologists and geneticists. Results In this manuscript, we present a findable, accessible, interactive, and reusable (FAIR) bioinformatics platform, i.e., GVViZ (visualizing genes with disease-causing variants). GVViZ is a user-friendly, cross-platform, and database application for RNA-seq-driven variable and complex gene-disease data annotation and expression analysis with a dynamic heat map visualization. GVViZ has the potential to find patterns across millions of features and extract actionable information, which can support the early detection of complex disorders and the development of new therapies for personalized patient care. The execution of GVViZ is based on a set of simple instructions that users without a computational background can follow to design and perform customized data analysis. It can assimilate patients’ transcriptomics data with the public, proprietary, and our in-house developed gene-disease databases to query, easily explore, and access information on gene annotation and classified disease phenotypes with greater visibility and customization. To test its performance and understand the clinical and scientific impact of GVViZ, we present GVViZ analysis for different chronic diseases and conditions, including Alzheimer’s disease, arthritis, asthma, diabetes mellitus, heart failure, hypertension, obesity, osteoporosis, and multiple cancer disorders. The results are visualized using GVViZ and can be exported as image (PNF/TIFF) and text (CSV) files that include gene names, Ensembl (ENSG) IDs, quantified abundances, expressed transcript lengths, and annotated oncology and non-oncology diseases. Conclusions We emphasize that automated and interactive visualization should be an indispensable component of modern RNA-seq analysis, which is currently not the case. However, experts in clinics and researchers in life sciences can use GVViZ to visualize and interpret the transcriptomics data, making it a powerful tool to study the dynamics of gene expression and regulation. Furthermore, with successful deployment in clinical settings, GVViZ has the potential to enable high-throughput correlations between patient diagnoses based on clinical and transcriptomics data.

scholarly journals An Evaluation of the Formative Experiences of Students Enrolled in Postgraduate Studies in Education: Case Study in Northern Mexico

2021 ◽  
Vol 13 (9) ◽  
pp. 4790
Author(s):  
Brenda Imelda Boroel Cervantes ◽  
José Alfonso Jiménez Moreno ◽  
Salvador Ponce Ceballos ◽  
José Sánchez Santamaría
Keyword(s):  
Data Analysis ◽  
Focus Groups ◽  
Teaching Staff ◽  
Training Context ◽  
Northern Mexico ◽  
Postgraduate Studies ◽  
Successful Design ◽  
Formative Experiences

The educational journey in postgraduate programs is linked to the actors, processes and results, setting the tone for different approaches from the perspective of characterization, development and evaluation. It is summarized in a sequential manner in four stages: entry to the program, progress within the program, and the final educational stretch, where the instructor/tutor plays an important part and obtaining the diploma or degree. The goal of this research was to evaluate, using the students’ perceptions, formative experiences as a result of their academic journey in postgraduate programs within education in Northern Mexico. We have used a case study based on the focus groups technique, applied to a sample of cases comprised of students enrolled in their final educational stage. The information was analyzed using inductive data analysis. The main results were grouped into three meta categories: (1) development of professional skills for the successful design of the intervention proposal, which unfolded into four categories; (2) the role of the tutor during the formative process, consisting of four analysis categories and (3) contributions of the teaching staff in their profession, consisting of two categories. These trends also evidence the formative abundance in the personal, academic and social training context of the students.

scholarly journals Evaluation of Cell Type Annotation R Packages on Single-cell RNA-seq Data

2020 ◽  
Author(s):  
Qianhui Huang ◽  
Yu Liu ◽  
Yuheng Du ◽  
Lana X. Garmire
Keyword(s):  
Single Cell ◽  
Rna Seq ◽  
Cell Type ◽  
R Packages
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