scholarly journals MultiDataSet: an R package for encapsulating multiple data sets with application to omic data integration

2017 ◽  
Vol 18 (1) ◽  
Author(s):  
Carles Hernandez-Ferrer ◽  
Carlos Ruiz-Arenas ◽  
Alba Beltran-Gomila ◽  
Juan R. González
Keyword(s):  
Data Integration ◽  
R Package ◽  
Data Sets ◽  
Multiple Data ◽  
Multiple Data Sets ◽  
Omic Data Integration ◽  
Omic Data

scholarly journals Two-stage Linked Component Analysis for Joint Decomposition of Multiple Biologically Related Data Sets

2021 ◽  
Author(s):  
By Huan Chen ◽  
Brian Caffo ◽  
Genevieve Stein-O’Brien ◽  
Jinrui Liu ◽  
Ben Langmead ◽  
...  
Keyword(s):  
R Package ◽  
Component Analysis ◽  
Biological Data ◽  
Joint Analysis ◽  
Data Sets ◽  
Biological Processes ◽  
Two Stage ◽  
Data Set ◽  
Multiple Data ◽  
Multiple Data Sets

SummaryIntegrative analysis of multiple data sets has the potential of fully leveraging the vast amount of high throughput biological data being generated. In particular such analysis will be powerful in making inference from publicly available collections of genetic, transcriptomic and epigenetic data sets which are designed to study shared biological processes, but which vary in their target measurements, biological variation, unwanted noise, and batch variation. Thus, methods that enable the joint analysis of multiple data sets are needed to gain insights into shared biological processes that would otherwise be hidden by unwanted intra-data set variation. Here, we propose a method called two-stage linked component analysis (2s-LCA) to jointly decompose multiple biologically related experimental data sets with biological and technological relationships that can be structured into the decomposition. The consistency of the proposed method is established and its empirical performance is evaluated via simulation studies. We apply 2s-LCA to jointly analyze four data sets focused on human brain development and identify meaningful patterns of gene expression in human neurogenesis that have shared structure across these data sets. The code to conduct 2s-LCA has been complied into an R package “PJD”, which is available at https://github.com/CHuanSite/PJD.

scholarly journals PyLiger: Scalable single-cell multi-omic data integration in Python

2021 ◽  
Author(s):  
Lu Lu ◽  
Joshua D Welch
Keyword(s):  
Gene Ontology ◽  
Data Integration ◽  
Single Cell ◽  
Scientific Computing ◽  
Enrichment Analysis ◽  
R Package ◽  
Gene Ontology Enrichment Analysis ◽  
Omic Data Integration ◽  
Omic Data ◽  
Python Package

Motivation: LIGER is a widely-used R package for single-cell multi-omic data integration. However, many users prefer to analyze their single-cell datasets in Python, which offers an attractive syntax and highly-optimized scientific computing libraries for increased efficiency. Results: We developed PyLiger, a Python package for integrating single-cell multi-omic datasets. PyLiger offers faster performance than the previous R implementation (2-5× speedup), interoperability with AnnData format, flexible on-disk or in-memory analysis capability, and new functionality for gene ontology enrichment analysis. The on-disk capability enables analysis of arbitrarily large single-cell datasets using fixed memory.

scholarly journals Assessment of batch-correction methods for scRNA-seq data with a new test metric

2017 ◽  
Author(s):  
Maren Büttner ◽  
Zhichao Miao ◽  
F Alexander Wolf ◽  
Sarah A Teichmann ◽  
Fabian J Theis
Keyword(s):  
Data Integration ◽  
Principal Component ◽  
R Package ◽  
Batch Effect ◽  
Data Sets ◽  
Batch Effects ◽  
Visual Evaluation ◽  
Batch Correction ◽  
Multiple Data Sets ◽  
Reduced Representations

AbstractSingle-cell transcriptomics is a versatile tool for exploring heterogeneous cell populations. As with all genomics experiments, batch effects can hamper data integration and interpretation. The success of batch effect correction is often evaluated by visual inspection of dimension-reduced representations such as principal component analysis. This is inherently imprecise due to the high number of genes and non-normal distribution of gene expression. Here, we present a k-nearest neighbour batch effect test (kBET, https://github.com/theislab/kBET) to quantitatively measure batch effects. kBET is easier to interpret, more sensitive and more robust than visual evaluation and other measures of batch effects. We use kBET to assess commonly used batch regression and normalisation approaches, and quantify the extent to which they remove batch effects while preserving biological variability. Our results illustrate that batch correction based on log-transformation or scran pooling followed by ComBat reduced the batch effect while preserving structure across data sets. Finally we show that kBET can pinpoint successful data integration methods across multiple data sets, in this case from different publications all charting mouse embryonic development. This has important implications for future data integration efforts, which will be central to projects such as the Human Cell Atlas where data for the same tissue may be generated in multiple locations around the world.[Before final publication, we will upload the R package to Bioconductor]

The development of nurses’ foundational values

2021 ◽  
pp. 096973302110032
Author(s):  
Sastrawan Sastrawan ◽  
Jennifer Weller-Newton ◽  
Gabrielle Brand ◽  
Gulzar Malik
Keyword(s):  
Professional Training ◽  
Reference Points ◽  
Constructivist Grounded Theory ◽  
Professional Values ◽  
Data Sets ◽  
Value System ◽  
Institutional Values ◽  
Multiple Data ◽  
Human Ethics ◽  
Multiple Data Sets

Background: In the ever-changing and complex healthcare environment, nurses encounter challenging situations that may involve a clash between their personal and professional values resulting in a profound impact on their practice. Nevertheless, there is a dearth of literature on how nurses develop their personal–professional values. Aim: The aim of this study was to understand how nurses develop their foundational values as the base for their value system. Research design: A constructivist grounded theory methodology was employed to collect multiple data sets, including face-to-face focus group and individual interviews, along with anecdote and reflective stories. Participants and research context: Fifty-four nurses working across various nursing settings in Indonesia were recruited to participate. Ethical considerations: Ethics approval was obtained from the Monash University Human Ethics Committee, project approval number 1553. Findings: Foundational values acquisition was achieved through family upbringing, professional nurse education and organisational/institutional values reinforcement. These values are framed through three reference points: religious lens, humanity perspective and professionalism. This framing results in a unique combination of personal–professional values that comprise nurses’ values system. Values are transferred to other nurses either in a formal or informal way as part of one’s professional responsibility and customary social interaction via telling and sharing in person or through social media. Discussion: Values and ethics are inherently interweaved during nursing practice. Ethical and moral values are part of professional training, but other values are often buried in a hidden curriculum, and attained and activated through interactions during nurses’ training. Conclusion: Developing a value system is a complex undertaking that involves basic social processes of attaining, enacting and socialising values. These processes encompass several intertwined entities such as the sources of values, the pool of foundational values, value perspectives and framings, initial value structures, and methods of value transference.

scholarly journals Evaluation of daily precipitation statistics and monsoon onset/retreat over western Sahel in multiple data sets

2014 ◽  
Vol 45 (5-6) ◽  
pp. 1325-1354 ◽  
Author(s):  
Emilia Paula Diaconescu ◽  
Philippe Gachon ◽  
John Scinocca ◽  
René Laprise
Keyword(s):  
Daily Precipitation ◽  
Monsoon Onset ◽  
Data Sets ◽  
Multiple Data ◽  
Western Sahel ◽  
Multiple Data Sets

Can earning much lead to doing good? Firm performance implications for corporate social responsibility

2021 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Siyu Hou ◽  
Zhaoyang Guo ◽  
Chuangneng Cai ◽  
Xiaobo Jiao
Keyword(s):  
Corporate Social Responsibility ◽  
Firm Performance ◽  
Social Responsibility ◽  
State Ownership ◽  
Data Sets ◽  
Content Type ◽  
Multiple Data ◽  
Instrumental Variable Regression ◽  
Multiple Data Sets ◽  
Corporate Social

Purpose The purpose of this study is to examine the influence of firm performance on corporate social responsibility (CSR) and its possible moderating effect. Despite the significance of CSR, there remains an extensive debate about how it is affected by firm performance. Design/methodology/approach The conceptual model is mainly built on goal-setting theory. Based on archival data from multiple data sets on 1,650 companies, collected from 2010 to 2017, the hypotheses are tested using the two-stage instrumental variable regression method. Findings There is an inverted U-shaped relationship between firm performance and CSR that first increases and then decreases. In addition, considering the boundary conditions, state ownership makes the inverted U-shaped curve steeper, while high executive wage concentration makes the inverted U-shaped curve flatter. Research limitations/implications This study harmonizes the traditional contradictory findings of the influence of firm performance on CSR, that is, it supports a positive, negative or neutral relationship between the two. Originality/value This research provides a necessary structure for the CSR literature. By delving deeply into the relationship between firm performance and CSR, it enables scholars to better address the critical management question of whether earning more will lead to doing good.

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