Büyükaltay, Kaan
Microbiome studies mainly use two different approaches: metagenomic and amplicon analysis. The metagenomic analysis is based on a whole-genome shotgun approach. It is possible to acquire taxonomic resolution to species and strain level but requires high computational power and is expensive. In the amplicon analysis approach, marker genes like 16S, 18S, and ITS are used to identify the sequences. These genes are highly conserved but contain hypervariable regions, allowing researchers to acquire taxonomic resolution at the genus level. The downside of this approach is due to the biases introduced with PCR and its high error rate. QIIME 2 is a tool consisting of many plugins for amplicon analysis. QIIME 2 team has a decentralized development approach so that third parties can develop new plugins and share them with the community. Although there are different options for visualizations in QIIME 2, there is no tool for visualizing the contents of the features table for a single sample. On the other hand, Krona is a tool that visualizes hierarchical data as multi-layered pie charts. While this visualization is desired, it is not a straightforward task, as the QIIME 2 and Krona do not share the same data formats. This study aims to fill this gap by developing a plugin that will transfer QIIME2 outputs into Krona to ease the visualization of QIIME 2 analysis results with Krona without additional script or manipulation during amplicon analysis.


Performance outcomes of interorganizational trust in buyer-seller relationships: the case of the relationship between a pharmacy and a drug wholesaler
Şengün, Ayşe Elif; Wasti Pamuksuz, Syeda Nazlı; Department of Business Administration (2005)
This study examines the performance outcomes of interorganizational trust using both qualitative and quantitative methods. Using qualitative data from four informants and drawing on the literature on trust, we define interorganizational trust and derive a model of its outcomes. Regression analysis results indicate that trust is negatively related to transaction costs and positively related to cooperation, conflict resolution, satisfaction, and risk taking tendency. Dependence has a moderating effect on trus...
A strategic planning for a gypsum plasterboard producing company
Özaydın, Elif; Çağlar, Güven; Department of Industrial Engineering (2007)
This thesis creates a specific methodology for strategy development while drawing on approaches reported in the literature. The analysis is done at a company that produces gypsum, gypsum board, and related products. A sequential planning method is used where an environmental analysis is conducted in order to define the features of the environment that the company operates in. Then a capability analysis reveals the strengths and weaknesses of the company. For strategy development, this thesis introduces a po...
Shame-proneness vs guilt-proneness and their relationship to attributional styles, coping strategies and depressive symptom levels of university students
İnandılar Topaç, Hicran; Gençöz, Faruk; Department of Psychology (2010)
The purpose of the present study is to investigate the link between shame-proneness, guilt-proneness, attributional styles, and coping strategies, and then to determine which of these variables are significantly related to depressive symptomatology in the sample of Turkish undergraduates. Moreover, the association between shame-proneness, guilt-proneness and depressive symptomatology through attributional styles and coping strategies is examined. Four hundred undergraduates from different universities compl...
Connectivity enforced bayesian superpixels
Eker, Onur; Alatan, A. Aydın.; Department of Electrical and Electronics Engineering (2019)
In this study a general flow for clustering-based superpixel (SP) extraction methods is presented, while each step is analyzed in detail, and improvements are proposed. Considering general SP extraction method steps, initial grid alternatives are examined. The necessity of initial grid refinement is studied and unlike current approaches, a novel Edge Based Refinement step which does not break regular grid structure is proposed. Label update constraints are also analyzed in terms of preserving regular initia...
Development of a dynamic strategy map incorporating scenario analysis and system dynamics: a simulation test on an international construction company
Yıldız, Açelya Ecem; Dikmen Toker, İrem; Department of Civil Engineering (2018)
The balanced scorecard (BSC) and strategy map (SM) methods developed by Kaplan and Norton [1] are widely utilized both in academic studies and in practice to measure organizational performance. On the other hand, these methods are criticized in the literature due to their inability in quantifying bi-directional causalities among strategies, aggregating performance measures, reflecting dynamic nature of real-life behavior, and making simulations to understand implications of future scenarios to support strat...
Citation Formats
K. Büyükaltay, “IMPLEMENTATION OF KRONA INTO QIIME 2,” M.S. - Master of Science, Middle East Technical University, 2022.