scholarly journals HiCEnterprise: Identifying long range chromosomal contacts in HiC data

2019 ◽  
Author(s):  
Hanna Kranas ◽  
Irina Tuszyńska ◽  
Bartek Wilczynski
Keyword(s):  
Statistical Analysis ◽  
Long Range ◽  
Computational Analysis ◽  
Software Tool ◽  
Experimental Techniques ◽  
Input Output ◽  
Accurate Identification ◽  
Rapid Advance ◽  
Chromosome Domains ◽  
Growing Body

Computational analysis of chromosomal capture data is currently gaining popularity with the rapid advance in experimental techniques providing access to growing body of data. An important problem in this area is the identification of long-range contacts be- tween distinct chromatin regions. Such loops were shown to exist at different scales, either mediating interactions between enhancers and promoters or providing much longer interactions between functionally interacting distant chromosome domains. A proper statistical analysis is crucial for accurate identification of such interactions from experi- mental data. We present HiCEnterprise, a software tool for identification of long-range chromatin contacts. It implements three different sta- tistical tests for identification of significant contacts at different scales as well as necessary functions for input, output and visualization of chromosome contact matrices.

scholarly journals HiCEnterprise: Identifying long range chromosomal contacts in HiC data

2019 ◽  
Author(s):  
Hanna Kranas ◽  
Irina Tuszyńska ◽  
Bartek Wilczynski
Keyword(s):  
Statistical Analysis ◽  
Long Range ◽  
Computational Analysis ◽  
Software Tool ◽  
Experimental Techniques ◽  
Input Output ◽  
Accurate Identification ◽  
Rapid Advance ◽  
Chromosome Domains ◽  
Growing Body

Computational analysis of chromosomal capture data is currently gaining popularity with the rapid advance in experimental techniques providing access to growing body of data. An important problem in this area is the identification of long-range contacts be- tween distinct chromatin regions. Such loops were shown to exist at different scales, either mediating interactions between enhancers and promoters or providing much longer interactions between functionally interacting distant chromosome domains. A proper statistical analysis is crucial for accurate identification of such interactions from experi- mental data. We present HiCEnterprise, a software tool for identification of long-range chromatin contacts. It implements three different sta- tistical tests for identification of significant contacts at different scales as well as necessary functions for input, output and visualization of chromosome contact matrices.

scholarly journals HiCEnterprise: identifying long range chromosomal contacts in Hi-C data

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10558
Author(s):  
Hanna Kranas ◽  
Irina Tuszynska ◽  
Bartek Wilczynski
Keyword(s):  
Long Range ◽  
Short Range ◽  
Computational Analysis ◽  
Statistical Tests ◽  
Software Tool ◽  
Research Community ◽  
Supplementary Information ◽  
Chromosome Domains ◽  
Growing Body ◽  
Contact Data

Motivation Computational analysis of chromosomal contact data is currently gaining popularity with the rapid advance in experimental techniques providing access to a growing body of data. An important problem in this area is the identification of long range contacts between distinct chromatin regions. Such loops were shown to exist at different scales, either mediating relatively short range interactions between enhancers and promoters or providing interactions between much larger, distant chromosome domains. A proper statistical analysis as well as availability to a wide research community are crucial in a tool for this task. Results We present HiCEnterprise, a first freely available software tool for identification of long range chromatin contacts not only between small regions, but also between chromosomal domains. It implements four different statistical tests for identification of significant contacts for user defined regions or domains as well as necessary functions for input, output and visualization of chromosome contacts. Availability The software and the corresponding documentation are available at: github.com/regulomics/HiCEnterprise. Supplementary information Supplemental data are available in the online version of the article and at the website regulomics.mimuw.edu.pl/wp/hicenterprise.

Long-Range Vocal Interactions Between Groups of Gibbons (Hylobates Lar)

Behaviour ◽  
1985 ◽  
Vol 95 (1-2) ◽  
pp. 26-44 ◽  
Author(s):  
Jeremy J. Raemaekers ◽  
Patricia M. Raemaekers
Keyword(s):  
Statistical Analysis ◽  
Long Range ◽  
Distinctive Pattern ◽  
Hylobates Lar ◽  
Leaders And Followers ◽  
Vocal Interactions

AbstractWe report on long-range duet interactions among twelve wild groups of lar gibbons (Hylobates lar) in Thailand. Statistical analysis demonstrates that groups were more likely to respond with an answering duet to a duet sung by a neighbouring group than to one sung by a non-neighbouring group in the population. A distinctive pattern of response among neighbours was to wait until a neighbouring group had finished its duet before immediately answering with a duet, resulting in avoidance of overlap between the two duets. Non-neighbours did not exhibit this pattern. The effect is shown to be due solely to neighbour status and not to the degree of mutual audibility of the duets. There was no evidence that, when duets overlapped, the first group to sing modified the length of its duet in response to the second duet, whether given by a neighbour or by a non-neighbour. In general, among those groups which responded to one another's duets, there were no identifiable leaders and followers: the order of duetting groups was random. We discuss why neighbours interact more by duet than do non-neighbours, and consider what may be the functions of avoiding overlap of duets.

scholarly journals CHR: An Integrated Software Tool for chilling requirements

2020 ◽  
Author(s):  
Chen Chen ◽  
Wanyu Xu ◽  
Ningning Gou ◽  
Lasu Bai ◽  
Lin Wang ◽  
...  
Keyword(s):  
Statistical Analysis ◽  
Software Tool ◽  
Fruit Trees ◽  
Cold Weather ◽  
Chilling Requirements ◽  
Deciduous Fruit ◽  
Heat Requirement ◽  
Integrated Software ◽  
User Friendly ◽  
Analyze Data

Abstract Background Bud dormancy in deciduous fruit trees enables plants to survive cold weather. The buds adopt dormant state and resume growth after satisfying the chilling requirements. Chilling requirements play a key role in flowering time. So far, several chilling models, including ≤ 7.2 °C model, the 0–7.2 °C model, Utah model, and Dynamic Model, have been developed; however, it is still time-consuming to determine the chilling requirements employing any model. This calls for efficient tools that can analyze data. Results In this study, we developed novel software Chilling and Heat Requirement (CHR), by flexibly integrating data conversions, model selection, calculations, statistical analysis, and plotting. Conclusion CHR is a tool for chilling requirements estimation, which will be very useful to researchers. It is very simple, easy, and user-friendly.

scholarly journals Computational Analysis of Biophilic Scale Distributions of Façades in Kaunas City Centre

2021 ◽  
Vol 18 ◽  
pp. 16-28
Author(s):  
Marius Ivaskevicius ◽  
Huriye Armagan Dogan
Keyword(s):  
Statistical Analysis ◽  
Linear Regression ◽  
Regression Model ◽  
Linear Regression Model ◽  
Computational Analysis ◽  
Fractal Dimensions ◽  
Health Problems ◽  
Medical Emergency ◽  
City Centre ◽  
Emotional Tension

The results of numerous studies which are performed on the concepts of Biophilic architecture demonstrate that it can influence emotional tension and health of the observers. Moreover Biophilic research exhibits that not only natural plants induce biophilic response, but also artificial, human creations with certain fractal dimensions or distributions of scales can have an impact. In that regard, the aim of this research is to describe the relation between measurable Biophilic properties of façades and the emotional tension inducing health problems measured with the count of medical emergency arrivals in the vicinity of the façades. To achieve the aim several tasks were completed, such as the development of a methodology of façade analysis, and application of it in an experiment to test the validity. The engineered features found by this research are based on statistical analysis of distributions of line lengths and distances between lines in a drawing of a façade. To test the methodology, a linear regression model with six features was trained and it achieved a 37 % confidence, measured with R² adjusted, predicting the number of medical emergency arrivals. Simplicity of the model allowed to make additional insights into the specificity of façade properties, and their importance to Biophilia, which establishes the scientific novelty and the significance of this research.

scholarly journals Disentangling Meritocracy Among the Long-Range Upwardly Mobile: The Chilean Case

2020 ◽  
pp. 136078042096339
Author(s):  
Malik Fercovic
Keyword(s):  
Long Range ◽  
Social Mobility ◽  
Latin American ◽  
Future Study ◽  
External Factors ◽  
Neoliberal Reforms ◽  
The Us ◽  
Growing Body ◽  
Wealth Inequalities ◽  
The Individual

In a world of rising income and wealth inequalities, studying popular concern or consent about inequality, social mobility and meritocracy is increasingly relevant. However, while there is growing body of research on the explanations individuals provide for inequality in the US and Europe, there is a striking absence of studies addressing how people experiencing long-range upward mobility relate to meritocratic values in Latin American societies. In this article I draw upon on 60 life-course interviews to examine how long-range upwardly mobile individuals – those who best embody the meritocratic ideal – explain their success in Chilean society. Internationally well-known for the implementation of radical neoliberal reforms since the mid 1970s, Chile has both elevated levels of inequality and high rates of occupational mobility. Contrary to the individual-centred approach to meritocratic success dominant in the existing literature, my findings reveal a strong collective framing in respondents’ accounts and the acknowledgement of external factors shaping their upward trajectories. These findings bear important conceptual, methodological and geographical implications for the future study of social mobility and meritocratic values.

The OECD software tool for screening chemicals for persistence and long-range transport potential

2009 ◽  
Vol 24 (2) ◽  
pp. 228-237 ◽  
Author(s):  
Fabio Wegmann ◽  
Laurent Cavin ◽  
Matthew MacLeod ◽  
Martin Scheringer ◽  
Konrad Hungerbühler
Keyword(s):  
Long Range ◽  
Software Tool ◽  
Long Range Transport ◽  
Range Transport ◽  
Transport Potential

scholarly journals A Software Tool for Assisting Experimentation in Dynamic Environments

2015 ◽  
Vol 2015 ◽  
pp. 1-12
Author(s):  
Pavel Novoa-Hernández ◽  
Carlos Cruz Corona ◽  
David A. Pelta
Keyword(s):  
Statistical Analysis ◽  
User Interface ◽  
Graphical User Interface ◽  
Optimization Problems ◽  
Software Tool ◽  
Dynamic Environments ◽  
Experiment Management ◽  
And Performance ◽  
Main Components

In real world, many optimization problems are dynamic, which means that their model elements vary with time. These problems have received increasing attention over time, especially from the viewpoint of metaheuristics methods. In this context, experimentation is a crucial task because of the stochastic nature of both algorithms and problems. Currently, there are several technologies whose methods, problems, and performance measures can be implemented. However, in most of them, certain features that make the experimentation process easy are not present. Examples of such features are the statistical analysis of the results and a graphical user interface (GUI) that allows an easy management of the experimentation process. Bearing in mind these limitations, in the present work, we present DynOptLab, a software tool for experimental analysis in dynamic environments. DynOptLab has two main components: (1) an object-oriented framework to facilitate the implementation of new proposals and (2) a graphical user interface for the experiment management and the statistical analysis of the results. With the aim of verifying the benefits of DynOptLab’s main features, a typical case study on experimentation in dynamic environments was carried out.

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