Search results for "PACKAGE"
showing 10 items of 116 documents
The MIRS computer package for modeling the rovibrational spectra of polyatomic molecules
2003
International audience; The MIRS spectroscopic software for the modeling of ro-vibrational spectra of polyatomic molecules is presented. It is designed for the global treatment of complex band systems of molecules to take full account of symmetry properties. It includes e cient algorithms based on the irreducible tensor formalism. Predictions and simultaneous data fi tting (positions and intensities) are implemented as well as advanced options related to group theory algebra. Illustrative examples on CH3D, CH4, CH3Cl and PH3 are reported and the present status of data available is given. It is written in C++ for standard PC computer operating under Windows. The full package including on-lin…
Northern European Salmo trutta (L.) populations are genetically divergent across geographical regions and environmental gradients
2020
The salmonid fish Brown trout is iconic as a model for the application of conservation genetics to understand and manage local interspecific variation. However, there is still scant information about relationships between local and large-scale population structure, and to what extent geographical and environmental variables are associated with barriers to gene flow. We used information from 3,782 mapped SNPs developed for the present study and conducted outlier tests and gene–environment association (GEA) analyses in order to examine drivers of population structure. Analyses comprised >2,600 fish from 72 riverine populations spanning a central part of the species' distribution in norther…
paco: implementing Procrustean Approach to Cophylogeny in R
2017
Summary The concordance of evolutionary histories and extant species interactions provides a useful metric for addressing questions of how the structure of ecological communities is influenced by macro-evolutionary processes. We introduce paco (v0.3.1), an R package to perform Procrustean Approach to Cophylogeny. This method assesses the phylogenetic congruence, or evolutionary dependence, of two groups of interacting species using both ecological interaction networks and their phylogenetic history. We demonstrate the functionality of paco through its application to empirical host-parasite and plant-pollinator communities. Although the package is intended to assess the phylogenetic congruen…
iSEE: Interactive SummarizedExperiment Explorer
2018
Data exploration is critical to the comprehension of large biological data sets generated by high-throughput assays such as sequencing. However, most existing tools for interactive visualisation are limited to specific assays or analyses. Here, we present the iSEE (Interactive SummarizedExperiment Explorer) software package, which provides a general visual interface for exploring data in a SummarizedExperiment object. iSEE is directly compatible with many existing R/Bioconductor packages for analysing high-throughput biological data, and provides useful features such as simultaneous examination of (meta)data and analysis results, dynamic linking between plots and code tracking for reproduci…
LipidMS: An R Package for Lipid Annotation in Untargeted Liquid Chromatography-Data Independent Acquisition-Mass Spectrometry Lipidomics.
2018
High resolution LC-MS untargeted lipidomics using data independent acquisition (DIA) has the potential to increase lipidome coverage, as it enables the continuous and unbiased acquisition of all eluting ions. However, the loss of the link between the precursor and the product ions combined with the high dimensionality of DIA data sets hinder accurate feature annotation. Here, we present LipidMS, an R package aimed to confidently identify lipid species in untargeted LC-DIA-MS. To this end, LipidMS combines a coelution score, which links precursor and fragment ions with fragmentation and intensity rules. Depending on the MS evidence reached by the identification function survey, LipidMS provi…
A Two-Cohort RNA-seq Study Reveals Changes in Endometrial and Blood miRNome in Fertile and Infertile Women
2018
The endometrium undergoes extensive changes to prepare for embryo implantation and microRNAs (miRNAs) have been described as playing a significant role in the regulation of endometrial receptivity. However, there is no consensus about the miRNAs involved in mid-secretory endometrial functions. We analysed the complete endometrial miRNome from early secretory (pre-receptive) and mid-secretory (receptive) phases from fertile women and from patients with recurrent implantation failure (RIF) to reveal differentially expressed (DE) miRNAs in the mid-secretory endometrium. Furthermore, we investigated whether the overall changes during early to mid-secretory phase transition and with RIF conditio…
Association between DNA methylation and ADHD symptoms from birth to school age: a prospective meta-analysis
2020
Funder: Gouvernement du Canada | Canadian Institutes of Health Research (Instituts de Recherche en Santé du Canada); doi: https://doi.org/10.13039/501100000024
MetProc: Separating Measurement Artifacts from True Metabolites in an Untargeted Metabolomics Experiment
2019
High-throughput metabolomics using liquid chromatography and mass spectrometry (LC/MS) provides a useful method to identify biomarkers of disease and explore biological systems. However, the majority of metabolic features detected from untargeted metabolomics experiments have unknown ion signatures, making it critical that data should be thoroughly quality controlled to avoid analyzing false signals. Here, we present a postalignment method relying on intermittent pooled study samples to separate genuine metabolic features from potential measurement artifacts. We apply the method to lipid metabolite data from the PREDIMED (PREvención con DIeta MEDi-terránea) study to demonstrate clear remova…
A multilevel statistical toolkit to study animal social networks: Animal Network Toolkit (ANT) R package
2018
AbstractHow animals interact and develop social relationships regarding, individual attributes, sociodemographic and ecological pressures is of great interest. New methodologies, in particular Social Network Analysis, allow us to elucidate these types of questions. However, the different methodologies developed to that end and the speed at which they emerge make their use difficult. Moreover, the lack of communication between the different software developed to provide an answer to the same/different research questions is a source of confusion. The R package Animal Network Toolkit (ANT) was developed with the aim of implementing in one package the many different social network analysis tech…
Validation of ThermoHuman automatic thermographic software for assessing foot temperature before and after running
2020
The aim of the study was to evaluate an automatic thermographic software package (ThermoHuman®) for assessing skin temperature on the soles of the feet before and after running and to compare it with two manual definitions of the regions of interest (ROIs). 120 thermal images of the soles of the feet of 30 participants, at two measurement points (before and after running 30 min) and on two measurement days were analyzed. Three different models of thermographic image analyses were used to obtain the mean temperature of 9 ROIs: A) ThermoHuman (automatic definition of ROIs using ThermoHuman® software), B) Manual (manual delimitation of ROIs by proportion criteria), and C) Manual-TH (manual del…