psresearch/NER-RE-for-Software-Mentions · Datasets at Hugging Face

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Statistical analyses were performed using STATA version 11 ( StataCorp , College Station , TX ) .
Instead , we applied a custom built MATLAB routine ( using the speech processing toolbox ‘ voicebox ’ in MATLAB v. R 2014a ) to extract acoustic ‘ features ’ ( mel - frequency cepstral coefficients ; MFCCs ) from single screams and chorus excerpts .
We recruited 768 online participants on Amazon ’ s Mechanical Turk and TurkPrime [47] to “ rate 50 very brief audio clips of people laughing ” in exchange for $ 2 ( all participation occurred May 11 - 12 , 2017 ) .
Statistical Analysis
Data were entered into excel ( Microsoft 2010 ) database and analysed using excel functions .
The statistical analysis was done with Stata 14.1 ( Stata Corp LP , College station , Texas ) .
Off - line EEG processing and analyses were performed by adopting custom MATLAB ( MathWorks ) scripts using functions from the EEGLAB environment [38] .
We used ‘ R - bipartite ’ [48] to quantitatively assess interacting and distributional patterns between trophic levels of each sub - network and the set of tree hollows assessed .
The Pearson correlation coefficient between the two analyses was calculated using IBM Statistical Package for Social Sciences software ( SPSS , ver. 21 ; IMB SPSS Inc . , Chicago , IL , USA ) and differences were considered as statistically significant if the p - Value was < 0.05 .
Protein - protein interaction data and functional findings were extracted from QIAGEN ’ s Ingenuity Pathway Analysis ( IPA , QIAGEN Redwood City , www.qiagen.com/ingenuity ) , manually analysed and supplemented by literature curation .
Statistical analyses were performed using SPSS for Windows software version 15.0 ( SPSS Inc . , Chicago , IL ) .
Computation of the Gower index was implemented using the ' Gower ' computer program version 1.1 ( www.pbarrett.net/software.html ) .
Statistical significance was set at p ≤ 0.05 , and analysis was performed using SAS software program ( version 9.1 ; SAS Institute Inc . , Cary , NC ) .
Statistical analyses were conducted using Statistical Package for the Social Sciences Version 20.0 ( SPSS 20.0 ) and Analysis of Moment Structures Version 20.0 ( AMOS 20.0 ) .
The anatomical localization of activated brain regions was assessed both by the SPM anatomy toolbox [34] and the WFU - Pickatlas [35] .
Preprocessing of the fMRI ' s was accomplished using ANFI and FSL tools [18,19] .
Alignments were first conducted using Clustal W [43] integrated into MEGA v. 4.1 [41] while employing default parameters .
The hypergeometric test was implemented in the Database for Annotation , Visualization and Integrated Discovery ( DAVID , http://david.abcc.ncifcrf.gov ) [23,24] .
Households in selected clusters were mapped using Global Positioning System ( GPS ) software ( CDC GPS Sample for Windows Mobile devices https://sites.google.com/a/wolkon.com/gps-sample/ ) .
Such a procedure combines the experimenter ' s prior knowledge ( tGuess = − 1 , tGuessSd = 5.0 , beta = 3.5 , delta = 0.01 , gamma = 0.5 in QUEST software of Psychophysics Toolbox [36] ) and the observer ' s responses ( i.e. , right or left ) in past trials in choosing the signal strength for the next trial , and , in the end , estimating threshold .
Facial stimuli were presented to the subjects in 4 different blocks using MATLAB 7.0 ™ ( Mathworks Inc . , Sherborn , USA ) .
All statistical analyses of this study were performed using SAS version 9.3 and STATA IC / SE 14 .
The DTI images were analysed using DTV.II SR toolbox software ( Image Computing and Analysis Laboratory [ UTRAD / ICAL ] Department of Radiology , The University of Tokyo Hospital , extension of Volume 1 , package [ http://www.volume-one.org/ ] ) with the following parameters to determine the degree of sensitivity for generating DTI tracts : Fractional Anisotropy ( FA ) = 0.05 , steps = 160 ; Apparent Diffusion Coefficient ( ADC ) ( x1K ) : any ; So < 80 ; Angle : any .
More details : Software name : CBFA plugin for Optflux Project home page : http://www.optflux.org/ Methods details and application tutorial : http://www.optflux.org/cbfa Operating system ( s ) : Platform independent Programming languages : Java Other requirements : Java JRE 1.7 .x ( for Mac OS users the installation of JDK 1.7 is recommended ) , GLPK License : GNU - GPL , version 3 "
Statistical analyses were conducted using GraphPad InStat version 3.10 ( GraphPad Software , Inc . , La Jolla , CA , USA ) .
Variants were further evaluated with respect to their functions ( e.g. , missense , coding - synonymous ) , using the in - house Genome Variation Server , and predicted functional effects ( e.g. , benign , possibly damaging ) , using PolyPhen [85] and the Combined Annotation Dependent Depletion ( CADD ) scores [86] .
This classification module was incorporated into our karyotyping software tool , called MetaSel , which was written from scratch using C # on Microsoft Windows 7 operating system .
All statistic analyses were computed using Statistical Package for Social Science ( SPSS , Chicago , Illinois , USA ) software version 19.0 for Windows .
Data were edited , coded and entered using EPI Info version 3.02 and then transferred to Stata version 14.2 for statistical analysis .
R language [30] ( version 3.2.2 ; R Foundation , Vienna , Austria ) was used for statistical analysis and creation of several figures .
The data analysis was done using Stata version 11 ( College Station , TX : StataCorp LP . ) .
In a further regression analysis , we investigated the impact of N on the relationship between SPQ subscales and post - conflict adjustment .
Data were analyzed with the Statistical Package for the Social Sciences ( SPSS ) for Windows ( Version 19.0 ) .
We have developed the HMMER web site ( http://hmmer.janelia.org ) to not only provide downloadable HMMER binaries , documentation and source code as it has done in the past , but now also to provide an interface for performing protein sequence searches with near interactive response times .
The data were analyzed with MIXED procedure in the IBM SPSS Statistics software , version 21 ( IBM Corporation , Armonk , New York , USA ) .
Statistical analyses
Analysis was then done by one researcher ( SS ) using MSOffice ( Word and Excel , Microsoft Corp . ) and NVivo ( QSR International ) software for qualitative data analysis .
We analyzed data using JMP ™ v. 8.0 ( SAS Institute Inc . , Cary , NC ) , comparing males and females for all variables using a t - test and considered results significant if α ≤ 0.05 [47] .
Diatom and pollen assemblages were plotted as stratigraphies using C2 [64] ; C2 was also used to ordinate the samples using Detrended Correspondence Analysis ( DCA ) .
The open reading frames ( ORFs ) were identified and automatically annotated using de Rapid Annotation using Subsystem Technology ( RAST , http://rast.nmpdr.org/ ) .
Given the exploratory nature of these analyses , statistical significance level was set at 0.05 , without corrections for multiple comparisons .
Analyses were performed using Stata , version 13 ( StataCorp LP , TX ) .
Data extracted included study characteristics : study publication year , study period in years , study location , i.e. city , state , and country , study site , e.g. clinic , community - based , school - based , or other , and study type , i.e. cohort , cross - sectional study , etc .
All further preprocessing steps were carried out using Nilearn 0.2.5 [30] in Python 2.7 .
All data were analyzed using Prism 6.0f 2014 , GraphPad Software , Inc . with 95 % confidence limits .
Bioinformatic analyses were performed using R [17] , version 2.15 , and BioConductor [18] , release 2.10 .
Immunoratio [16] , for example , is an open - source software based on ImageJ [17] , another open - source software available as either a stand - alone or Web application .
To investigate the relationship between the physiological correlates ( HRV and IS ) and ER as well as parental psychopathology , partial correlation tests were calculated ( alpha = .05 , two - tailed ) with the SPSS software package ( version 20 , IBM , Chicago , IL , USA ) .
The general techniques used for this part of the analysis are summarised in Section “ Evaluation Methods ” .
Data analyses were conducted , using SAS software ( version 9.2 , SAS Institute , Cary , NC , USA ) by JM ( biostatistician at Radboud University Nijmegen Medical Centre ) .
Ages were re - modelled for the Upper Mallot Lake pollen record using the top of the core ( 1993 AD ) , the three radiocarbon dates included in the database record , and the Ambrosia rise ( 15 cm depth ) with the clam package for R [53] ; pollen assemblages were ordinated using DCA and axis scores were plotted .
Descriptive statistics for all measures for the total sample , and the groups high and low on CU traits , are presented in Table 3 .
The study was undertaken in 2008 in three districts in the Eastern Cape and KwaZulu - Natal provinces of South Africa .
All the statistical analyses were conducted using IBM SPSS Statistics , version 20.0 .
Installation on Linux ( Ubuntu ) is supported via PyPi .
Statistical analyses were performed using Stata 11.0 ( StataCorp , College Station , Texas , USA ) .
Reliability analysis of the data and univariate analyses were performed using SPSS version 16.0 ( SPSS Inc . , Chicago , IL , USA ) for Windows , and the SEM was produced using LISREL 8.5 .
The cellXpress installation packages for 64 - bit Windows and Linux , user manual , installation guide , and datasets used in this analysis can be downloaded freely from http://www.cellXpress.org .
Our pharmacokinetic modeling and simulation were performed by use of ADAPT II program [44] and a MATLAB program developed in our own lab for numerical solution of differential equations defined in Eqs . ( 1 ) and ( 2 ) [45] , [46] , [47] .
However , studies were eligible if these graphs or the separate summary estimates were not available , but the general findings or implications of the cumulative meta - analyses were reported .
To accomplish this , we used the Artifact Rejection Toolbox ( ART ; http://www.nitrc.org/projects/artifact_detect/ ) to create confound regressors for motion parameters ( 3 translation and 3 rotation parameters ) , and additional confound regressors for specific image frames with outliers based on brain activation and head movement .
Data were analysed using SPSS version 22 [48] .
Tests for departures from Hardy - Weinberg equilibrium were performed using the Hardy - Weinberg probability function with default Markov chain parameters in Option One of GENEPOP 3.1 software [12] .
IBD among the four groups of populations and within groups including at least four clusters ( northeast and west ) was tested by comparing pairwise geographic distance ( log transformed ) with pairwise ( FST / [ 1 − FST ] ) and ( RST / [ 1 − RST ] ) using ARLEQUIN and SPAGeDI 1.3 [62] , respectively .
We used the AMOS extension to IBM SPSS ( v. 21.0 ) for structural equation modeling in order to identify associations of AR CAG repeat number , ethnicity and age with the number of children , mediated through BPAQ aggression scores .
All analyses accounted for complex survey design using SUDAAN 11.0 ( RTI , Research Triangle Park , North Carolina ) and were weighted to account for the selection of HCHS / SOL participants with unequal probabilities [24] and were performed using SAS version 9.3 ( SAS Institute , Cary , NC ) and SUDAAN release 11.0.1 ( RTI International , Research Triangle Park , NC ) .
Availability : ProDy is open source and freely available under GNU General Public License from http://www.csb.pitt.edu/ProDy/ .
The analysis was performed using SPSS 17 ( PASW ) for Windows ( SPSS Inc . , Chicago , Illinois , USA ) .
The characteristics collected from each study were : author , year of publication , country , age , AHI , sample size , diagnosis criteria , genotype , allele frequency , and specific technique of analysis .
All HB analyses used WinBugs 1.4 , available from ( http://www.mrc-bsu.cam.ac.uk/bugs/ ) , and the R 2WinBUGS package version 2.1 - 16 .
We classified each sequence at the family level , and used blast [36] to identify those OTUs that had been previously found in bees ( blastn , e - value < 0.0001 ) .
Transcriptional data were evaluated using Ingenuity Pathway Analysis ( IPA , Systems Inc . , USA ) and prediction ( increase of decrease ) of biological activities occurring in the tissue was established .
Random effects meta - regressions were also performed in Stata using the package metareg [44] .
Choroidal segmentation and thickness analyses were performed automatically with custom MATLAB ( MATLAB 2017b , The MathWorks , Inc . , Natick , MA , USA ) software for choroid segmentation [21] .
Online responses were exported from an integrated research platform ( Globalpark ) by Opinion Matters personnel into a survey reporting software program ( SNAP ) , and from thence were converted into an Excel spreadsheet .
For all community multivariate analyses , PCORD ( version 4.25 ) was used [19] .
Availability : FunciSNP is available from Bioconductor ( bioconductor.org ) .
The best - fitting nucleotide substitution model for each gene ( 16S : GTR + I + G , Cytb : GTR + G , D - loop : HKY + I + G ) was selected based on the Akaike Information Criterion as implemented in Modeltest v. 3.7 [50] using default parameters .
Statistical analyses were performed using Stata 13 ( StataCorp , College Station , TX ) .
MIiSR natively supports positions files from Leica GSD - SR Ground - State Depletion microscopes , Zeiss ELYRA PS 1 dSTORM microscopes , and any microscope running QuickPALM software [34] .
We defined the surface searchlights [44] in PyMVPA [45] ( http://www.pymvpa.org ) as cortical disks .
Data were pre - processed and analysed using SPM 8 ( Wellcome Department of Cognitive Neurology , London UK ) ( http://www.fil.ion.ucl.ac.uk/spm ) running on MATLAB 2007b ( Mathworks Inc . , Natick , MA ) .
The anatomical borders for each area of interest were defined by using overlays generated by the Wake Forest University ( WFU ) Pickatlas [31] toolbox for SPM .
Statistical analysis was performed using JMP ( JMP 7.0 , SAS Institute Inc . , NC , USA ) .
This evidence indicated that the present results were statistically stable and reliable .
The data were analyzed using the Statistical Package for the Social Science ( SPSS ) , version 17.0 .
Doppler scans were replayed back on the quantification software ( Q - LAB v 6 , Philips Healthcare , Andover , MA , USA ) and three images per ovary with the greatest area of blood flow were chosen for quantification by two observers blinded to the treatment groups .
Project name : PyMS Project home page : http://code.google.com/p/pyms/ Operating system ( s ) : Platform independent Programming language : Python Other requirements : NumPy , Netcdf , Pycdf , Pycluster , matplotlib , tcl , tk License : GNU GPL 2 Any restrictions to use by non - academics : No "
Statistical analysis was carried out using STATA 11.2 [18] .
All statistical analyses were performed using SAS System for Windows version 9.3 ( SAS Institute , Cary , NC ) .
Generalized Linear Mixed Models ( GLMM ) analyses were conducted , using IBM SPSS Statistics , Version 25 , to examine the effects of tDCS on patients ’ performance on social cognitive , neurocognitive , and EEG measures .
The collected data were analyzed in IBM SPSS for Windows - version 19 .
The scPipe package is written in R and C + + and uses the Rcpp package [ 16 , 17 ] to wrap the C + + code into R functions and the Rhtslib package [18] for BAM input / output .
Primer 3 Input version 0.4 , online software , was used to design forward and reverse primers ( Table 2 ) from DNA sequences obtained from Ensembl Genome Browser , sequences were checked for specificity using Basic Local Alignment Search Tool and validity confirmed as previously described [26] .
Data processing and statistical analyses were conducted using IBM SPSS 22.0 ( IBM Corp . , Armonk , NY ) , MATLAB R 2015a ( The MathWorks , Natick , MA ) , R 3.3.2 ( http://www.R-project.org/ ) , and Python libraries for scientific computation ( NumPy , and SciPy ) [39] .
All the analyses presented here are new .
In detail , cluster analysis was performed with genes belonging to the ERBB 2 amplicon after performing median centering of the amplicon genes using Cluster 3.0 and TreeView softwares .
" Project name : DCE @ urLAB 1.0Project home page : http://www.die.upm.es/im/archives/DCEurLAB/Operating system ( s ) : Microsoft Windows 7 / Vista / XPProgramming language : IDLOther requirements : IDL 6.4 or higher , IDL Virtual Machine 6.4 or higherLicense : BSD license "
Samples were classified according to the six consensus classes of MIBC using the R - based consensus MIBC classification tool ( n = 121 ) [15] .
The Fast Louvain and Spectral algorithms were carried out using the Matlab “ Brain Connectivity Toolbox ” ( http://www.brain-connectivity-toolbox.net/ , accessed 15th June 2013 ) [49] .

Statistical analyses were performed using STATA version 11 ( StataCorp , College Station , TX ) .

Instead , we applied a custom built MATLAB routine ( using the speech processing toolbox ‘ voicebox ’ in MATLAB v. R 2014a ) to extract acoustic ‘ features ’ ( mel - frequency cepstral coefficients ; MFCCs ) from single screams and chorus excerpts .

We recruited 768 online participants on Amazon ’ s Mechanical Turk and TurkPrime [47] to “ rate 50 very brief audio clips of people laughing ” in exchange for $ 2 ( all participation occurred May 11 - 12 , 2017 ) .

Statistical Analysis

Data were entered into excel ( Microsoft 2010 ) database and analysed using excel functions .

The statistical analysis was done with Stata 14.1 ( Stata Corp LP , College station , Texas ) .

Off - line EEG processing and analyses were performed by adopting custom MATLAB ( MathWorks ) scripts using functions from the EEGLAB environment [38] .

We used ‘ R - bipartite ’ [48] to quantitatively assess interacting and distributional patterns between trophic levels of each sub - network and the set of tree hollows assessed .

The Pearson correlation coefficient between the two analyses was calculated using IBM Statistical Package for Social Sciences software ( SPSS , ver. 21 ; IMB SPSS Inc . , Chicago , IL , USA ) and differences were considered as statistically significant if the p - Value was < 0.05 .

Protein - protein interaction data and functional findings were extracted from QIAGEN ’ s Ingenuity Pathway Analysis ( IPA , QIAGEN Redwood City , www.qiagen.com/ingenuity ) , manually analysed and supplemented by literature curation .

Statistical analyses were performed using SPSS for Windows software version 15.0 ( SPSS Inc . , Chicago , IL ) .

Computation of the Gower index was implemented using the ' Gower ' computer program version 1.1 ( www.pbarrett.net/software.html ) .

Statistical significance was set at p ≤ 0.05 , and analysis was performed using SAS software program ( version 9.1 ; SAS Institute Inc . , Cary , NC ) .

Statistical analyses were conducted using Statistical Package for the Social Sciences Version 20.0 ( SPSS 20.0 ) and Analysis of Moment Structures Version 20.0 ( AMOS 20.0 ) .

The anatomical localization of activated brain regions was assessed both by the SPM anatomy toolbox [34] and the WFU - Pickatlas [35] .

Preprocessing of the fMRI ' s was accomplished using ANFI and FSL tools [18,19] .

Alignments were first conducted using Clustal W [43] integrated into MEGA v. 4.1 [41] while employing default parameters .

The hypergeometric test was implemented in the Database for Annotation , Visualization and Integrated Discovery ( DAVID , http://david.abcc.ncifcrf.gov ) [23,24] .

Households in selected clusters were mapped using Global Positioning System ( GPS ) software ( CDC GPS Sample for Windows Mobile devices https://sites.google.com/a/wolkon.com/gps-sample/ ) .

Such a procedure combines the experimenter ' s prior knowledge ( tGuess = − 1 , tGuessSd = 5.0 , beta = 3.5 , delta = 0.01 , gamma = 0.5 in QUEST software of Psychophysics Toolbox [36] ) and the observer ' s responses ( i.e. , right or left ) in past trials in choosing the signal strength for the next trial , and , in the end , estimating threshold .

Facial stimuli were presented to the subjects in 4 different blocks using MATLAB 7.0 ™ ( Mathworks Inc . , Sherborn , USA ) .

All statistical analyses of this study were performed using SAS version 9.3 and STATA IC / SE 14 .

The DTI images were analysed using DTV.II SR toolbox software ( Image Computing and Analysis Laboratory [ UTRAD / ICAL ] Department of Radiology , The University of Tokyo Hospital , extension of Volume 1 , package [ http://www.volume-one.org/ ] ) with the following parameters to determine the degree of sensitivity for generating DTI tracts : Fractional Anisotropy ( FA ) = 0.05 , steps = 160 ; Apparent Diffusion Coefficient ( ADC ) ( x1K ) : any ; So < 80 ; Angle : any .

More details : Software name : CBFA plugin for Optflux Project home page : http://www.optflux.org/ Methods details and application tutorial : http://www.optflux.org/cbfa Operating system ( s ) : Platform independent Programming languages : Java Other requirements : Java JRE 1.7 .x ( for Mac OS users the installation of JDK 1.7 is recommended ) , GLPK License : GNU - GPL , version 3 "

Statistical analyses were conducted using GraphPad InStat version 3.10 ( GraphPad Software , Inc . , La Jolla , CA , USA ) .

Variants were further evaluated with respect to their functions ( e.g. , missense , coding - synonymous ) , using the in - house Genome Variation Server , and predicted functional effects ( e.g. , benign , possibly damaging ) , using PolyPhen [85] and the Combined Annotation Dependent Depletion ( CADD ) scores [86] .

This classification module was incorporated into our karyotyping software tool , called MetaSel , which was written from scratch using C # on Microsoft Windows 7 operating system .

All statistic analyses were computed using Statistical Package for Social Science ( SPSS , Chicago , Illinois , USA ) software version 19.0 for Windows .

Data were edited , coded and entered using EPI Info version 3.02 and then transferred to Stata version 14.2 for statistical analysis .

R language [30] ( version 3.2.2 ; R Foundation , Vienna , Austria ) was used for statistical analysis and creation of several figures .

The data analysis was done using Stata version 11 ( College Station , TX : StataCorp LP . ) .

In a further regression analysis , we investigated the impact of N on the relationship between SPQ subscales and post - conflict adjustment .

Data were analyzed with the Statistical Package for the Social Sciences ( SPSS ) for Windows ( Version 19.0 ) .

We have developed the HMMER web site ( http://hmmer.janelia.org ) to not only provide downloadable HMMER binaries , documentation and source code as it has done in the past , but now also to provide an interface for performing protein sequence searches with near interactive response times .

The data were analyzed with MIXED procedure in the IBM SPSS Statistics software , version 21 ( IBM Corporation , Armonk , New York , USA ) .

Statistical analyses

Analysis was then done by one researcher ( SS ) using MSOffice ( Word and Excel , Microsoft Corp . ) and NVivo ( QSR International ) software for qualitative data analysis .

We analyzed data using JMP ™ v. 8.0 ( SAS Institute Inc . , Cary , NC ) , comparing males and females for all variables using a t - test and considered results significant if α ≤ 0.05 [47] .

Diatom and pollen assemblages were plotted as stratigraphies using C2 [64] ; C2 was also used to ordinate the samples using Detrended Correspondence Analysis ( DCA ) .

The open reading frames ( ORFs ) were identified and automatically annotated using de Rapid Annotation using Subsystem Technology ( RAST , http://rast.nmpdr.org/ ) .

Given the exploratory nature of these analyses , statistical significance level was set at 0.05 , without corrections for multiple comparisons .

Analyses were performed using Stata , version 13 ( StataCorp LP , TX ) .

Data extracted included study characteristics : study publication year , study period in years , study location , i.e. city , state , and country , study site , e.g. clinic , community - based , school - based , or other , and study type , i.e. cohort , cross - sectional study , etc .

All further preprocessing steps were carried out using Nilearn 0.2.5 [30] in Python 2.7 .

All data were analyzed using Prism 6.0f 2014 , GraphPad Software , Inc . with 95 % confidence limits .

Bioinformatic analyses were performed using R [17] , version 2.15 , and BioConductor [18] , release 2.10 .

Immunoratio [16] , for example , is an open - source software based on ImageJ [17] , another open - source software available as either a stand - alone or Web application .

To investigate the relationship between the physiological correlates ( HRV and IS ) and ER as well as parental psychopathology , partial correlation tests were calculated ( alpha = .05 , two - tailed ) with the SPSS software package ( version 20 , IBM , Chicago , IL , USA ) .

The general techniques used for this part of the analysis are summarised in Section “ Evaluation Methods ” .

Data analyses were conducted , using SAS software ( version 9.2 , SAS Institute , Cary , NC , USA ) by JM ( biostatistician at Radboud University Nijmegen Medical Centre ) .

Ages were re - modelled for the Upper Mallot Lake pollen record using the top of the core ( 1993 AD ) , the three radiocarbon dates included in the database record , and the Ambrosia rise ( 15 cm depth ) with the clam package for R [53] ; pollen assemblages were ordinated using DCA and axis scores were plotted .

Descriptive statistics for all measures for the total sample , and the groups high and low on CU traits , are presented in Table 3 .

The study was undertaken in 2008 in three districts in the Eastern Cape and KwaZulu - Natal provinces of South Africa .

All the statistical analyses were conducted using IBM SPSS Statistics , version 20.0 .

Installation on Linux ( Ubuntu ) is supported via PyPi .

Statistical analyses were performed using Stata 11.0 ( StataCorp , College Station , Texas , USA ) .

Reliability analysis of the data and univariate analyses were performed using SPSS version 16.0 ( SPSS Inc . , Chicago , IL , USA ) for Windows , and the SEM was produced using LISREL 8.5 .

The cellXpress installation packages for 64 - bit Windows and Linux , user manual , installation guide , and datasets used in this analysis can be downloaded freely from http://www.cellXpress.org .

Our pharmacokinetic modeling and simulation were performed by use of ADAPT II program [44] and a MATLAB program developed in our own lab for numerical solution of differential equations defined in Eqs . ( 1 ) and ( 2 ) [45] , [46] , [47] .

However , studies were eligible if these graphs or the separate summary estimates were not available , but the general findings or implications of the cumulative meta - analyses were reported .

To accomplish this , we used the Artifact Rejection Toolbox ( ART ; http://www.nitrc.org/projects/artifact_detect/ ) to create confound regressors for motion parameters ( 3 translation and 3 rotation parameters ) , and additional confound regressors for specific image frames with outliers based on brain activation and head movement .

Data were analysed using SPSS version 22 [48] .

Tests for departures from Hardy - Weinberg equilibrium were performed using the Hardy - Weinberg probability function with default Markov chain parameters in Option One of GENEPOP 3.1 software [12] .

IBD among the four groups of populations and within groups including at least four clusters ( northeast and west ) was tested by comparing pairwise geographic distance ( log transformed ) with pairwise ( FST / [ 1 − FST ] ) and ( RST / [ 1 − RST ] ) using ARLEQUIN and SPAGeDI 1.3 [62] , respectively .

We used the AMOS extension to IBM SPSS ( v. 21.0 ) for structural equation modeling in order to identify associations of AR CAG repeat number , ethnicity and age with the number of children , mediated through BPAQ aggression scores .

All analyses accounted for complex survey design using SUDAAN 11.0 ( RTI , Research Triangle Park , North Carolina ) and were weighted to account for the selection of HCHS / SOL participants with unequal probabilities [24] and were performed using SAS version 9.3 ( SAS Institute , Cary , NC ) and SUDAAN release 11.0.1 ( RTI International , Research Triangle Park , NC ) .

Availability : ProDy is open source and freely available under GNU General Public License from http://www.csb.pitt.edu/ProDy/ .

The analysis was performed using SPSS 17 ( PASW ) for Windows ( SPSS Inc . , Chicago , Illinois , USA ) .

The characteristics collected from each study were : author , year of publication , country , age , AHI , sample size , diagnosis criteria , genotype , allele frequency , and specific technique of analysis .

All HB analyses used WinBugs 1.4 , available from ( http://www.mrc-bsu.cam.ac.uk/bugs/ ) , and the R 2WinBUGS package version 2.1 - 16 .

We classified each sequence at the family level , and used blast [36] to identify those OTUs that had been previously found in bees ( blastn , e - value < 0.0001 ) .

Transcriptional data were evaluated using Ingenuity Pathway Analysis ( IPA , Systems Inc . , USA ) and prediction ( increase of decrease ) of biological activities occurring in the tissue was established .

Random effects meta - regressions were also performed in Stata using the package metareg [44] .

Choroidal segmentation and thickness analyses were performed automatically with custom MATLAB ( MATLAB 2017b , The MathWorks , Inc . , Natick , MA , USA ) software for choroid segmentation [21] .

Online responses were exported from an integrated research platform ( Globalpark ) by Opinion Matters personnel into a survey reporting software program ( SNAP ) , and from thence were converted into an Excel spreadsheet .

For all community multivariate analyses , PCORD ( version 4.25 ) was used [19] .

Availability : FunciSNP is available from Bioconductor ( bioconductor.org ) .

The best - fitting nucleotide substitution model for each gene ( 16S : GTR + I + G , Cytb : GTR + G , D - loop : HKY + I + G ) was selected based on the Akaike Information Criterion as implemented in Modeltest v. 3.7 [50] using default parameters .

Statistical analyses were performed using Stata 13 ( StataCorp , College Station , TX ) .

MIiSR natively supports positions files from Leica GSD - SR Ground - State Depletion microscopes , Zeiss ELYRA PS 1 dSTORM microscopes , and any microscope running QuickPALM software [34] .

We defined the surface searchlights [44] in PyMVPA [45] ( http://www.pymvpa.org ) as cortical disks .

Data were pre - processed and analysed using SPM 8 ( Wellcome Department of Cognitive Neurology , London UK ) ( http://www.fil.ion.ucl.ac.uk/spm ) running on MATLAB 2007b ( Mathworks Inc . , Natick , MA ) .

The anatomical borders for each area of interest were defined by using overlays generated by the Wake Forest University ( WFU ) Pickatlas [31] toolbox for SPM .

Statistical analysis was performed using JMP ( JMP 7.0 , SAS Institute Inc . , NC , USA ) .

This evidence indicated that the present results were statistically stable and reliable .

The data were analyzed using the Statistical Package for the Social Science ( SPSS ) , version 17.0 .

Doppler scans were replayed back on the quantification software ( Q - LAB v 6 , Philips Healthcare , Andover , MA , USA ) and three images per ovary with the greatest area of blood flow were chosen for quantification by two observers blinded to the treatment groups .

Project name : PyMS Project home page : http://code.google.com/p/pyms/ Operating system ( s ) : Platform independent Programming language : Python Other requirements : NumPy , Netcdf , Pycdf , Pycluster , matplotlib , tcl , tk License : GNU GPL 2 Any restrictions to use by non - academics : No "

Statistical analysis was carried out using STATA 11.2 [18] .

All statistical analyses were performed using SAS System for Windows version 9.3 ( SAS Institute , Cary , NC ) .

Generalized Linear Mixed Models ( GLMM ) analyses were conducted , using IBM SPSS Statistics , Version 25 , to examine the effects of tDCS on patients ’ performance on social cognitive , neurocognitive , and EEG measures .

The collected data were analyzed in IBM SPSS for Windows - version 19 .

The scPipe package is written in R and C + + and uses the Rcpp package [ 16 , 17 ] to wrap the C + + code into R functions and the Rhtslib package [18] for BAM input / output .

Primer 3 Input version 0.4 , online software , was used to design forward and reverse primers ( Table 2 ) from DNA sequences obtained from Ensembl Genome Browser , sequences were checked for specificity using Basic Local Alignment Search Tool and validity confirmed as previously described [26] .

Data processing and statistical analyses were conducted using IBM SPSS 22.0 ( IBM Corp . , Armonk , NY ) , MATLAB R 2015a ( The MathWorks , Natick , MA ) , R 3.3.2 ( http://www.R-project.org/ ) , and Python libraries for scientific computation ( NumPy , and SciPy ) [39] .

All the analyses presented here are new .

In detail , cluster analysis was performed with genes belonging to the ERBB 2 amplicon after performing median centering of the amplicon genes using Cluster 3.0 and TreeView softwares .

" Project name : DCE @ urLAB 1.0Project home page : http://www.die.upm.es/im/archives/DCEurLAB/Operating system ( s ) : Microsoft Windows 7 / Vista / XPProgramming language : IDLOther requirements : IDL 6.4 or higher , IDL Virtual Machine 6.4 or higherLicense : BSD license "

Samples were classified according to the six consensus classes of MIBC using the R - based consensus MIBC classification tool ( n = 121 ) [15] .

The Fast Louvain and Spectral algorithms were carried out using the Matlab “ Brain Connectivity Toolbox ” ( http://www.brain-connectivity-toolbox.net/ , accessed 15th June 2013 ) [49] .