Sentence examples for using the following software from inspiring English sources

Data analysis for this study was performed using the following software: R (R Core Team 2016) with the geoR package (Ribeiro Júnior and Diggle 2001), WEKA 3.8 (Frank et al. 2016), and ArcGis version 10.1 (Esri 2010) with Geostatistical Analyst extension (Esri 2010).

Bioinformatic analysis included de novo assembly, assembly overlap and validation using the following software: VELVET, version 0.7.54, SeqMan, version 8 and MAQ, version 0.7.1.

Structural annotation was performed using the following software: FgenesB: gene predictor (www.softberry.com); RNAmmer: rRNA predictor [79]; tRNA-scan-SE: tRNA predictor [80]; and Tandem Repeat Finder: repetitive DNA predictor (tandem.bu.edu/trf/trf.html).html

Structure analysis was carried using the following software (referenced in [24]) SwissPBD Viewer and PyMol (www.pymol.org) for visualization; HotPatch [48] for hydrophobicity and PDB2PQR [49], PropKa [50] and APBS [51] for charged surface calculation.

The following dynamic exclusion parameters were used: repeat count -1, repeat duration – 30, list size – 100, exclusion duration – 80. MS2 and MS3 spectra were analyzed using the following software analysis protocol.

Statistical analysis was performed using the following software: SPSS IBMM, Armonk, NY, USA), Stata (StataCorp, College Station, TX, USA; command ci) and Excel (Microsoft, Redmond, WA, USA).

Software: We will use the following software.

We used the following software to run these methods: R packages fabia [ 68] and biclust [ 69], BicAT [ 70], (Evo- Bexpa [ 66] and Evo- Bexpa 71].

We used the following software: for (1)–(3) our R package 'fabia', for (4) the software http://www-stat.stanford.edu/∼owen/plaid/, for (5) the R package 'isa2', for (6) the software BicAT (Barkow et al., 2006), for (7) the software EXPANDER (Shamir et al., 2005), for (8)–(13) the R package 'biclust' (Kaiser and Leisch, 2008).

Phase analysis of gated myocardial perfusion single-photon emission computed tomography (SPECT) for assessment of left ventricular (LV) dyssynchrony was investigated using the following dedicated software packages: Corridor4DM (4DM), cardioREPO (cREPO), Emory Cardiac Toolbox (ECTb), and quantitative gated SPECT (QGS).

The statistical analysis was conducted using the following statistical software: SPSS for Windows (version 15.0, IBM Corporation, NY and SASS (version 9.3, SAS Institute Inc., Cary, NC).