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In all cases, the output of the script was used for subsequent trajectory planning.
The output of the script for the sentence in Figure 1 is shown in Table 1 (to reduce space requirement, some irrelevant columns are omitted in the table).
Guide currently uses the voom [ 22] function in the limma package for differential expression analysis, and the output of the script is a modified version of the topTable function from limma, which includes logFC and adjusted p-values.
The final output of the script was directed through two routes, a graphical dot-plot style representation of the mate-pair associations using an interface to the GridMap Java applet [ 23] and also a spreadsheet format summary of the details underlying each significant association (clone identifiers, HSP coordinates and gene models, strand dispositions).
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The output of this script is an excel file in which all transposon insertion sites are tabulated by their collective frequency in each annotated gene of the genome.
The output of that script is a panel of graph layouts, with each cluster's most abundant class of element, in addition to the genome percentage and number of paired-end reads belonging to the cluster.
The output of the Perl script is included as a supplemental file [see Additional file 3]. 3. The Perl script getdoub.pl implements algorithm 2 to extract phrases from the text corpora composed of sequences of doublets included in the original nomenclature and exceeding 4 words in length [see Additional file 4].
Because the Perl script used in the simulation experiments produces neither sequences nor trees (i.e., the output of the simulation script is a list with the total number of gene copies of an OG in each species), it was not possible to evaluate the GT-ST reconciliation procedure using those simulations.
The output of the normalization script (Normalized Molecule) is presented to the user, who can accept the changes prior the submission of the molecule.
Detailed evaluation and annotation of the tandem mass spectra, 1H NMR spectra, output of the Python script, and information on the IC50 calculation, are available in the online version of this article.
Fig. 3 displays an example of the output of the graphical script designed for stage III.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com