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Our procedure is implemented as CotQuest, a suite of scripts designed for use with the statistics package SAS.
There is a suite of scripts, called dax, that allows users to run some common CIAO tasks from within ds9.
To further identify the functional categories that were present within the dataset independent of enrichment, we developed a suite of scripts that are available at https://github.com/saralinker/GONetwork. Briefly, these scripts calculated a distance measurement between each gene in a set based on similarities in GO terms.
We also report the availability of Datgan, the suite of scripts that was developed to construct GDP.
CASAVA1.8 is a suite of scripts including sequence alignment of the complete genome (build37), counting and detection of allelic variants (SNPs and Indels).
We also report the availability of Datgan (Welsh, meaning 'to express'), the suite of scripts that was used to construct both the underlying data tables and the web interface that form GDP. Datgan was written in the python language.
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Briefly, in this suite of script, BLASTN is used to compare a genome against itself for short hits at least 11 bp-long, distant of 750 bp at most, and in inverted orientation (TIRs).
This script to track lava level is one of a suite of Matlab scripts that comprise the thermal camera image acquisition scheme described by Patrick et al. (2014).
The promoter sequences of L1 elements from L1Xplorer or the UCSC genome database were extracted using a suite of Perl scripts that detect and extract the core L1 promoter sequences by performing BLAST searches.
Data were collected using a suite of Perl scripts (available from the authors on request), accessing Ensembl and Vega via the Perl API (Bio::EnsEMBL) and other sources (dbSNP and HapMap) via an automated user script to access each relevant website, to construct a database using MySQL (software version MySQL 5.0.67-0ubuntu6).
All small RNA data were processed by a suite of perl scripts.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com