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Differential expression of annotated genes and novel transcribed units was tested using Cuffdiff, a program part of the Cufflinks package for testing differential gene expression [ 35].
This is an R package for testing whether two tumors from the same patient are clonal (metastasis) or independent (synchronous primaries) based on their genome wide copy number profiles.
Simulation cases are prepared using the ATP-EMTP package for testing purposes.
Successful changes developed in the prototype phase were complied into a "Change Package" for testing and adaption by other facilities as the project spread (Table 1).
All datasets used for these examples are supplied with pepgrep package for testing purposes.
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§ 178.602 Preparation of packagings and packages for testing.
The branch-site model and site-specific model of the likelihood method were performed using the program codeML implemented in PAML 4.2 software package [58] for testing positive selection on individual sites along a specific lineage and at different sites, respectively.
The Fisher's exact test was implemented using the fisher python package v0.14) for testing gene set enrichments.
The ampoules were tested without blinding to product packaging, as information on the packaging is required for testing.
20 Samples could be posted in prepaid secure packaging for testing by means of nucleic acid amplification tests.
The Bioconductor package GOstats shows substantial improvements for testing the association between Gene Ontology (GO) terms and a given gene list [ 23].
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