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Publication for Sphinx
Genetic variation among 82 pharmacogenes: The PGRNseq data from the eMERGE network
[…] nt, thus all further results refer to 82 pharmacogenes. Although both insertion/deletions (INDELs) and SNVs were called, only SNV calls were used for subsequent analyses and are currently provided in SPHINX. Raw variant calls failing any of the following filters were dropped: QUAL <50; ABHet >0.75; QD <5.0. Raw genotype calls failing any of the following filters were also dropped: GQ <50; Heterozy […]
Single cell Transcriptome Study as Big Data
[…] TMM) , remove unwanted variation (RUV) , Poisson beta , and Sphinx utilize statistical modeling to infer normalized read counts. Owing to the distribution assumed, DESeq, TMM, RUV, Poisson beta, and Sphinx allow over-dispersion on read counts. In particular, Poisson beta and Sphinx can identify transcriptional status through bimodality, which characterizes the single-cell RNA-seq signal profiles. […]
Imputation of TPMT defective alleles for the identification of patients with high risk phenotypes
[…] egration of information on actionable pharmacogenetic variants, such as TPMT alleles, into clinical practice using EMR technologies (Gottesman et al., ). One of the goals of eMERGE is the creation of SPHINX (Sequence, Phenotype, and pHarmacogenomics INtegration eXchange http://www.emergesphinx.org/), a web accessible repository of genomic variants derived from a panel of 84 genes involved in the p […]
Best Practices for Scientific Computing
[…] l update the documentation at the same time.Embedded documentation usually takes the form of specially-formatted and placed comments. Typically, a documentation generator such as Javadoc, Doxygen, or Sphinx extracts these comments and generates well-formatted web pages and other human-friendly documents (http://en.wikipedia.org/wiki/Comparison_of_documentation_generators). Alternatively, code can […]
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