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Articles 1 - 3 of 3
Full-Text Articles in Bioinformatics
Iam Hiq—A Novel Pair Of Accuracy Indices For Imputed Genotypes, Albert Rosenberger, Viola Tozzi, Heike Bickeböller, Susanne M. Arnold, The Integral-Ilcco Consortium
Iam Hiq—A Novel Pair Of Accuracy Indices For Imputed Genotypes, Albert Rosenberger, Viola Tozzi, Heike Bickeböller, Susanne M. Arnold, The Integral-Ilcco Consortium
Markey Cancer Center Faculty Publications
Background: Imputation of untyped markers is a standard tool in genome-wide association studies to close the gap between directly genotyped and other known DNA variants. However, high accuracy with which genotypes are imputed is fundamental. Several accuracy measures have been proposed and some are implemented in imputation software, unfortunately diversely across platforms. In the present paper, we introduce Iam hiQ, an independent pair of accuracy measures that can be applied to dosage files, the output of all imputation software. Iam (imputation accuracy measure) quantifies the average amount of individual-specific versus population-specific genotype information in a linear manner. …
The Mwtab Python Library For Restful Access And Enhanced Quality Control, Deposition, And Curation Of The Metabolomics Workbench Data Repository, Christian D. Powell, Hunter N. B. Moseley
The Mwtab Python Library For Restful Access And Enhanced Quality Control, Deposition, And Curation Of The Metabolomics Workbench Data Repository, Christian D. Powell, Hunter N. B. Moseley
Markey Cancer Center Faculty Publications
The Metabolomics Workbench (MW) is a public scientific data repository consisting of experimental data and metadata from metabolomics studies collected with mass spectroscopy (MS) and nuclear magnetic resonance (NMR) analyses. MW has been constantly evolving; updating its ‘mwTab’ text file format, adding a JavaScript Object Notation (JSON) file format, implementing a REpresentational State Transfer (REST) interface, and nearly quadrupling the number of datasets hosted on the repository within the last three years. In order to keep up with the quickly evolving state of the MW repository, the ‘mwtab’ Python library and package have been continuously updated to mirror the changes …
Genome-Wide Dna Methylation Profiling In Human Breast Tissue By Illumina Truseq Methyl Capture Epic Sequencing And Infinium Methylationepic Beadchip Microarray, Nan Lin, Jinpeng Liu, James Castle, Jun Wan, Aditi Shendre, Yunlong Liu, Chi Wang, Chunyan He
Genome-Wide Dna Methylation Profiling In Human Breast Tissue By Illumina Truseq Methyl Capture Epic Sequencing And Infinium Methylationepic Beadchip Microarray, Nan Lin, Jinpeng Liu, James Castle, Jun Wan, Aditi Shendre, Yunlong Liu, Chi Wang, Chunyan He
Markey Cancer Center Faculty Publications
A newly-developed platform, the Illumina TruSeq Methyl Capture EPIC library prep (TruSeq EPIC), builds on the content of the Infinium MethylationEPIC Beadchip Microarray (EPIC-array) and leverages the power of next-generation sequencing for targeted bisulphite sequencing. We empirically examined the performance of TruSeq EPIC and EPIC-array in assessing genome-wide DNA methylation in breast tissue samples. TruSeq EPIC provided data with a much higher density in the regions when compared to EPIC-array (~2.74 million CpGs with at least 10X coverage vs ~752 K CpGs, respectively). Approximately 398 K CpGs were common and measured across the two platforms in every sample. Overall, there …