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Title:
Bioconductor - ppcseq
Description:
Relative transcript abundance has proven to be a valuable tool for understanding the function of genes in biological systems. For the differential analysis of transcript abundance using RNA sequencing data, the negative binomial model is by far the most frequently adopted. However, common methods that are based on a negative binomial model are not robust to extreme outliers, which we found to be abundant in public datasets. So far, no rigorous and probabilistic methods for detection of outliers have been developed for RNA sequencing data, leaving the identification mostly to visual inspection. Recent advances in Bayesian computation allow large-scale comparison of observed data against its theoretical distribution given in a statistical model. Here we propose ppcseq, a key quality-control tool for identifying transcripts that include outlier data points in differential expression analysis, which do not follow a negative binomial distribution. Applying ppcseq to analyse several publicly available datasets using popular tools, we show that from 3 to 10 percent of differentially abundant transcripts across algorithms and datasets had statistics inflated by the presence of outliers.
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Keywords {🔍}

package, bioconductor, ppcseq, version, packages, sequencing, rna, release, data, source, probabilistic, outlier, identification, negative, binomial, model, methods, outliers, datasets, mangiola, enter, install, reports, binary, learn, developers, started, software, generalized, linear, models, transcript, abundance, tool, differential, analysis, abundant, distribution, qualitycontrol, transcripts, follow, stefano, installation, start, documentation, system, details, bioc, stats, url,

Topics {✒️}

org/packages/ppcseq source repository key quality-control tool /stemangiola/ppcseq bug reports joint galaxy/bioconductor conference bioconductor release tgz source repository source package rna sequencing data gnu make url release //code bioconductor support site /stemangiola/ppcseq/issues ppcseq package large-scale comparison script reference manual gz windows binary zip macos binary tgz macos binary negative binomial model negative binomial distribution probabilistic outlier identification stefano mangiola [aut �probabilistic outlier identification package installed git clone https relative transcript abundance differential expression analysis details biocviews utils system requirements package version 1 differentially abundant transcripts packages started install package valuable tool differential analysis transcript abundance observed data propose ppcseq applying ppcseq bioconductor //bioconductor statistical model theoretical distribution identifying transcripts probabilistic methods registration open biological systems frequently adopted

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