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ROTS – reproducible RNA-Seq biomarker detector

ROTS – reproducible RNA-Seq biomarker detector

Recent comprehensive assessments of RNA-seq technology support its utility in quantifying gene expression in various samples. The next step of rigorously quantifying differences between sample groups, however, still lacks well-defined best practices. Although a number of advanced statistical methods have ...

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A sleuth for RNA-Seq

A sleuth for RNA-Seq

from Bits of DNA by Lior Pachter Today my student Harold Pimentel released the beta version of his new RNA-Seq analysis method and software program called sleuth. A sleuth for RNA-Seq begins with the quantification of samples with kallisto, and together a sleuth ...

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PathwaySeq – Pathway analysis for RNA-Seq data

PathwaySeq – Pathway analysis for RNA-Seq data

A variety of pathway/gene-set approaches have been proposed to provide evidence of higher-level biological phenomena in the association of expression with experimental condition or clinical outcome. Among these approaches, it has been repeatedly shown that resampling methods are far preferable ...

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Predicting Protein Functions at the Isoform Level

Predicting Protein Functions at the Isoform Level

Integrate isoform co-expression networks for protein isoform function prediction. Propose a novel hybrid method of multiple-instance and semi-supervised graph learning. Predict isoform-isoform interactions and discover isoform functional modules. Over the past few decades, many computational methods have been developed to ...

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