Data Analysis

PROPER – Comprehensive Power Evaluation for Differential Expression using RNA-seq

rna-seq

RNA-seq has become a routine technique in differential expression (DE) identification. Scientists face a number of experimental design decisions including the sample size. The power for detecting differential expression is affected by several factors including the fraction of DE genes, ...

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RNA-seq Data – Challenges in and Recommendations for Experimental Design and Analysis

rna-seq

RNA-seq is widely used to determine differential expression of genes or transcripts as well as identify novel transcripts, identify allele-specific expression, and precisely measure translation of transcripts. Thoughtful experimental design and choice of analysis tools are critical to ensure high-quality ...

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Open-access synthetic spike-in mRNA-seq data for cancer gene fusions

rna-seq

Oncogenic fusion genes underlie the mechanism of several common cancers. Next-generation sequencing based RNA-seq analyses have revealed an increasing number of recurrent fusions in a variety of cancers. However, absence of a publicly available gene-fusion focused RNA-seq data impedes comparative ...

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BADGE – A novel Bayesian model for accurate abundance quantification and differential analysis of RNA-Seq data

RNA-Seq

Recent advances in RNA sequencing (RNA-Seq) technology have offered unprecedented scope and resolution for transcriptome analysis. However, precise quantification of mRNA abundance and identification of differentially expressed genes are complicated due to biological and technical variations in RNA-Seq data. Researchers ...

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Astroid – transcriptome reconstruction on the basis of a flow network

rna-seq

The advancement of RNA sequencing (RNA-seq) has provided an unprecedented opportunity to assess both the diversity and quantity of transcript isoforms in an mRNA transcriptome. In this paper, researchers from the University of Kentucky revisit the computational problem of transcript ...

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Methods for Joint Imaging and RNA-seq Data Analysis

rna-seq

Emerging integrative analysis of genomic and anatomical imaging data which has not been well developed, provides invaluable information for the holistic discovery of the genomic structure of disease and has the potential to open a new avenue for discovering novel ...

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OrthoClust: an orthology-based network framework for clustering data across multiple species

RNA-Seq

Increasingly, high-dimensional genomics data are becoming available for many organisms. Now, researchers from Yale University have developed OrthoClust for simultaneously clustering data across multiple species. OrthoClust is a computational framework that integrates the co-association networks of individual species by utilizing ...

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Power analysis and sample size estimation for RNA-Seq differential expression

rna-seq

It is crucial for researchers to optimize RNA-seq experimental designs for differential expression detection. Currently, the field lacks general methods to estimate power and sample size for RNA-Seq in complex experimental designs, under the assumption of the negative binomial distribution. ...

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Quality control method for RNA-seq using single nucleotide polymorphism allele frequency

rna-seq

RNA sequencing (RNA-seq) provides information not only about the level of expression of individual genes but also about genomic sequences of host cells. When we use transcriptome data with whole-genome single nucleotide polymorphism (SNP) variant information, the allele frequency can ...

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PLEK: a tool for predicting long non-coding RNAs and messenger RNAs based on an improved k-mer scheme

rna-seq

High-throughput transcriptome sequencing (RNA-seq) technology promises to discover novel protein-coding and non-coding transcripts, particularly the identification of long non-coding RNAs (lncRNAs) from de novo sequencing data. This requires tools that are not restricted by prior gene annotations, genomic sequences and ...

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