AuPairWise – a method to estimate RNA-seq replicability through co-expression

March 25, 2016 Leave a comment 2,873 Views

In addition to detecting novel transcripts and higher dynamic range, a principal claim for RNA-sequencing has been greater replicability, typically measured in sample-sample correlations of gene expression levels. Through a re-analysis of ENCODE data, researchers at Cold Spring Harbor Laboratory ...

SPARSE: Quadratic Time Simultaneous Alignment and Folding of RNAs Without Sequence-Based Heuristics

April 8, 2015 Leave a comment 3,411 Views

RNA-Seq experiments have revealed a multitude of novel ncRNAs. The gold standard for their analysis based on simultaneous alignment and folding (Sankoff, 1985) suffers from extreme time complexity of O(n6). Subsequently, numerous faster “Sankoff-style” approaches have been suggested. Commonly, the ...

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Tag Archives: Heuristics

AuPairWise – a method to estimate RNA-seq replicability through co-expression

SPARSE: Quadratic Time Simultaneous Alignment and Folding of RNAs Without Sequence-Based Heuristics

Kassandra – precise reconstruction of the TME using bulk RNA-seq and a machine learning algorithm trained on artificial transcriptomes

RNA Sequencing identifies potential targets for treating a common type of chronic, non-healing wound

Kyoto scientists use mathematics to extract clear signals from single-cell RNA sequencing data

SMaSH – a scalable, general marker gene identification framework for single-cell RNA-sequencing

PlaqView 2.0 – A comprehensive web portal for cardiovascular single-cell genomics

Sample-multiplexing approaches for single-cell sequencing

Researchers use single-cell approaches and deep learning to map all stages of fruit fly embryo development