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RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR

RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR

The ability to easily and efficiently analyse RNA-sequencing data is a key strength of the Bioconductor project. Starting with counts summarised at the gene-level, a typical analysis involves pre-processing, exploratory data analysis, differential expression testing and pathway analysis with the ...

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Assessment of single cell RNA-seq normalization methods

Assessment of single cell RNA-seq normalization methods

UCSD researchers have assessed the performance of seven normalization methods for single cell RNA-seq using data generated from dilution of RNA samples. Their analyses showed that methods considering spike-in ERCC RNA molecules significantly outperformed those not considering ERCCs. This work ...

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Combinatorial Analysis Performed Using gSELEX-Seq and RNA-Seq

Combinatorial Analysis Performed Using gSELEX-Seq and RNA-Seq

For identifying the genes that are regulated by a transcription factor (TF), Nagoya University researchers have established an analytical pipeline that combines genomic systematic evolution of ligands by exponential enrichment (gSELEX)-Seq and RNA-Seq. Here, SELEX was used to select DNA ...

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gsa4mirna – Integrated gene set analysis for microRNA studies

gsa4mirna – Integrated gene set analysis for microRNA studies

Functional interpretation of miRNA expression data is currently done in a three step procedure: select differentially expressed miRNAs, find their target genes, and carry out gene set overrepresentation analysis Nevertheless, major limitations of this approach have already been described at ...

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Rapid and efficient analysis of 20,000 RNA-seq samples with Toil

Rapid and efficient analysis of 20,000 RNA-seq samples with Toil

Toil is portable, open-source workflow software that supports contemporary workflow definition languages and can be used to securely and reproducibly run scientific workflows efficiently at large-scale. To demonstrate Toil, University of California Santa Cruz researchers processed over 20,000 RNA-seq samples ...

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