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Pseudotime Estimation – Deconfounding Single Cell Time Series

Pseudotime Estimation – Deconfounding Single Cell Time Series

Repeated cross-sectional time series single cell data confound several sources of variation, with contributions from measurement noise, stochastic cell-to-cell variation and cell progression at different rates. Time series from single cell assays are particularly susceptible to confounding as the measurements ...

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CONDOP – an R package for CONdition-Dependent Operon Predictions

CONDOP – an R package for CONdition-Dependent Operon Predictions

The use of high-throughput RNA sequencing to predict dynamic operon structures in prokaryotic genomes has recently gained popularity in bioinformatics. Researchers from the Finnish Institute of Occupational Health provide the R implementation of a novel method that uses transcriptomic features ...

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TarPmiR – a new approach for microRNA target site prediction

TarPmiR – a new approach for microRNA target site prediction

The identification of microRNA (miRNA) target sites is fundamentally important for studying gene regulation. There are dozens of computational methods available for miRNA target site prediction. Despite their existence, we still cannot reliably identify miRNA target sites, partially due to ...

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Improving microRNA target prediction with gene expression profiles

Improving microRNA target prediction with gene expression profiles

Mammalian genomes encode for thousands of microRNAs, which can potentially regulate the majority of protein-coding genes. They have been implicated in development and disease, leading to great interest in understanding their function, with computational methods being widely used to predict ...

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New to RNA-Seq Bioinformatics? Try GeneGazer

New to RNA-Seq Bioinformatics? Try GeneGazer

Next-generation sequencing provides useful information about gene mutations, gene expression, epigenetic modification, microRNA expression, and copy number variations. More and more computing tools have been developed to analyze this large quantity of information. However, to test and find suitable analytical ...

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You might be ruining your RNA-Seq data

You might be ruining your RNA-Seq data

High-throughput RNA-Sequencing (RNA-Seq) has become the preferred technique for studying gene expression differences between biological samples and for discovering novel isoforms, though the techniques to analyze the resulting data are still immature. One pre-processing step that is widely but heterogeneously ...

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