Analysis Pipelines

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Implementation of an Open Source Software solution for Laboratory Information Management and automated RNA-seq data analysis

Implementation of an Open Source Software solution for Laboratory Information Management and automated RNA-seq data analysis

Large-scale cancer genomics initiatives and next-generation sequencing for transcriptome profiling allow for detailed molecular characterization of tumors, and provide opportunities for clinical tools to improve diagnosis, prognosis, and treatment decisions. Laboratory information, data management, and data sharing in large-scale genomics ...

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RDDpred – a condition-specific RNA-editing prediction model from RNA-seq data

RDDpred – a condition-specific RNA-editing prediction model from RNA-seq data

RNA-editing is an important post-transcriptional RNA sequence modification performed by two catalytic enzymes, “ADAR”(A-to-I) and “APOBEC”(C-to-U). By utilizing high-throughput sequencing technologies, the biological function of RNA-editing has been actively investigated. Currently, RNA-editing is considered to be a key regulator that ...

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A survey of best practices for RNA-seq data analysis

A survey of best practices for RNA-seq data analysis

RNA-sequencing (RNA-seq) has a wide variety of applications, but no single analysis pipeline can be used in all cases. A multi-national team led by researchers from the University of Florida reviews all of the major steps in RNA-seq data analysis, including ...

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SINCERA – A Pipeline for Single-Cell RNA-Seq Profiling Analysis

SINCERA – A Pipeline for Single-Cell RNA-Seq Profiling Analysis

A major challenge in developmental biology is to understand the genetic and cellular processes/programs driving organ formation and differentiation of the diverse cell types that comprise the embryo. While recent studies using single cell transcriptome analysis illustrate the power to ...

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