RNA-Seq Blog Transcriptome Research & Industry News
Researchers from University of Lausanne have developed BgeeDB, a collection of functions to import into R re-annotated, quality-controlled and reprocessed expression data available in the Bgee database. This includes data from thousands of...
Read More »iSEE – an interactive Shiny-based graphical user interface for exploring data stored in SummarizedExperiment objects
Data exploration is critical to the comprehension of large biological datasets obtained by high-throughput assays such as sequencing. Interactive exploration fosters the generation of novel data-driven hypotheses...
Read More »clusterExperiment and RSEC – A Bioconductor package and framework for clustering of single-cell and other large gene expression datasets
Clustering of genes and/or samples is a common task in gene expression analysis. The goals in clustering can vary, but an important scenario is that of...
Read More »CEMiTool – gene co-expression network analysis
The analysis of modular gene co-expression networks is a well-established method commonly used for discovering the systems-level functionality of genes. In addition, these studies provide a basis for the discovery of clinically relevant molecular pathways underlying different diseases and conditions. ...
Read More »EGSEA – easy and efficient ensemble gene set testing
Gene set enrichment analysis is a popular approach for prioritising the biological processes perturbed in genomic datasets. The Bioconductor project hosts over 80 software packages capable of gene set...
Read More »Reproducible Bioconductor workflows using browser-based interactive notebooks and containers
Bioinformatics publications typically include complex software workflows that are difficult to describe in a manuscript. University of Washington, Tacoma researchers describe and demonstrate the use of interactive software notebooks to document and distribute bioinformatics research. They provide a user-friendly tool, ...
Read More »Upcoming workshop – RNA-seq differential expression with Bioconductor
Speaker – Davide Risso Start Date: October 27, 2017 End Date: October 27, 2017 Time: 5:00 pm To 7:00 pm Location: 430 East 67th Street – Room RRL-116 Website: http://bit.ly/2kWIQqF Description: In this hands-on workshop I will show you how ...
Read More »RNA-Seq-Based Comparative Transcriptomics – RNA Preparation and Bioinformatics
Transcriptome analysis is the determination of differentially expressed genes across experimental conditions. For this, the next-generation sequencing of RNA (RNA-seq) is an increasingly cost-effective technology for the analysis of transcriptomes with several advantages over gene expression microarrays, such as its ...
Read More »RNA-Seq with R-Bioconductor
RNA-Seq with R-Bioconductor from bcbbslides Maarten Leerkes PhD Genome Analysis Specialist Bioinformatics and Computational Biosciences Branch Office of Cyber Infrastructure and Computational Biology RNA-seq with R-bioconductor
Read More »RNA-Seq analysis is easy as 1-2-3
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 ...
Read More »