Tag Archives: 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

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 ...

The position is in the Channing Division of Network Medicine at Brigham and Women’s Hospital and Harvard Medical School, Boston, MA. Brigham and Women’s Hospital is consistently ranked one of the top 10 hospitals in the United States, and the ...

Single-cell RNA sequencing (scRNA-seq) is widely used to profile the transcriptome of individual cells. This provides biological resolution that cannot be matched by bulk RNA sequencing, at the cost of increased technical noise and data complexity. The differences between scRNA-seq ...

Current computational methods for estimating transcript abundance from RNA-seq data can lead to hundreds of false-positive results. Researchers from the Dana-Farber Cancer Institute show that these systematic errors stem largely from a failure to model fragment GC content bias. Sample-specific ...

The ribosome profiling technique (Ribo-seq) allows the selective sequencing of translated RNA regions. Recently, the analysis of genomic sequences associated to Ribo-seq reads has been widely employed to assess their coding potential. These analyses led to the identification of differentially ...

Single-cell RNA sequencing is fast becoming one the standard method for gene expression measurement, providing unique insights into cellular processes. A number of methods, based on general dimensionality reduction techniques, have been suggested to help infer and visualise the underlying ...

PCR clonal artefacts originating from NGS library preparation can affect both genomic as well as RNA-Seq applications when protocols are pushed to their limits. In RNA-Seq however the artifactual reads are not easy to tell apart from normal read duplication ...

Here the authors walk through an end-to-end gene-level RNA-Seq differential expression workflow using Bioconductor packages. They start from the FASTQ files, show how these were aligned to the reference genome, and prepare a count matrix which tallies the number of ...

RNA sequencing (RNA-seq) has revolutionized transcriptome analysis through profiling the expression of thousands of genes at the same time. Systematic analysis of orthologous transcripts across species is critical for understanding the evolution of gene expression and uncovering important information in ...