Experiments involving high-throughput sequencing are widely used for analyses of chromatin function and gene expression. Common examples are the use of chromatin immunoprecipitation for the analysis of chromatin modifications or factor binding, enzymatic digestions for chromatin structure assays, and RNA ...
Read More »How well do RNA-Seq differential gene expression tools perform in higher eukaryotes?
RNA-seq experiments are usually carried out in three or fewer replicates. In order to work well with so few samples, Differential Gene Expression (DGE) tools typically assume the form of the underlying distribution of gene expression. A recent highly replicated ...
Read More »A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor
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 ...
Read More »Rascaf – Improving Genome Assembly with RNA Sequencing Data
Abundant but short second-generation sequencing reads make assembly difficult, leading to fragmented genomes and gene annotations. Gene structure information from RNA sequences can be used to improve the completeness and contiguity of an assembly, but bioinformatics methods have been lacking. ...
Read More »InFusion – Discovery of Fusion Genes and Chimeric Transcripts from Deep RNA-Sequencing Data
Analysis of fusion transcripts has become increasingly important due to their link with cancer development. Since high-throughput sequencing approaches survey fusion events exhaustively, several computational methods for the detection of gene fusions from RNA-seq data have been developed. This kind ...
Read More »Docker Pipelines for RNA-Seq Alignment and Analyses
Background: Docker (https://www.docker.com) is an application that packages binary executables and scripts into modules (containers) with their software dependencies. Containers can be freely mixed and matched to form workflows that give identical results on any platform which supports Docker. The ...
Read More »SCODE – An efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation
The analysis of RNA-Seq data from individual differentiating cells enables us to reconstruct the differentiation process and the degree of differentiation (in pseudo-time) of each cell. Such analyses can reveal detailed expression dynamics and functional relationships for differentiation. To further ...
Read More »VirusDetect – a new pipeline for virus identification
Researchers studying the viruses that affect agricultural production or human health now have a new tool for investigating where viruses have spread, on a local, national, or even global scale. VirusDetect is a free, open-source bioinformatics pipeline that can efficiently ...
Read More »Analysis of EBV Transcription Using High-Throughput RNA Sequencing
High-throughput sequencing of RNA is used to analyze the transcriptomes of viruses and cells, providing information about transcript structure and abundance. A wide array of programs and pipelines has been created to manage and interpret the abundance of data generated ...
Read More »Plastid – nucleotide-resolution analysis of next-generation sequencing and genomics data
Next-generation sequencing (NGS) informs many biological questions with unprecedented depth and nucleotide resolution. These assays have created a need for analytical tools that enable users to manipulate data nucleotide-by-nucleotide robustly and easily. Furthermore, because many NGS assays encode information jointly ...
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