VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis

BACKGROUND: RNA sequencing has become a ubiquitous technology used throughout life sciences as an effective method of measuring RNA abundance quantitatively in tissues and cells. The increase in use of RNA-seq technology has led to the continuous development of new tools for every step of analysis from alignment to downstream pathway analysis. However, effectively using these analysis tools in a scalable and reproducible way can be challenging, especially for non-experts. RESULTS: Using the workflow management system Snakemake we have developed a user friendly, fast, efficient, and comprehensive pipeline for RNA-seq analysis. VIPER (Visualization Pipeline for RNA-seq analysis) is an analysis workflow that combines some of the most popular tools to take RNA-seq analysis from raw sequencing data, through alignment and quality control, into downstream differential expression and pathway analysis. VIPER has been created in a modular fashion to allow for the rapid incorporation of new tools to expand the capabilities. This capacity has already been exploited to include very recently developed tools that explore immune infiltrate and T-cell CDR (Complementarity-Determining Regions) reconstruction abilities. The pipeline has been conveniently packaged such that minimal computational skills are required to download and install the dozens of software packages that VIPER uses. CONCLUSIONS: VIPER is a comprehensive solution that performs most standard RNA-seq analyses quickly and effectively with a built-in capacity for customization and expansion

CistromeMap: a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human

Summary: Transcription and chromatin regulators, and histone modifications play essential roles in gene expression regulation. We have created CistromeMap as a web server to provide a comprehensive knowledgebase of all of the publicly available ChIP-Seq and DNase-Seq data in mouse and human. We have also manually curated metadata to ensure annotation consistency, and developed a user-friendly display matrix for quick navigation and retrieval of data for specific factors, cells, and papers. Finally, we provide users with summary statistics of ChIP-Seq and DNase-Seq studies. Availability: Freely available on the web a

Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse

Chromatin immunoprecipitation, DNase I hypersensitivity and transposase-accessibility assays combined with high-throughput sequencing enable the genome-wide study of chromatin dynamics, transcription factor binding and gene regulation. Although rapidly accumulating publicly available ChIP-seq, DNase-seq and ATAC-seq data are a valuable resource for the systematic investigation of gene regulation processes, a lack of standardized curation, quality control and analysis procedures have hindered extensive reuse of these data. To overcome this challenge, we built the Cistrome database, a collection of ChIP-seq and chromatin accessibility data (DNase-seq and ATAC-seq) published before January 1, 2016, including 13 366 human and 9953 mouse samples. All the data have been carefully curated and processed with a streamlined analysis pipeline and evaluated with comprehensive quality control metrics. We have also created a user-friendly web server for data query, exploration and visualization. The resulting Cistrome DB (Cistrome Data Browser), available online at http://cistrome.org/db, is expected to become a valuable resource for transcriptional and epigenetic regulation studies

Quality of life of patients with oesophageal cancer in Taiwan: validation and application of the Taiwan Chinese (Mandarin) version of the EORTC QLQ-OES18: a brief communication

[[abstract]]Purpose: The aim of this study was to examine the reliability and validity, and the application of the Taiwan Chinese Version of the EORTC QLQ-OES18. Methods: The authors translated the questionnaire according to the guideline of the EORTC. Ninety-five patients with oesophageal cancer in National Taiwan University Hospital were interviewed using the questionnaire and the EORTC QLQ-C30 between October 2002 and September 2007. Answer distribution and psychometric properties of the EORTC QLQ-OES18 were examined. Results: The mean age of the patients was 60?years (SD 12?years). Most of the patients were in advanced stages of disease, with two-thirds off-treatment. The Cronbach's alpha coefficients were satisfactory (0.77-0.82) or near-satisfactory (pain: 0.67). The item-to-own and item-to-other scale correlations showed satisfactory results. Patients who were on-treatment versus off-treatment had significantly poorer quality of life scores in dysphagia, dry mouth, and taste, and a borderline poorer score in cough. Opposite situations were seen in the scales of reflux and choking. Conclusions: The EORTC QLQ-OES18 is a valid instrument to assess quality of life issues in patients with oesophageal cancer in Taiwan

The corrosion/dissolution behaviour of aluminium in solutions containing both chloride and fluoride ions

The corrosion behaviour of aluminium in sodium chloride or sodium fluoride solution is at the present time reasonably well understood. In chloride solution, localised attack on the oxide is the most usual problem encountered. In fluoride solution, the Al2O3 film is initially found to be removed to be replaced by a complex oxyfluoride film which subsequently determines the corrosion behaviour. In the present work, potentiodynamic, potentiostatic, open circuit potential and impedance tests are used to elucidate the corrosion behaviour of aluminium in solutions containing both chloride and fluoride ions. It has been found that the presence of fluoride does not lead to localised attack, but that it modifies the surface oxide in such a way as to facilitate attack by chloride. Surprisingly however, for a fixed 0.5 M chloride concentration, these effects of fluoride are only manifest in the concentration range 0.25–10−3 M fluoride at 20°C. Concentrations in excess of 0.25 M have no apparent activating influence. At higher temperatures, lower fluoride levels are sufficient to cause these oxide modifications. The presence of fluoride even in very small quantities prevents ‘film improvement’ reactions similar to those observed in chloride only solutions