scholarly journals ImmunoDataAnalyzer: a bioinformatics pipeline for processing barcoded and UMI tagged immunological NGS data

2022 ◽  
Vol 23 (1) ◽  
Author(s):  
Julia Vetter ◽  
Susanne Schaller ◽  
Andreas Heinzel ◽  
Constantin Aschauer ◽  
Roman Reindl-Schwaighofer ◽  
...  
Keyword(s):  
Quality Control ◽  
Data Analysis ◽  
Gene Segment ◽  
Cell Receptor ◽  
Relevant Information ◽  
Ease Of Use ◽  
Immune Repertoire ◽  
Bioinformatics Pipeline ◽  
Depth Analysis ◽  
Ngs Data

Abstract Background Next-generation sequencing (NGS) is nowadays the most used high-throughput technology for DNA sequencing. Among others NGS enables the in-depth analysis of immune repertoires. Research in the field of T cell receptor (TCR) and immunoglobulin (IG) repertoires aids in understanding immunological diseases. A main objective is the analysis of the V(D)J recombination defining the structure and specificity of the immune repertoire. Accurate processing, evaluation and visualization of immune repertoire NGS data is important for better understanding immune responses and immunological behavior. Results ImmunoDataAnalyzer (IMDA) is a pipeline we have developed for automatizing the analysis of immunological NGS data. IMDA unites the functionality from carefully selected immune repertoire analysis software tools and covers the whole spectrum from initial quality control up to the comparison of multiple immune repertoires. It provides methods for automated pre-processing of barcoded and UMI tagged immune repertoire NGS data, facilitates the assembly of clonotypes and calculates key figures for describing the immune repertoire. These include commonly used clonality and diversity measures, as well as indicators for V(D)J gene segment usage and between sample similarity. IMDA reports all relevant information in a compact summary containing visualizations, calculations, and sample details, all of which serve for a more detailed overview. IMDA further generates an output file including key figures for all samples, designed to serve as input for machine learning frameworks to find models for differentiating between specific traits of samples. Conclusions IMDA constructs TCR and IG repertoire data from raw NGS reads and facilitates descriptive data analysis and comparison of immune repertoires. The IMDA workflow focus on quality control and ease of use for non-computer scientists. The provided output directly facilitates the interpretation of input data and includes information about clonality, diversity, clonotype overlap as well as similarity, and V(D)J gene segment usage. IMDA further supports the detection of sample swaps and cross-sample contamination that potentially occurred during sample preparation. In summary, IMDA reduces the effort usually required for immune repertoire data analysis by providing an automated workflow for processing raw NGS data into immune repertoires and subsequent analysis. The implementation is open-source and available on https://bioinformatics.fh-hagenberg.at/immunoanalyzer/.

scholarly journals FastqCleaner: an interactive Bioconductor application for quality-control, filtering and trimming of FASTQ files

2018 ◽  
Author(s):  
Leandro Gabriel Roser ◽  
Fernán Agüero ◽  
Daniel Oscar Sánchez
Keyword(s):  
Quality Control ◽  
Data Analysis ◽  
The Novel ◽  
Web Environment ◽  
Ngs Data Analysis ◽  
Novel Concept ◽  
Next Generation Sequencing Ngs ◽  
User Friendly ◽  
Ngs Data ◽  
Analysis Platform

AbstractBackgroundExploration and processing of FASTQ files are the first steps in state-of-the-art data analysis workflows of Next Generation Sequencing (NGS) platforms. The large amount of data generated by these technologies has put a challenge in terms of rapid analysis and visualization of sequencing information. Recent integration of the R data analysis platform with web visual frameworks has stimulated the development of user-friendly, powerful, and dynamic NGS data analysis applications.ResultsThis paper presents FastqCleaner, a Bioconductor visual application for both quality-control (QC) and pre-processing of FASTQ files. The interface shows diagnostic information for the input and output data and allows to select a series of filtering and trimming operations in an interactive framework. FastqCleaner combines the technology of Bioconductor for NGS data analysis with the data visualization advantages of a web environment.ConclusionsFastqCleaner is an user-friendly, offline-capable tool that enables access to advanced Bioconductor infrastructure. The novel concept of a Bioconductor interactive application that can be used without the need for programming skills, makes FastqCleaner a valuable resource for NGS data analysis.

An Empirical Study on the Adoption of E-Commerce in Pondicherry.

Think India ◽  
2019 ◽  
Vol 22 (2) ◽  
pp. 305-314
Author(s):  
Kishore Raaj Suresh
Keyword(s):  
Data Analysis ◽  
Design Methodology ◽  
Measurement Instrument ◽  
Ease Of Use ◽  
Perceived Usefulness ◽  
Perceived Ease Of Use ◽  
Validity And Reliability ◽  
Personal Cost ◽  
Perceived Security ◽  
Perceived Enjoyment

Purpose – This study investigates the consumer’s technology adoption toward electronic commerce. In addition to the variables perceived usefulness and perceived ease of use derived from TAM, the study included and tested factors like perceived security, perceived product value, personal cost, perceived enjoyment, perceived cost and perceived quality. Design/methodology/approach – A questionnaire was developed primarily based on the available scales in the already published literature. All model constructs requested participants to indicate their perceptions of Likert-style responses. The data analysis was executed using Smart PLS to test the validity and reliability of the measurement instrument.

scholarly journals A Review of the Botany, Traditional Use, Phytochemistry, Analytical Methods, Pharmacological Effects, and Toxicity of Angelicae Pubescentis Radix

2020 ◽  
Vol 2020 ◽  
pp. 1-28
Author(s):  
Liu Yang ◽  
Ajiao Hou ◽  
Song Wang ◽  
Jiaxu Zhang ◽  
Wenjing Man ◽  
...  
Keyword(s):  
Quality Control ◽  
Mechanism Of Action ◽  
Analytical Methods ◽  
Lumbar Disc ◽  
Pharmacological Study ◽  
Relevant Information ◽  
Chemical Components ◽  
Pharmacological Effects ◽  
Bioactive Constituents ◽  
Traditional Use

Angelicae Pubescentis Radix (AP), as a traditional Chinese medicine (TCM), has been used for thousands of years in China. In this paper, the botany, traditional use, phytochemistry, analytical methods, quality control, pharmacological effects, and toxicity of AP were reviewed. It can provide a reference for the further research and lay a foundation for the rational clinical application of AP. The relevant information on AP was collected from scientific databases (such as Baidu Scholar, CNKI, Google Scholar, PubMed, Science Direct, Web of Science, and SciFinder Scholar), Chinese herbal classics, Chinese Pharmacopoeia, PhD and MSc dissertations, and so on. The components which have been isolated and identified in AP include coumarins, volatile oils, organic acids, terpenes, polysaccharides, flavonoids, sterols, and trace elements. Most of them were analyzed by HPLC and GC. A pharmacological study shows that the AP has extensive pharmacological effects, including anti-inflammatory, antirheumatism, sedative and hypnotic, neuroprotection, antioxidation, antitumor, and allergy, and it is widely used in the treatment of the rheumatoid arthritis, knee osteoarthritis, lumbar disc, ankylosing spondylitis, headaches, stroke hemiplegia, Alzheimer’s, and arrhythmia. AP is a valuable natural medicinal plant. So far, significant advances have been made in phytochemistry and pharmacology. Some traditional uses have been demonstrated by modern pharmacology. However, the chemical components and pharmacological effects of AP are complex and varied, and there are different standards for the evaluation of its quality and efficacy. The mechanism of action, the structure-activity relationship among the components, and the potential synergistic and antagonistic effects remain to be studied. At the same time, there are few studies on the specific compounds related to its pharmacodynamics. In order to better develop and utilize AP, we should establish a more reasonable, reliable, and accurate quality control standard and focus on the study of bioactive constituents and the demonstration of their mechanism of action.

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