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| galaxy for rna seq analysis: Hi-C Data Analysis Silvio Bicciato, Francesco Ferrari, 2022-09-04 This volume details a comprehensive set of methods and tools for Hi-C data processing, analysis, and interpretation. Chapters cover applications of Hi-C to address a variety of biological problems, with a specific focus on state-of-the-art computational procedures adopted for the data analysis. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Hi-C Data Analysis: Methods and Protocols aims to help computational and molecular biologists working in the field of chromatin 3D architecture and transcription regulation. |
| galaxy for rna seq analysis: A Practical Guide To Cancer Systems Biology Hsueh-fen Juan, Hsuan-cheng Huang, 2017-11-29 Systems biology combines computational and experimental approaches to analyze complex biological systems and focuses on understanding functional activities from a systems-wide perspective. It provides an iterative process of experimental measurements, data analysis, and computational simulation to model biological behavior. This book provides explained protocols for high-throughput experiments and computational analysis procedures central to cancer systems biology research and education. Readers will learn how to generate and analyze high-throughput data, therapeutic target protein structure modeling and docking simulation for drug discovery. This is the first practical guide for students and scientists who wish to become systems biologists or utilize the approach for cancer research. |
| galaxy for rna seq analysis: Applications of RNA-Seq and Omics Strategies Fabio Marchi, Priscila Cirillo, Elvis Cueva Mateo, 2017-09-13 The large potential of RNA sequencing and other omics techniques has contributed to the production of a huge amount of data pursuing to answer many different questions that surround the science's great unknowns. This book presents an overview about powerful and cost-efficient methods for a comprehensive analysis of RNA-Seq data, introducing and revising advanced concepts in data analysis using the most current algorithms. A holistic view about the entire context where transcriptome is inserted is also discussed here encompassing biological areas with remarkable technological advances in the study of systems biology, from microorganisms to precision medicine. |
| galaxy for rna seq analysis: The Kiwifruit Genome Raffaele Testolin, Hong-Wen Huang, Allan Ross Ferguson, 2016-05-02 This book describes the basic botanical features of kiwifruit and its wild relatives, reports on the steps that led to its genome sequencing, and discusses the results obtained with the assembly and annotation. The core chapters provide essential insights into the main gene families that characterize this species as a crop, including the genes controlling sugar and starch metabolism, pigment biosynthesis and degradation, the ascorbic-acid pathway, fruit softening and postharvest metabolism, allergens, and resistance to pests and diseases. The book offers a valuable reference guide for taxonomists, geneticists and horticulturists. Further, since information gained from the genome sequence is extraordinarily useful in assessing the breeding value of individuals based on whole-genome scans, it will especially benefit plant breeders. Accordingly, chapters are included that focus on gene introgression from wild relatives and genome-based breeding. |
| galaxy for rna seq analysis: RNA-Seq Analysis: Methods, Applications and Challenges Filippo Geraci, Indrajit Saha, Monica Bianchini, 2020-06-08 |
| galaxy for rna seq analysis: Genome Data Analysis Ju Han Kim, 2019-04-30 This textbook describes recent advances in genomics and bioinformatics and provides numerous examples of genome data analysis that illustrate its relevance to real world problems and will improve the reader’s bioinformatics skills. Basic data preprocessing with normalization and filtering, primary pattern analysis, and machine learning algorithms using R and Python are demonstrated for gene-expression microarrays, genotyping microarrays, next-generation sequencing data, epigenomic data, and biological network and semantic analyses. In addition, detailed attention is devoted to integrative genomic data analysis, including multivariate data projection, gene-metabolic pathway mapping, automated biomolecular annotation, text mining of factual and literature databases, and integrated management of biomolecular databases. The textbook is primarily intended for life scientists, medical scientists, statisticians, data processing researchers, engineers, and other beginners in bioinformatics who are experiencing difficulty in approaching the field. However, it will also serve as a simple guideline for experts unfamiliar with the new, developing subfield of genomic analysis within bioinformatics. |
| galaxy for rna seq analysis: 6th International Conference on Practical Applications of Computational Biology & Bioinformatics Miguel P. Rocha, Nicholas Luscombe, Florentino Fdez-Riverola, Juan M. Corchado Rodríguez, 2012-03-05 The growth in the Bioinformatics and Computational Biology fields over the last few years has been remarkable and the trend is to increase its pace. In fact, the need for computational techniques that can efficiently handle the huge amounts of data produced by the new experimental techniques in Biology is still increasing driven by new advances in Next Generation Sequencing, several types of the so called omics data and image acquisition, just to name a few. The analysis of the datasets that produces and its integration call for new algorithms and approaches from fields such as Databases, Statistics, Data Mining, Machine Learning, Optimization, Computer Science and Artificial Intelligence. Within this scenario of increasing data availability, Systems Biology has also been emerging as an alternative to the reductionist view that dominated biological research in the last decades. Indeed, Biology is more and more a science of information requiring tools from the computational sciences. In the last few years, we have seen the surge of a new generation of interdisciplinary scientists that have a strong background in the biological and computational sciences. In this context, the interaction of researchers from different scientific fields is, more than ever, of foremost importance boosting the research efforts in the field and contributing to the education of a new generation of Bioinformatics scientists. PACBB‘12 hopes to contribute to this effort promoting this fruitful interaction. PACBB'12 technical program included 32 papers from a submission pool of 61 papers spanning many different sub-fields in Bioinformatics and Computational Biology. Therefore, the conference will certainly have promoted the interaction of scientists from diverse research groups and with a distinct background (computer scientists, mathematicians, biologists). The scientific content will certainly be challenging and will promote the improvement of the work that is being developed by each of the participants. |
| galaxy for rna seq analysis: Interactive Web-Based Data Visualization with R, plotly, and shiny Carson Sievert, 2020-01-30 The richly illustrated Interactive Web-Based Data Visualization with R, plotly, and shiny focuses on the process of programming interactive web graphics for multidimensional data analysis. It is written for the data analyst who wants to leverage the capabilities of interactive web graphics without having to learn web programming. Through many R code examples, you will learn how to tap the extensive functionality of these tools to enhance the presentation and exploration of data. By mastering these concepts and tools, you will impress your colleagues with your ability to quickly generate more informative, engaging, and reproducible interactive graphics using free and open source software that you can share over email, export to pdf, and more. Key Features: Convert static ggplot2 graphics to an interactive web-based form Link, animate, and arrange multiple plots in standalone HTML from R Embed, modify, and respond to plotly graphics in a shiny app Learn best practices for visualizing continuous, discrete, and multivariate data Learn numerous ways to visualize geo-spatial data This book makes heavy use of plotly for graphical rendering, but you will also learn about other R packages that support different phases of a data science workflow, such as tidyr, dplyr, and tidyverse. Along the way, you will gain insight into best practices for visualization of high-dimensional data, statistical graphics, and graphical perception. The printed book is complemented by an interactive website where readers can view movies demonstrating the examples and interact with graphics. |
| galaxy for rna seq analysis: Deep Sequencing Data Analysis Noam Shomron, 2013-07-20 The new genetic revolution is fuelled by Deep Sequencing (or Next Generation Sequencing) apparatuses which, in essence, read billions of nucleotides per reaction. Effectively, when carefully planned, any experimental question which can be translated into reading nucleic acids can be applied.In Deep Sequencing Data Analysis, expert researchers in the field detail methods which are now commonly used to study the multi-facet deep sequencing data field. These included techniques for compressing of data generated, Chromatin Immunoprecipitation (ChIP-seq), and various approaches for the identification of sequence variants. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of necessary materials and reagents, step-by-step, readily reproducible protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Deep Sequencing Data Analysis seeks to aid scientists in the further understanding of key data analysis procedures for deep sequencing data interpretation. |
| galaxy for rna seq analysis: Transcriptome Data Analysis Yejun Wang, Ming-an Sun, 2019-03-20 This detailed volume provides comprehensive practical guidance on transcriptome data analysis for a variety of scientific purposes. Beginning with general protocols, the collection moves on to explore protocols for gene characterization analysis with RNA-seq data as well as protocols on several new applications of transcriptome studies. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and useful, Transcriptome Data Analysis: Methods and Protocols serves as an ideal guide to the expanding purposes of this field of study. |
| galaxy for rna seq analysis: Field Guidelines for Genetic Experimental Designs in High-Throughput Sequencing Ana M. Aransay, José Luis Lavín Trueba, 2016-06-02 High throughput sequencing (HTS) technologies have conquered the genomics and epigenomics worlds. The applications of HTS methods are wide, and can be used to sequence everything from whole or partial genomes, transcriptomes, non-coding RNAs, ribosome profiling, to single-cell sequencing. Having such diversity of alternatives, there is a demand for information by research scientists without experience in HTS that need to choose the most suitable methodology or combination of platforms and to define their experimental designs to achieve their specific objectives. Field Guidelines for Genetic Experimental Designs in High-Throughput Sequencing aims to collect in a single volume all aspects that should be taken into account when HTS technologies are being incorporated into a research project and the reasons behind them. Moreover, examples of several successful strategies will be analyzed to make the point of the crucial features. This book will be of use to all scientist that are unfamiliar with HTS and want to incorporate such technologies to their research. |
| galaxy for rna seq analysis: Bioinformatics and Functional Genomics Jonathan Pevsner, 2005-03-04 Wiley is proud to announce the publication of the first ever broad-based textbook introduction to Bioinformatics and Functional Genomics by a trained biologist, experienced researcher, and award-winning instructor. In this new text, author Jonathan Pevsner, winner of the 2001 Johns Hopkins University Teacher of the Year award, explains problem-solving using bioinformatic approaches using real examples such as breast cancer, HIV-1, and retinal-binding protein throughout. His book includes 375 figures and over 170 tables. Each chapter includes: Problems, discussion of Pitfalls, Boxes explaining key techniques and math/stats principles, Summary, Recommended Reading list, and URLs for freely available software. The text is suitable for professionals and students at every level, including those with little to no background in computer science. |
| galaxy for rna seq analysis: Computational Genomics with R Altuna Akalin, 2020-12-16 Computational Genomics with R provides a starting point for beginners in genomic data analysis and also guides more advanced practitioners to sophisticated data analysis techniques in genomics. The book covers topics from R programming, to machine learning and statistics, to the latest genomic data analysis techniques. The text provides accessible information and explanations, always with the genomics context in the background. This also contains practical and well-documented examples in R so readers can analyze their data by simply reusing the code presented. As the field of computational genomics is interdisciplinary, it requires different starting points for people with different backgrounds. For example, a biologist might skip sections on basic genome biology and start with R programming, whereas a computer scientist might want to start with genome biology. After reading: You will have the basics of R and be able to dive right into specialized uses of R for computational genomics such as using Bioconductor packages. You will be familiar with statistics, supervised and unsupervised learning techniques that are important in data modeling, and exploratory analysis of high-dimensional data. You will understand genomic intervals and operations on them that are used for tasks such as aligned read counting and genomic feature annotation. You will know the basics of processing and quality checking high-throughput sequencing data. You will be able to do sequence analysis, such as calculating GC content for parts of a genome or finding transcription factor binding sites. You will know about visualization techniques used in genomics, such as heatmaps, meta-gene plots, and genomic track visualization. You will be familiar with analysis of different high-throughput sequencing data sets, such as RNA-seq, ChIP-seq, and BS-seq. You will know basic techniques for integrating and interpreting multi-omics datasets. Altuna Akalin is a group leader and head of the Bioinformatics and Omics Data Science Platform at the Berlin Institute of Medical Systems Biology, Max Delbrück Center, Berlin. He has been developing computational methods for analyzing and integrating large-scale genomics data sets since 2002. He has published an extensive body of work in this area. The framework for this book grew out of the yearly computational genomics courses he has been organizing and teaching since 2015. |
| galaxy for rna seq analysis: Fog Computing Assad Abbas, Samee U. Khan, Albert Y. Zomaya, 2020-04-21 Summarizes the current state and upcoming trends within the area of fog computing Written by some of the leading experts in the field, Fog Computing: Theory and Practice focuses on the technological aspects of employing fog computing in various application domains, such as smart healthcare, industrial process control and improvement, smart cities, and virtual learning environments. In addition, the Machine-to-Machine (M2M) communication methods for fog computing environments are covered in depth. Presented in two parts—Fog Computing Systems and Architectures, and Fog Computing Techniques and Application—this book covers such important topics as energy efficiency and Quality of Service (QoS) issues, reliability and fault tolerance, load balancing, and scheduling in fog computing systems. It also devotes special attention to emerging trends and the industry needs associated with utilizing the mobile edge computing, Internet of Things (IoT), resource and pricing estimation, and virtualization in the fog environments. Includes chapters on deep learning, mobile edge computing, smart grid, and intelligent transportation systems beyond the theoretical and foundational concepts Explores real-time traffic surveillance from video streams and interoperability of fog computing architectures Presents the latest research on data quality in the IoT, privacy, security, and trust issues in fog computing Fog Computing: Theory and Practice provides a platform for researchers, practitioners, and graduate students from computer science, computer engineering, and various other disciplines to gain a deep understanding of fog computing. |
| galaxy for rna seq analysis: The Burrows-Wheeler Transform: Donald Adjeroh, Timothy Bell, Amar Mukherjee, 2008-06-17 The Burrows-Wheeler Transform is one of the best lossless compression me- ods available. It is an intriguing — even puzzling — approach to squeezing redundancy out of data, it has an interesting history, and it has applications well beyond its original purpose as a compression method. It is a relatively late addition to the compression canon, and hence our motivation to write this book, looking at the method in detail, bringing together the threads that led to its discovery and development, and speculating on what future ideas might grow out of it. The book is aimed at a wide audience, ranging from those interested in learning a little more than the short descriptions of the BWT given in st- dard texts, through to those whose research is building on what we know about compression and pattern matching. The ?rst few chapters are a careful description suitable for readers with an elementary computer science ba- ground (and these chapters have been used in undergraduate courses), but later chapters collect a wide range of detailed developments, some of which are built on advanced concepts from a range of computer science topics (for example, some of the advanced material has been used in a graduate c- puter science course in string algorithms). Some of the later explanations require some mathematical sophistication, but most should be accessible to those with a broad background in computer science. |
| galaxy for rna seq analysis: MicroRNA Protocols Shao-Yao Ying, 2008-02-04 MicroRNA Protocols provides diverse, novel, and useful descriptions of miRNAs in several species, including plants, worms, flies, fish, chicks, mice, and humans. These include some useful adaptations and applications that could be relevant to the wider research community who are already familiar with the identification of miRNAs. This volume will stimulate the reader to explore diverse ways to understanding the mechanism in which miRNAs facilitate the molecular aspects of the biomedical research. |
| galaxy for rna seq analysis: Next Generation Sequencing Jerzy Kulski, 2016-01-14 Next generation sequencing (NGS) has surpassed the traditional Sanger sequencing method to become the main choice for large-scale, genome-wide sequencing studies with ultra-high-throughput production and a huge reduction in costs. The NGS technologies have had enormous impact on the studies of structural and functional genomics in all the life sciences. In this book, Next Generation Sequencing Advances, Applications and Challenges, the sixteen chapters written by experts cover various aspects of NGS including genomics, transcriptomics and methylomics, the sequencing platforms, and the bioinformatics challenges in processing and analysing huge amounts of sequencing data. Following an overview of the evolution of NGS in the brave new world of omics, the book examines the advances and challenges of NGS applications in basic and applied research on microorganisms, agricultural plants and humans. This book is of value to all who are interested in DNA sequencing and bioinformatics across all fields of the life sciences. |
| galaxy for rna seq analysis: Integrative analysis of single-cell and/or bulk multi-omics sequencing data Geng Chen, Xingdong Chen, Rongshan Yu, Zhichao Liu, 2023-03-13 |
| galaxy for rna seq analysis: Data Integration in the Life Sciences Sarah Cohen-Boulakia, 2008-06-11 This book constitutes the refereed proceedings of the 5th International Workshop on Data Integration in the Life Sciences, DILS 2008, held in Evry, France in June 2008. The 18 revised full papers presented together with 3 keynote talks and a tutorial paper were carefully reviewed and selected from 54 submissions. The papers adress all current issues in data integration and data management from the life science point of view and are organized in topical sections on Semantic Web for the life sciences, designing and evaluating architectures to integrate biological data, new architectures and experience on using systems, systems using technologies from the Semantic Web for the life sciences, mining integrated biological data, and new features of major resources for biomolecular data. |
| galaxy for rna seq analysis: Gene Prediction Martin Kollmar, 2019-05-19 This volume introduces software used for gene prediction with focus on eukaryotic genomes. The chapters in this book describe software and web server usage as applied in common use-cases, and explain ways to simplify re-annotation of long available genome assemblies. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary computational requirements, step-by-step, readily reproducible computational protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and thorough, Gene Prediction: Methods and Protocols is a valuable resource for researchers and research groups working on the assembly and annotation of single species or small groups of species. Chapter 3 is available open access under a CC BY 4.0 license via link.springer.com. |
| galaxy for rna seq analysis: RNA-Seq in Drug Discovery and Development Feng Cheng, Robert Morris, 2023-08-17 The research and development process in modern drug discovery and development is a complex and challenging task. Using traditional biological test methods such as PCR to measure the expression levels or function of these genes is costly and time-consuming. RNA-seq can measure the expression patterns of thousands of genes simultaneously and provide insights into functional pathways or regulations in biological processes, which has revolutionized the way biological scientists examine gene functions. This book addresses the various aspects of the RNA-seq technique, especially its application in drug discovery and development. Features • One of the few books that focuses on the applications of the RNA-seq technique in drug discovery and development. • Comprehensive and timely publication which relates RNA sequencing to drug targets, mechanisms of action, and resistance. • The editor has extensive experience in the field of computational medicinal chemistry, computational biophysics, and bioinformatics. • Chapter authors are at the frontline of the academic and industrial science in this particular area of RNA sequencing. |
| galaxy for rna seq analysis: Gene Expression Analysis Nalini Raghavachari, Natàlia Garcia-Reyero, 2018-05-17 This volume provides experimental and bioinformatics approaches related to different aspects of gene expression analysis. Divided in three sections chapters detail wet-lab protocols, bioinformatics approaches, single-cell gene expression, highly multiplexed amplicon sequencing, multi-omics techniques, and targeted sequencing. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Gene Expression Analysis: Methods and Protocols aims provide useful information to researchers worldwide. |
| galaxy for rna seq analysis: Computational Systems Biology Tao Huang, 2018-03-14 This volume introduces the reader to the latest experimental and bioinformatics methods for DNA sequencing, RNA sequencing, cell-free tumour DNA sequencing, single cell sequencing, single-cell proteomics and metabolomics. Chapters detail advanced analysis methods, such as Genome-Wide Association Studies (GWAS), machine learning, reconstruction and analysis of gene regulatory networks and differential coexpression network analysis, and gave a practical guide for how to choose and use the right algorithm or software to handle specific high throughput data or multi-omics data. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Computational Systems Biology: Methods and Protocols aims to ensure successful results in the further study of this vital field. |
| galaxy for rna seq analysis: Methicillin-Resistant Staphylococcus Aureus (MRSA) Protocols Yinduo Ji, 2019-09-16 This third edition volume expands on the previous editions with an update on the latest techniques used for the detection, genotyping, and investigating pathogenesis of Staphylococcus aureus in vitro and in vivo. The methods covered in this book mostly focus on routine clinical diagnosis, surveillance, research, and practice for treatment of patients infected by multi-drug resistant S. aureus. The book also covers the epidemiology of MRSA, molecular typing approaches, clinical treatment of MRSA infections, and animal models of drug discovery. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Informative and cutting-edge, Methicillin-Resistant Staphylococcus Aureus (MRSA) Protocols: Cutting-Edge Technologies and Advancements, Third Edition is a valuable resource for researchers looking to set up new methods to study S. aureus, and will also be very useful for technicians and scientists working on other bacterial pathogens. |
| galaxy for rna seq analysis: Next-Generation Genome Sequencing Michal Janitz, 2011-08-24 Written by leading experts from industry and academia, this first single comprehensive resource addresses recent developments in next generation DNA sequencing technology and their impact on genome research, drug discovery and health care. As such, it presents a detailed comparative analysis of commercially available platforms as well as insights into alternative, emerging sequencing techniques. In addition, the book not only covers the principles of DNA sequencing techniques but also social, ethical and commercial aspects, the concept of personalized medicine and a five-year perspective of DNA sequencing. |
| galaxy for rna seq analysis: RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods Jan Gorodkin, Walter L. Ruzzo, 2014-03-18 The existence of genes for RNA molecules not coding for proteins (ncRNAs) has been recognized since the 1950's, but until recently, aside from the critically important ribosomal and transfer RNA genes, most focus has been on protein coding genes. However, a long series of striking discoveries, from RNA's ability to carry out catalytic function, to discovery of riboswitches, microRNAs and other ribo-regulators performing critical tasks in essentially all living organisms, has created a burgeoning interest in this primordial component of the biosphere. However, the structural characteristics and evolutionary constraints on RNA molecules are very different from those of proteins, necessitating development of a completely new suite of informatic tools to address these challenges. In RNA Sequence, Structure, Function: Computational and Bioinformatic Methods, expert researchers in the field describe a substantial and relevant fraction of these methodologies from both practical and computational/algorithmic perspectives. Focusing on both of these directions addresses both the biologist interested in knowing more about RNA bioinformatics as well as the bioinformaticist interested in more detailed aspects of the algorithms. Written in the highly successful Methods in Molecular Biology series format, the chapters include the kind of detailed description and implementation advice that is crucial for getting optimal results. Thorough and intuitive, RNA Sequence, Structure, Function: Computational and Bioinformatic Methods aids scientists in continuing to study key methods and principles of RNA bioinformatics. |
| galaxy for rna seq analysis: Tumor Immunology and Immunotherapy - Cellular Methods Part B , 2020-01-28 Tumor Immunology and Immunotherapy - Cellular Methods Part B, Volume 632, the latest release in the Methods in Enzymology series, continues the legacy of this premier serial with quality chapters authored by leaders in the field. Topics covered include Quantitation of calreticulin exposure associated with immunogenic cell death, Side-by-side comparisons of flow cytometry and immunohistochemistry for detection of calreticulin exposure in the course of immunogenic cell death, Quantitative determination of phagocytosis by bone marrow-derived dendritic cells via imaging flow cytometry, Cytofluorometric assessment of dendritic cell-mediated uptake of cancer cell apoptotic bodies, Methods to assess DC-dependent priming of T cell responses by dying cells, and more. |
| galaxy for rna seq analysis: Kubernetes: Up and Running Kelsey Hightower, Brendan Burns, Joe Beda, 2017-09-07 Legend has it that Google deploys over two billion application containers a week. How’s that possible? Google revealed the secret through a project called Kubernetes, an open source cluster orchestrator (based on its internal Borg system) that radically simplifies the task of building, deploying, and maintaining scalable distributed systems in the cloud. This practical guide shows you how Kubernetes and container technology can help you achieve new levels of velocity, agility, reliability, and efficiency. Authors Kelsey Hightower, Brendan Burns, and Joe Beda—who’ve worked on Kubernetes at Google and other organizatons—explain how this system fits into the lifecycle of a distributed application. You will learn how to use tools and APIs to automate scalable distributed systems, whether it is for online services, machine-learning applications, or a cluster of Raspberry Pi computers. Explore the distributed system challenges that Kubernetes addresses Dive into containerized application development, using containers such as Docker Create and run containers on Kubernetes, using the docker image format and container runtime Explore specialized objects essential for running applications in production Reliably roll out new software versions without downtime or errors Get examples of how to develop and deploy real-world applications in Kubernetes |
| galaxy for rna seq analysis: Cryptosporidium Jan R. Mead, Michael J. Arrowood, 2019-08-27 This book encompasses broad aspects of Cryptosporidium research with established methods that have been improved and expanded over the years as well as recent cutting-edge techniques. Within this collection are numerous molecular methods as well as protocols for genotyping and diagnostics, while also including room for in vitro cell culture techniques to address the issues with growing this difficult organism continuously. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Cryptosporidium: Methods and Protocols serves as an idea guide to the inherent challenges of working with cryptosporidial parasites to provide a foundation for new investigators to build upon. The chapter “Accessing Cryptosporidium Omic and Isolate Data via CryptoDB.org” is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com. |
| galaxy for rna seq analysis: Plant Long Non-Coding RNAs Julia A. Chekanova, Hsiao-Lin V. Wang, 2019-04-20 This volume focuses on various approaches to studying long non-coding RNAs (lncRNAs), including techniques for finding lncRNAs, localization, and observing their functions. The chapters in this book cover how to catalog lncRNAs in various plant species; determining subcellular localization; protein interactions; structures; and RNA modifications. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and innovative, Plant Long Non-Coding RNAs: Methods and Protocols is a valuable resource that aids researchers in understanding the functions of lncRNAs in different plant species, and helps them explore currently uncharted facets of plant biology. |
| galaxy for rna seq analysis: Version Control with Git Jon Loeliger, Matthew McCullough, 2012-08-14 Get up to speed on Git for tracking, branching, merging, and managing code revisions. Through a series of step-by-step tutorials, this practical guide takes you quickly from Git fundamentals to advanced techniques, and provides friendly yet rigorous advice for navigating the many functions of this open source version control system. This thoroughly revised edition also includes tips for manipulating trees, extended coverage of the reflog and stash, and a complete introduction to the GitHub repository. Git lets you manage code development in a virtually endless variety of ways, once you understand how to harness the system’s flexibility. This book shows you how. Learn how to use Git for several real-world development scenarios Gain insight into Git’s common-use cases, initial tasks, and basic functions Use the system for both centralized and distributed version control Learn how to manage merges, conflicts, patches, and diffs Apply advanced techniques such as rebasing, hooks, and ways to handle submodules Interact with Subversion (SVN) repositories—including SVN to Git conversions Navigate, use, and contribute to open source projects though GitHub |
| galaxy for rna seq analysis: Next-Generation Sequencing and Sequence Data Analysis Kuo Ping Chiu, 2015-11-04 Nucleic acid sequencing techniques have enabled researchers to determine the exact order of base pairs - and by extension, the information present - in the genome of living organisms. Consequently, our understanding of this information and its link to genetic expression at molecular and cellular levels has lead to rapid advances in biology, genetics, biotechnology and medicine. Next-Generation Sequencing and Sequence Data Analysis is a brief primer on DNA sequencing techniques and methods used to analyze sequence data. Readers will learn about recent concepts and methods in genomics such as sequence library preparation, cluster generation for PCR technologies, PED sequencing, genome assembly, exome sequencing, transcriptomics and more. This book serves as a textbook for students undertaking courses in bioinformatics and laboratory methods in applied biology. General readers interested in learning about DNA sequencing techniques may also benefit from the simple format of information presented in the book. |
| galaxy for rna seq analysis: Marine Metagenomics Takashi Gojobori, Tokio Wada, Takanori Kobayashi, Katsuhiko Mineta, 2019-07-24 This book presents the state-of-art marine metagenome research and explains the method of marine metagenomic analysis in an easy-to-understand manner. Changes in the marine environment due to global warming and pollution have become a major global problem. Maintaining a healthy marine ecosystem requires advanced environmental monitoring and assessment systems. As such, the book presents a novel metagenomic monitoring method, which has been developed for comprehensive analyses of the DNA of microorganisms living in seawater to further our understanding of the dynamics of the marine environment. The book can be used as a primer for new researchers and as a manual on experimental methods. |
| galaxy for rna seq analysis: Data Mining Techniques for the Life Sciences Oliviero Carugo, Frank Eisenhaber, 2016-08-23 Most life science researchers will agree that biology is not a truly theoretical branch of science. The hype around computational biology and bioinformatics beginning in the nineties of the 20th century was to be short lived (1, 2). When almost no value of practical importance such as the optimal dose of a drug or the three-dimensional structure of an orphan protein can be computed from fundamental principles, it is still more straightforward to determine them experimentally. Thus, experiments and observationsdogeneratetheoverwhelmingpartofinsightsintobiologyandmedicine. The extrapolation depth and the prediction power of the theoretical argument in life sciences still have a long way to go. Yet, two trends have qualitatively changed the way how biological research is done today. The number of researchers has dramatically grown and they, armed with the same protocols, have produced lots of similarly structured data. Finally, high-throu- put technologies such as DNA sequencing or array-based expression profiling have been around for just a decade. Nevertheless, with their high level of uniform data generation, they reach the threshold of totally describing a living organism at the biomolecular level for the first time in human history. Whereas getting exact data about living systems and the sophistication of experimental procedures have primarily absorbed the minds of researchers previously, the weight increasingly shifts to the problem of interpreting accumulated data in terms of biological function and bio- lecular mechanisms. |
| galaxy for rna seq analysis: Applications of RNA-Seq in Biology and Medicine Irina Vlasova-St. Louis, 2021-10-13 This book evaluates and comprehensively summarizes the scientific findings that have been achieved through RNA-sequencing (RNA-Seq) technology. RNA-Seq transcriptome profiling of healthy and diseased tissues allows FOR understanding the alterations in cellular phenotypes through the expression of differentially spliced RNA isoforms. Assessment of gene expression by RNA-Seq provides new insight into host response to pathogens, drugs, allergens, and other environmental triggers. RNA-Seq allows us to accurately capture all subtypes of RNA molecules, in any sequenced organism or single-cell type, under different experimental conditions. Merging genomics and transcriptomic profiling provides novel information underlying causative DNA mutations. Combining RNA-Seq with immunoprecipitation and cross-linking techniques is a clever multi-omics strategy assessing transcriptional, post-transcriptional and post-translational levels of gene expression regulation. |
| galaxy for rna seq analysis: Plant-Pathogen Interactions Paul Birch, John Jones, Jorunn Bos, 2014-03-19 Plant-Pathogen Interactions: Methods and Protocols, Second Edition expands upon the first edition with current, detailed protocols for the study of plant pathogen genome sequences. It contains new chapters on techniques to help identify and characterize effectors and to study their impacts on host immunity and their roles in pathogen biology. Additional chapters focus on protocols to identify avirulence and resistance genes, investigate the roles of effector targets and other defence-associated proteins in plant immunity. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Plant-Pathogen Interactions: Methods and Protocols, Second Edition seeks to aid scientists in the further study of plant immunity. |
| galaxy for rna seq analysis: The Baculoviruses Lois K. Miller, 1997-07-31 The past decade has witnessed an explosion of information on the molecular biology of insect viruses and a frenzy of activity in applying this information to medicine and agriculture. Genetically engineered baculoviruses are presently being tested for commercial use as pesticides, and the study of such viruses is also revealing remarkable insights into basic cellular processes such as apoptosis. This comprehensive volume provides readers with knowledge of basic and applied baculovirology so that current literature in the field can be appreciated. |
| galaxy for rna seq analysis: Human Preimplantation Embryo Selection Jacques Cohen, Kay Elder, 2007-09-26 The most profound dilemma in assisted reproduction to date is the inability to recognize potentially viable embryos before their replacement into the reproductive tract. Application of increasingly advanced new technology has allowed the field of embryo evaluation to evolve rapidly and dramatically over the past five years.Human Preimplantation Emb |
| galaxy for rna seq analysis: Regulation of Downstream Targets Rossen Donev, 2023-03-03 Regulation of Downstream Targets, Volume 134 in the Advances in Protein Chemistry and Structural Biology series, presents interesting chapters on topics such as Transcriptional regulatory mechanisms and signaling networks in Viral Infections, Identification of potential key genes associated with pathogenesis and prognosis of endometrial cancer based on Integrated Bioinformatics Approaches, Differential regulation of genes in stage IB pancreatic cancer associated with increased risk of metastasis, AMPK-related LKB1-downstream targets, A compilation of bioinformatic approaches to identify novel downstream targets for the detection and prophylaxis of cancer, Protein phosphatases and their targets: Critical determinants of signaling pathway in plants, and more. Other sections cover Calcium decoders and their targets: The holy alliance that regulate cellular responses, Importin alpha family NAAT/IBB domain: functions of a multi-faceted long chameleon sequence, Aurora Kinase A and related downstream molecules: A Potential Network for Cancer Therapy, Emerging Role of Heat Shock Proteins in Cardiovascular Diseases, Function, Structure, Evolution, Regulation and Drug Target Relevance of Arylalkylamine N-acetyltransferase, and Analysis of signaling cascades from myeloma cells treated with pristimerin. - Provides the authority and expertise of leading contributors from an international board of authors - Presents the latest release in the Advances in Protein Chemistry and Structural Biology series - Updated release includes the latest information on the Regulation of Downstream Targets |
| galaxy for rna seq analysis: Computational Biology of Non-Coding RNA Xin Lai, Shailendra Gupta, Julio Vera Gonzalez, 2025-01-09 |
RNA-Seq expression analysis in Galaxy From A to Z
In this workshop we demonstrate a typical analysis done by a bioinformatician working with RNA-seq data using Galaxy. This involves quality control, aligning sequencing data to a known …
lecture 6 Galaxy - University of Central Florida
Galaxy Usage • “RNA–Seq Data Analysis in Galaxy” is an academic article published on PubMed and SpringerLink • The purpose of this article is to showcase the tools and steps involved in …
RNA-Seq Differential Gene Expression analysis (Galaxy Server) …
RNA-seq is a powerful and versatile tool published widely over the last few years. RNA-seq used to investigate complex diseases and find new genes for functional analysis. RNA-seq used in one of …
RNA sequence data analysis via Galaxy, Part II Analyzing your …
RNA sequence data analysis via Galaxy, Part II Analyzing your results (Group Exercise) Learning objectives: - examine the results from the Galaxy RNA-Seq analysis workflow - Import data from …
Using Galaxy for NGS Analysis - Pennsylvania State University
Obtain datasets at the end of a sequencing run. Select Libraries and Histories, and Workflows to populate and run on sequenced samples. How does it all work?
Galaxy RNAseq tutorial - GCC2014
1 Do a typical RNA-seq analysis. Expression. 2 Workflows. Rerun the analysis with no effort. 3 Differential expression analysis. RNAseq in Galaxy June 29, 2014
RNA-seq Analysis with Galaxy - bioinformatics.bc.edu
Wang, Z. et al. RNA-Seq: a revolutionary tool for transcriptomics Nature Reviews Genetics (2009) Galaxy Project ToolShed The Galaxy Project Tool Shed contains contributed software and …
GL4HS BIOINFORMATICS MANUAL - NASA Technical …
RNA-seq is a powerful tool that enable us to analyze the expression profile of an entire organism’s genome. RNA-seq is more accurate than the previous microarray technology which was based …
RNA-seq Analysis - generegulation.org
Oct 15, 2020 · Throughout this practical, you will be using a platform called Galaxy, that integrates multiple state-of-the-art bioinformatics programs. Galaxy is intuitive and easy to use, and all …
RNA sequence data analysis via Galaxy, Part I Uploading data …
We will divide up into groups and use a Galaxy workflow to analyze RNAseq data from a study that examined gene expression in different Toxoplasma developmental stages: “An experimental …
RNA sequence data analysis via Galaxy, Part II Uploading data …
RNA sequence data analysis via Galaxy, Part II Uploading data and starting the workflow (Group Exercise) Learning objectives: - Examine Galaxy output results - Analyze output results - Export …
RNA-Seq expression analysis in Galaxy
Introduction Raw data to alignment Differential Gene Expression (DGE) analysis Wrap up RNA-Seq Central dogma RNA-Seq analysis in Galaxy July 5 2015
Differential gene expression analysis using RNA-Seq data and …
This course covers topics regarding experimental design, introduction and considerations for NGS sequencing, hands on sessions to get from raw sequencing data to count matrices using the …
RNA-seq using Galaxy
1. Do a typical RNA-seq analysis. • Expression. 2. Workflows. • Rerun the analysis with no effort. 3. Differential expression analysis. RNA-seq data analysis 16/17 Sunday, 30 June 2013
RNA sequence data analysis via Galaxy, Part I Uploading data …
The goal of this exercise is to use a Galaxy workflow to analyze RNA sequencing data. The datasets we will us are all feely available through the sequence repositories (SRA, ENA, DDBJ).
Using Galaxy: RNA-seq
Sep 23, 2014 · RNA-seq (RNA Sequencing), also called "Whole Transcriptome Shotgun Sequencing" ("WTSS"), is a technology that uses the capabilities of next-generation sequencing …
RNA sequence data analysis via VEuPathDB Galaxy, Part I …
VEuPathDB Galaxy-based workspace offers pre-loaded genomes, private data analysis and display, and the ability to share and export analysis results and also import certain datasets into private …
RNA-Seq analysis in Galaxy
RNA-Seq analysis in Galaxy June 30 2014 Introduction Single Nucleotide Variants (SNV) Differential Gene Expression (DGE) analysis References Hypothesis testing
RNA-Seq expression analysis in Galaxy From A to Z
In this workshop we demonstrate a typical analysis done by a bioinformatician working with RNA-seq data using Galaxy. This involves quality control, aligning sequencing data to a known …
lecture 6 Galaxy - University of Central Florida
Galaxy Usage • “RNA–Seq Data Analysis in Galaxy” is an academic article published on PubMed and SpringerLink • The purpose of this article is to showcase the tools and steps involved in …
RNA-Seq Differential Gene Expression analysis (Galaxy …
RNA-seq is a powerful and versatile tool published widely over the last few years. RNA-seq used to investigate complex diseases and find new genes for functional analysis. RNA-seq used in …
Chapter 20
Here, we describe how to perform a reference-based RNA-Seq analysis using Galaxy, from data upload to visualization and functional enrichment analysis of differentially expressed genes.
RNA sequence data analysis via Galaxy, Part II Analyzing …
RNA sequence data analysis via Galaxy, Part II Analyzing your results (Group Exercise) Learning objectives: - examine the results from the Galaxy RNA-Seq analysis workflow - Import data …
Using Galaxy for NGS Analysis - Pennsylvania State University
Obtain datasets at the end of a sequencing run. Select Libraries and Histories, and Workflows to populate and run on sequenced samples. How does it all work?
Galaxy RNAseq tutorial - GCC2014
1 Do a typical RNA-seq analysis. Expression. 2 Workflows. Rerun the analysis with no effort. 3 Differential expression analysis. RNAseq in Galaxy June 29, 2014
RNA-seq Analysis with Galaxy - bioinformatics.bc.edu
Wang, Z. et al. RNA-Seq: a revolutionary tool for transcriptomics Nature Reviews Genetics (2009) Galaxy Project ToolShed The Galaxy Project Tool Shed contains contributed software and …
GL4HS BIOINFORMATICS MANUAL - NASA Technical Reports …
RNA-seq is a powerful tool that enable us to analyze the expression profile of an entire organism’s genome. RNA-seq is more accurate than the previous microarray technology which was based …
RNA-seq Analysis - generegulation.org
Oct 15, 2020 · Throughout this practical, you will be using a platform called Galaxy, that integrates multiple state-of-the-art bioinformatics programs. Galaxy is intuitive and easy to use, and all …
RNA sequence data analysis via Galaxy, Part I Uploading …
We will divide up into groups and use a Galaxy workflow to analyze RNAseq data from a study that examined gene expression in different Toxoplasma developmental stages: “An …
RNA sequence data analysis via Galaxy, Part II Uploading …
RNA sequence data analysis via Galaxy, Part II Uploading data and starting the workflow (Group Exercise) Learning objectives: - Examine Galaxy output results - Analyze output results - …
RNA-Seq expression analysis in Galaxy
Introduction Raw data to alignment Differential Gene Expression (DGE) analysis Wrap up RNA-Seq Central dogma RNA-Seq analysis in Galaxy July 5 2015
Differential gene expression analysis using RNA-Seq data …
This course covers topics regarding experimental design, introduction and considerations for NGS sequencing, hands on sessions to get from raw sequencing data to count matrices using the …
RNA-seq using Galaxy
1. Do a typical RNA-seq analysis. • Expression. 2. Workflows. • Rerun the analysis with no effort. 3. Differential expression analysis. RNA-seq data analysis 16/17 Sunday, 30 June 2013
RNA sequence data analysis via Galaxy, Part I Uploading …
The goal of this exercise is to use a Galaxy workflow to analyze RNA sequencing data. The datasets we will us are all feely available through the sequence repositories (SRA, ENA, DDBJ).
Using Galaxy: RNA-seq
Sep 23, 2014 · RNA-seq (RNA Sequencing), also called "Whole Transcriptome Shotgun Sequencing" ("WTSS"), is a technology that uses the capabilities of next-generation …
RNA sequence data analysis via VEuPathDB Galaxy, Part I …
VEuPathDB Galaxy-based workspace offers pre-loaded genomes, private data analysis and display, and the ability to share and export analysis results and also import certain datasets …
RNA-Seq analysis in Galaxy
RNA-Seq analysis in Galaxy June 30 2014 Introduction Single Nucleotide Variants (SNV) Differential Gene Expression (DGE) analysis References Hypothesis testing
