Genetics Branch Journal club

Apr 10, 2011Download as PPT, PDF1 like314 views

The document describes a dataset containing cancer samples from multiple types. It includes 3131 cancer samples from 26 different cancer types with at least 20 samples per type. The majority of the samples, 2520, came from clinical samples while 541 came from cell lines. There were also 1480 normal samples for comparison.

Samples 3131 cancer samples 2965 from 26 cancer types, more than 20 samples per type; 17 types with 40 or more samples 2520 from clinical samples, 541 from cell lines 1480 normal samples Some paired, but unclear if this was used in the analysis.

This document discusses various topics related to cancer genome sequencing and analysis. It describes the exome capture process using RNA baits and targeted sequencing. It also discusses the data analysis pipeline including alignment, indel realignment, quality recalibration, and variant calling. Further, it covers challenges around repeats, copy number analysis from exomes, and complete genome sequencing. Finally, it briefly mentions workflows for analyzing germline and tumor/normal variants.

Public datatutorialoverviewSean Davis

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Introduction to RSean Davis

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OKC Grand Rounds 2009Sean Davis

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Sssc retreat.bioinfo resources.20110411Sean Davis

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Genomics TechnologiesSean Davis

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This document discusses high-resolution views of the cancer genome using various technologies including DNA microarrays, comparative genomic hybridization, tiling arrays, next-generation sequencing, and DNAse-Seq. It describes how these technologies can be used to analyze gene expression, copy number variation, chromatin structure, and more to better understand cancer at the genomic level. Integrating data from all these sources presents challenges but may help improve individual health outcomes.

2016 07 12_purdue_bigdatainomics_seandavisSean Davis

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RNA-seq: A High-resolution View of the TranscriptomeSean Davis

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The molecular microscopes that we use to examine human biology have advanced significantly with the advent of next generation sequencing. RNA-seq is one application of this technology that leads to a very high-resolution view of the transcriptome. With these new technologies come increased data analysis and data handling burdens as well as the promise of new discovery. These slides present a high-level overview of the RNA-seq technology with a focus on the analysis approaches, quality control challenges, and experimental design.

Lect 1 scientific-method-bsc-1010_f13_jcJunior Umeh

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The document provides an overview of the scientific method and examples of its application to understanding life and climate change. It discusses the key characteristics of life, levels of biological organization from atoms to cells to organisms, and an outline of the history of life on Earth. Examples of applying the scientific method include using observations, hypotheses, predictions and experiments to investigate evolution and determine whether climate change is occurring.

Rna seqSean Davis

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This document provides an overview of RNA-seq and its applications. It discusses key aspects of RNA-seq including transcriptome profiling, alignment, quantification, differential expression analysis, clustering and visualization. It also covers experimental design considerations and highlights some commonly used tools and software. The document is a comprehensive guide that describes the RNA-seq workflow and analysis from start to finish.

Bioc strucvariant seattle_11_09Sean Davis

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ShinySRAdb: an R package using shiny to wrap the SRAdb Bioconductor packageSean Davis

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This document describes a Shiny web application called ShinySRAdb that provides a user-friendly interface for querying, viewing, and interacting with data from the Sequence Read Archive (SRA) database. It was programmed using the Shiny Apps package in R to make functions from the SRAdb package more accessible. The application allows users to search the SRA, filter results, view information on selected records, export results, and perform operations like downloading FASTQ files or visualizing entity relationships.

Culture projectJunior Umeh

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The document discusses the author's interests in sports like football, soccer, and basketball as well as Igbo sports and wrestling. It also covers the author's languages of English and some Spanish and the various languages spoken in Igbo culture. Various types of music are listed for both the author and Igbo culture. Religious beliefs discussed include the author being Catholic and the various religions in Igbo culture. Igbo traditions such as weddings, gatherings with kola nuts, and masquerades are briefly outlined. Comparisons are made between the author and Igbo culture regarding music listened to, religious beliefs, and sports enjoyed.

RNA-seq Data Analysis OverviewSean Davis

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Lect 4-&-5 cells-bsc-1010_f13_jcJunior Umeh

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This document provides an outline and overview of key concepts about cells. It begins by defining a cell and describing the main types - prokaryotic and eukaryotic. It then discusses the main components of cells, including the cytoplasm, organelles, cytoskeleton, cell wall, extracellular matrix, and cell junctions. For each topic, it provides brief explanations and examples. Interactive questions are included throughout to test understanding. The goal is to introduce the fundamental building blocks and structures that make up prokaryotic and eukaryotic cells.

Lect 2 biomolecules-bsc-1010_f13_jcJunior Umeh

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This document provides an outline and overview of biological molecules, including the key elements of life like carbon, hydrogen, oxygen, nitrogen, phosphorus and sulfur. It discusses the macromolecules that make up living things like carbohydrates, nucleic acids, proteins and lipids. Carbohydrates include sugars and starch, nucleic acids include DNA and RNA, proteins are made of amino acids, and lipids encompass fatty acids, phospholipids and steroids. The document also examines the structures, functions and importance of these fundamental building blocks of life.

SRAdb Bioconductor Package OverviewSean Davis

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Patient- and Family Centered Care: "Resident Performance from the Patient's V...hanscomhh5

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This document summarizes a presentation about patient and family centered care (PFCC) in graduate medical education. It discusses the history and core values of PFCC, provides examples of how PFCC has been successfully implemented at institutions like the Medical College of Georgia, and shares results from a study that assessed resident performance through patient feedback surveys. The study found patient feedback improved residents' communication, patient care, and systems-based practice skills compared to traditional attending evaluations alone. The presentation concludes PFCC can enhance graduate medical education by providing meaningful feedback to help residents improve.