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Aaron Quinlan
United States
Приєднався 9 сер 2010
Programming, Statistics, and Bioinformatic Data Analysis with an emphasis on Genomics
Tips and Tricks: Block indentation in VSCode
This quick tutorial shows you how to use the block indentation and unindentation features in VSCode. These features are super useful for quickly manipulating lists, outlines, and code.
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Відео
Tips and Tricks: Block editing in VSCode
Переглядів 3,9 тис.2 роки тому
This quick tutorial shows you how to use the fantastic block editing feature in VSCode to, for example, apply the same command to many samples while only typing it once!
Applied Computational Genomics - BEDtools for Monte Carlo Overlap Enrichment Experiments
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From Aaron Quinlan's course on Applied Computational Genomics at the University of Utah (github.com/quinlan-lab/applied-computational-genomics.). This lecture introduces the concepts and considerations related to Monte Carlo experiments for testing whether overlaps between two genome interval datasets differ from expectation.
Applied Computational Genomics - bash_profile and UNIX tidbis
Переглядів 8553 роки тому
From Aaron Quinlan's course on Applied Computational Genomics at the University of Utah (github.com/quinlan-lab/applied-computational-genomics.). This lecture introduces VIM, the utility of the bash_profile, and new UNIX commands (ps, kill, top).
Applied Computational Genomics - Genome Annotation Concepts
Переглядів 2,5 тис.3 роки тому
From Aaron Quinlan's course on Applied Computational Genomics at the University of Utah (github.com/quinlan-lab/applied-computational-genomics). This lecture introduces the concepts of annotating new genome sequences using molecular and computational techniques.
Applied Computational Genomics - awk and bioawk
Переглядів 4,4 тис.3 роки тому
From Aaron Quinlan's course on Applied Computational Genomics at the University of Utah (github.com/quinlan-lab/applied-computational-genomics). This lecture introduces awk, one of the most powerful UNIX commands for manipulating and transforming data. We close with an introduction to bioawk from Heng Li, which extends awk to genomics file formats.
Applied Computational Genomics - 07 - DNA sequence mapping and alignment
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From Aaron Quinlan's course on Applied Computational Genomics at the University of Utah (github.com/quinlan-lab/applied-computational-genomics). This lecture introduces the concepts of DNA mapping and its complexities with hash-based mapping strategies. It also introduces the Smith-Waterman alignment algorithm to discern an optimal sequence alignment given a scoring scheme.
Applied Computational Genomics - 06 - Uncertainty in bulk RNA-seq
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From Aaron Quinlan's course on Applied Computational Genomics at the University of Utah (github.com/quinlan-lab/applie...). This lecture introduces discusses sources of Poisson and non-Poisson technical variation in RNA-seq that complicate biological interpretation.
Applied Computational Genomics - 05 - Poisson Processes in Biology
Переглядів 1,5 тис.3 роки тому
From Aaron Quinlan's course on Applied Computational Genomics at the University of Utah (github.com/quinlan-lab/applie...). This lecture introduces Poisson processes and its relevance to counting applications (e.g., RNA-seq) in biology.
Applied Computational Genomics - 04 - Dataframes, Precision/Accuracy, and Basic RNA-seq
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From Aaron Quinlan's course on Applied Computational Genomics at the University of Utah (github.com/quinlan-lab/applie...). This lecture digs deeper into R data frames, precision v. accuracy, and a basic introduction to RNA-seq. Level is beginner.
Applied Computational Genomics - 03- Introduction to R
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From Aaron Quinlan's course on Applied Computational Genomics at the University of Utah (github.com/quinlan-lab/applie...). This lecture introduces R (RStudio) through basic data analysis concepts and introductory commands. Level is beginner.
Applied Computational Genomics - 02- UNIX commands continued.
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From Aaron Quinlan's course on Applied Computational Genomics at the University of Utah (github.com/quinlan-lab/applie...). This lecture continues with UNIX by introducing the use of `cat`, `more`, `less`, `grep`, and `cut`.
Applied Computational Genomics - 01- Intro to UNIX
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From Aaron Quinlan's course on Applied Computational Genomics at the University of Utah (github.com/quinlan-lab/applie...). An introductory lecture to the history of computational biology and quick intro to UNIX.
Guest Lecturer: Susan Holmes, Stanford. Intro to expectation maximization and its applications.
Переглядів 4473 роки тому
SLLOBS was fortunate to have a guest lectures from Susan Holmes, Professor of Statistics at Stanford University (statweb.stanford.edu/~susan/). This lecture provides a wonderful introduction to Expectation Maximization and how it can be applied to biological questions.
Applied Computational Genomics - 20 - A Quick Overview of Supervised Machine Learning
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From Aaron Quinlan's course on Applied Computational Genomics at the University of Utah (github.com/quinlan-lab/applie...). This lecture introduces the the concepts of supervised machine learning through a conceptual demonstration of how handwriting recognition tools work. This covers the application of Bayes's Rule and Naive Bayes Classifiers.
Applied Computational Genomics - 15 - Monte Carlo analyses with bedtools
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Applied Computational Genomics - 15 - Monte Carlo analyses with bedtools
Applied Computational Genomics - 14 - Real-world analyses with bedtools
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Applied Computational Genomics - 14 - Real-world analyses with bedtools
Applied Computational Genomics - 13 - An introduction to bedtools.
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Applied Computational Genomics - 13 - An introduction to bedtools.
Applied Computational Genomics - 12 - Genome Annotation Formats
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Applied Computational Genomics - 12 - Genome Annotation Formats
Applied Computational Genomics - 11 - What is Structural Variation and how do we detect it?
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Applied Computational Genomics - 11 - What is Structural Variation and how do we detect it?
Applied Computational Genomics - 10 - VCF Annotation
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Applied Computational Genomics - 10 - VCF Annotation
Applied Computational Genomics - 09 - Variant Calling Format (VCF) and Hardy-Weinberg Equilibrium.
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Applied Computational Genomics - 09 - Variant Calling Format (VCF) and Hardy-Weinberg Equilibrium.
Applied Computational Genomics - 08 - Detecting Genetic Variation Part 2.
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Applied Computational Genomics - 08 - Detecting Genetic Variation Part 2.
Applied Computational Genomics - 07 - Detecting Genetic Variation Part 1.
Переглядів 2,6 тис.4 роки тому
Applied Computational Genomics - 07 - Detecting Genetic Variation Part 1.
Applied Computational Genomics - 06 - SAM, BAM, CRAM format.
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Applied Computational Genomics - 06 - SAM, BAM, CRAM format.
Applied Computational Genomics - 05 - Sequence Mapping and Alignment: Methods and Considerations.
Переглядів 3,7 тис.4 роки тому
Applied Computational Genomics - 05 - Sequence Mapping and Alignment: Methods and Considerations.
Applied Computational Genomics - 04 - DNA Sequencing Technologies, Sequencing Error, & FASTQ format.
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Applied Computational Genomics - 04 - DNA Sequencing Technologies, Sequencing Error, & FASTQ format.
Applied Computational Genomics - 03- Genetic Variation
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Applied Computational Genomics - 03- Genetic Variation
Applied Computational Genomics - 02- Pattern Matching in the Human Genome
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Applied Computational Genomics - 02- Pattern Matching in the Human Genome
Applied Computational Genomics - 01- The Human Genome
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Applied Computational Genomics - 01- The Human Genome