Practical Bioinformatics Mark Voorhies 5/23/2019 Mark Voorhies - PowerPoint PPT Presentation

Jan 09, 2023 •198 likes •330 views

Practical Bioinformatics Mark Voorhies 5/23/2019 Mark Voorhies Practical Bioinformatics JavaTreeView link-out for ENSEMBL Mouse http://www.ensembl.org/Mus musculus/Gene/Summary?g=HEADER Mark Voorhies Practical Bioinformatics Science! Mark

Practical Bioinformatics Mark Voorhies 5/23/2019 Mark Voorhies Practical Bioinformatics
JavaTreeView link-out for ENSEMBL Mouse http://www.ensembl.org/Mus musculus/Gene/Summary?g=HEADER Mark Voorhies Practical Bioinformatics
Science! Mark Voorhies Practical Bioinformatics
Example Pipeline: Overview Mark Voorhies Practical Bioinformatics
Example Pipeline: Details Mark Voorhies Practical Bioinformatics
GSE88801 Pipelines Mark Voorhies Practical Bioinformatics
Linear Least Squares Mark Voorhies Practical Bioinformatics
Linear Least Squares b i = y i σ i Mark Voorhies Practical Bioinformatics
Linear Least Squares A ij = f j ( x i ) σ i Mark Voorhies Practical Bioinformatics
Linear Least Squares χ 2 = | A · a − b | 2 Mark Voorhies Practical Bioinformatics
Linear Least Squares M � U i · b � � a = V i s i i Mark Voorhies Practical Bioinformatics
Multiple Hypothesis Testing http://xkcd.com/882/ Mark Voorhies Practical Bioinformatics
Homework live Explore today’s limma results for the uninfected | J 77 , 24 h comparison (choose two or more) : 1 Extract the gene names from limma1.J774.Live.24-J774.uninfected.24.t0.csv and paste them into the selection window in JavaTreeView. 2 Filter yesterday’s heatmap to create a new CDT file for just these differential genes. 3 Redo our PCA and clustering protocol for just these differential genes. 4 Find the corresponding set of differential genes from the “J774 Live vs Uninfected” tab of S2 of the paper. Use python sets to find differential genes common to the two analysis pipelines. 5 Repeat the above for other interesting comparisons. Mark Voorhies Practical Bioinformatics

Recommend

Practical Bioinformatics Mark Voorhies 5/ 24/ 2013 Mark Voorhies Practical Bioinformatics

Practical Bioinformatics Mark Voorhies 5/ 24/ 2013 Mark Voorhies Practical Bioinformatics Clustering exercises { Visualizing the distance matrix Mark Voorhies Practical Bioinformatics Scripting Cluster Running Cluster3 from the command line

401 views • 7 slides

Practical Bioinformatics Mark Voorhies 5/22/2015 Mark Voorhies Practical Bioinformatics PAM

Practical Bioinformatics Mark Voorhies 5/22/2015 Mark Voorhies Practical Bioinformatics PAM (Dayhoff) and BLOSUM matrices PAM1 matrix originally calculated from manual alignments of highly conserved sequences (myoglobin, cytochrome C, etc.)

979 views • 71 slides

Practical Bioinformatics Mark Voorhies 5/15/2015 Mark Voorhies Practical Bioinformatics

Practical Bioinformatics Mark Voorhies 5/15/2015 Mark Voorhies Practical Bioinformatics Gotchas Indentation matters Mark Voorhies Practical Bioinformatics Clustering exercises Visualizing the distance matrix Mark Voorhies Practical

705 views • 46 slides

Practical Bioinformatics Mark Voorhies 4/16/2018 Mark Voorhies Practical Bioinformatics

Practical Bioinformatics Mark Voorhies 4/16/2018 Mark Voorhies Practical Bioinformatics JavaTreeView link-out for ENSEMBL Mouse http://www.ensembl.org/Mus musculus/Gene/Summary?g=HEADER Mark Voorhies Practical Bioinformatics Science! Mark

767 views • 20 slides

Practical Bioinformatics Mark Voorhies 5/21/2019 Mark Voorhies Practical Bioinformatics Change

Practical Bioinformatics Mark Voorhies 5/21/2019 Mark Voorhies Practical Bioinformatics Change of Coordinates http://xkcd.com/123/ Mark Voorhies Practical Bioinformatics Principal Components Analysis (PCA) Is there a point of view that

264 views • 11 slides

Practical Bioinformatics Mark Voorhies 5/26/2015 Mark Voorhies Practical Bioinformatics Habits

Practical Bioinformatics Mark Voorhies 5/26/2015 Mark Voorhies Practical Bioinformatics Habits are things you get for free, without requiring any special work. Cory Doctorow Advice to Writers, 4/5/2012 Mark Voorhies Practical

521 views • 27 slides

Practical Bioinformatics Mark Voorhies 5/11/2015 Mark Voorhies Practical Bioinformatics

Introduction to Python Practical Bioinformatics Mark Voorhies 5/11/2015 Mark Voorhies Practical Bioinformatics Introduction to Python Good ideas shamelessly lifted from David Erle and Josh Pollack Mark Voorhies Practical Bioinformatics

718 views • 46 slides

Practical Bioinformatics Mark Voorhies 4/9/2018 Mark Voorhies Practical Bioinformatics

Practical Bioinformatics Mark Voorhies 4/9/2018 Mark Voorhies Practical Bioinformatics Clustering exercises Visualizing the distance matrix Mark Voorhies Practical Bioinformatics Dictionaries d i c t i o n a r y = { A : T ,

77 views • 5 slides

Practical Bioinformatics Mark Voorhies 5/14/2019 Mark Voorhies Practical Bioinformatics Course

Practical Bioinformatics Mark Voorhies 5/14/2019 Mark Voorhies Practical Bioinformatics Course platform: VirtualBox Host operating system (e.g., OS X) VirtualBox Debian Linux Web 8888 8088 Jupyter Browser launches Python3 Bash Bash

756 views • 32 slides

Practical Bioinformatics Mark Voorhies 4/19/2011 Mark Voorhies Practical Bioinformatics Review

Practical Bioinformatics Mark Voorhies 4/19/2011 Mark Voorhies Practical Bioinformatics Review Topic Learning Python Dive Into Python Types (string, int, float, list) 2 3 Assignment (=, +=) 2 3 Slicing and indexing 4 3.2 References

443 views • 6 slides

Practical Bioinformatics Mark Voorhies 4/29/2011 Mark Voorhies Practical Bioinformatics Our

Practical Bioinformatics Mark Voorhies 4/29/2011 Mark Voorhies Practical Bioinformatics Our current tool set data (strings, floats, lists, nested lists) logic (if/then, try/except, for, while) functions (def, import, reload) Mark Voorhies

615 views • 25 slides

Practical Bioinformatics Mark Voorhies 5/29/2019 Mark Voorhies Practical Bioinformatics

Practical Bioinformatics Mark Voorhies 5/29/2019 Mark Voorhies Practical Bioinformatics Example Pipeline: Overview Mark Voorhies Practical Bioinformatics Example Pipeline: Overview Generate Genome Transfer Pre-process Samples Coverage

521 views • 16 slides

Practical Bioinformatics Mark Voorhies 5/19/2015 Mark Voorhies Practical Bioinformatics Review

Practical Bioinformatics Mark Voorhies 5/19/2015 Mark Voorhies Practical Bioinformatics Review Documentation A program should communicate its intent to both the computer and human programmers. Comments Docstrings Mark Voorhies

495 views • 26 slides

Practical Bioinformatics Mark Voorhies 5/31/2013 Mark Voorhies Practical Bioinformatics

Practical Bioinformatics Mark Voorhies 5/31/2013 Mark Voorhies Practical Bioinformatics Exercise: Scoring a gapped alignment 1 Given two equal length gapped sequences (where - represents a gap) and a scoring matrix, calculate an

335 views • 5 slides

Practical Bioinformatics Mark Voorhies 4/2/2018 Mark Voorhies Practical Bioinformatics

Introduction to Python Practical Bioinformatics Mark Voorhies 4/2/2018 Mark Voorhies Practical Bioinformatics Introduction to Python Resources Course website: http://histo.ucsf.edu/BMS270/ Resources on the course website: Syllabus Papers

660 views • 37 slides

Practical Bioinformatics Mark Voorhies 4/24/2017 Mark Voorhies Practical Bioinformatics

Introduction to Python Practical Bioinformatics Mark Voorhies 4/24/2017 Mark Voorhies Practical Bioinformatics Introduction to Python Resources Course website: http://histo.ucsf.edu/BMS270/ Resources on the course website: Syllabus Papers

701 views • 43 slides

Practical Bioinformatics Mark Voorhies 5/13/2019 Mark Voorhies Practical Bioinformatics

Introduction to Python Practical Bioinformatics Mark Voorhies 5/13/2019 Mark Voorhies Practical Bioinformatics Introduction to Python Resources Course website: http://histo.ucsf.edu/BMS270/ Resources on the course website: Syllabus Papers

594 views • 42 slides

Practical Bioinformatics Mark Voorhies 4/6/2017 Mark Voorhies Practical Bioinformatics Loading

Practical Bioinformatics Mark Voorhies 4/6/2017 Mark Voorhies Practical Bioinformatics Loading and re-loading your functions # Use import the f i r s t time you load a module # (And keep using import u n t i l i t loads # s u c c

775 views • 32 slides

Practical Bioinformatics Mark Voorhies 5/12/2015 Mark Voorhies Practical Bioinformatics

Practical Bioinformatics Mark Voorhies 5/12/2015 Mark Voorhies Practical Bioinformatics Gotchas Strings are quoted, names of things are not. mystring = mystring Mark Voorhies Practical Bioinformatics Gotchas Strings are quoted,

554 views • 27 slides

Practical Bioinformatics Mark Voorhies 5/21/2013 Mark Voorhies Practical Bioinformatics

Practical Bioinformatics Mark Voorhies 5/21/2013 Mark Voorhies Practical Bioinformatics Gotchas Enclosing symbols (,,(),[],...) need to be matched Mark Voorhies Practical Bioinformatics Gotchas Enclosing symbols

99 views • 7 slides

Practical Bioinformatics Mark Voorhies 4/20/2011 Mark Voorhies Practical Bioinformatics Review

Practical Bioinformatics Mark Voorhies 4/20/2011 Mark Voorhies Practical Bioinformatics Review Corrected slides for days 1 and 2 are on the website Mark Voorhies Practical Bioinformatics Review Corrected slides for days 1 and 2 are on the

248 views • 10 slides

Practical Bioinformatics Mark Voorhies 4/28/2017 Mark Voorhies Practical Bioinformatics

Practical Bioinformatics Mark Voorhies 4/28/2017 Mark Voorhies Practical Bioinformatics Pearson distances Pearson similarity N i ( x i x offset )( y i y offset ) s ( x , y ) = N N i ( x i x offset ) 2 i ( y i

502 views • 28 slides

Intro to NGS Theoretical and Practical HiC Workshop: Wet-lab and Bioinformatics November 4th,

Intro to NGS Theoretical and Practical HiC Workshop: Wet-lab and Bioinformatics November 4th, 2019 Selene L. Fernndez-Valverde regRNAlab.github.io @SelFdz 1 Learning objectives In this class we will learn How high-throughput (NGS)

728 views • 30 slides

Algorithms in Bioinformatics: A f Practical Introduction Practical Introduction Peptide

Algorithms in Bioinformatics: A f Practical Introduction Practical Introduction Peptide Sequencing Peptide Sequencing What is Peptide Sequencing? g High-throughput Protein Sequencing is to deduce the amino acid sequence of a d d h i

669 views • 53 slides