bluuebunny/crossref_metadata_2025 huggingface dataset:
Excel Template for Mapping Four 96-Well Plates to One 384-Well Plate
Authors: Turner Stephen
Published: December 2024

Daniel Cook in Jeff Murray's lab at the University of Iowa put together this handy Excel template for keeping track of how samples from four 96-well plates are interleaved to configure a single 384-well plate using robotic liquid handling systems, like the Hydra II. Paste in lists of samples on your 96-well plates: And you'll get out a map of how the 384-well plate layout: And a summary list: You can download the Excel file here.
PCG Journal Club Articles, 7/17
Authors:   Unknown
Published: December 2024

Here are citations for the articles discussed at our most recent meeting (July 17). Our next meeting is scheduled for July 31.~JuliaBianconi G, Pin P, Marsili M. Assessing the relevance of node features for network structure.
Keep up with what's happening at ASHG 2010
Authors: Turner Stephen
Published: December 2024

As this year's ASHG meeting starts to wind down be sure to check out Variable Genome where Larry Parnell is summarizing what's going on at the talks he's been to. Also see the commentary on Genetic Inference by Luke Jostins. The 1000 Genomes tutorial from Wednesday night will be made available on genome.gov soon, and the presidential address, plenary sessions, and distinguished speaker symposium talks were recorded and will also soon be online.
Useful Unix/Linux One-Liners for Bioinformatics
Authors: Turner Stephen
Published: December 2024

Much of the work that bioinformaticians do is munging and wrangling around massive amounts of text. While there are some "standardized" file formats (FASTQ, SAM, VCF, etc.) and some tools for manipulating them (fastx toolkit, samtools, vcftools, etc.), there are still times where knowing a little bit of Unix/Linux is extremely helpful, namely awk, sed, cut, grep, GNU parallel, and others.
Introduction to single molecule real time (SMRT) sequencing from Pac Bio's Curtis Fideler
Authors: Turner Stephen
Published: December 2024

Definitely a seminar not to miss: Curtis Fideler, director of Sales at Pacific Biosciences, will be giving a special seminar here at Vanderbilt Thursday, May 20, 11:00a-noon in 202 Light Hall entitled "An Introduction to SMRT Sequencing: A description of Pacific Biosciences single molecule real time sequencing technology." Science: Real-Time DNA Sequencing from Single
Google Developers R Programming Video Lectures
Authors: Turner Stephen
Published: December 2024

Google Developers recognized that most developers learn R in bits and pieces, which can leave significant knowledge gaps. To help fill these gaps, they created a series of introductory R programming videos. These videos provide a solid foundation for programming tools, data manipulation, and functions in the R language and software.
Top 10 Algorithms in Data Mining
Authors: Turner Stephen
Published: December 2024

The authors here invited ACM KDD Innovation Award and IEEE ICDM Research Contributions Award winners to each nominate up to 10 best-known algorithms in data mining, including the algorithm name, justification for nomination, and a representative publication reference. The list was voted on by other IEEE and ACM award winners to narrow this down to a top 10 list.
Efficient Mixed-Model Association in GWAS using R
Authors: Turner Stephen
Published: December 2024

I recently did an analysis for the eMERGE network where I had lots of individuals from a small town in central Wisconsin where many of the subjects were related to one another. The subjects could not be treated as independent, but I could not use a family-based design either. I ended up using a mixed model approach using previously mentioned GenABEL.
Journal Club 4/16/2010
Authors: Turner Stephen
Published: December 2024

Our Program in Computation Genomics Journal Club is starting again, now the 3rd Friday of each month. The next meeting is this Friday, April 16, at 3pm in the CHGR conference room. As usual, please bring in any articles you've found recently and give a brief overview of why you thought it was interesting.
Split a Data Frame into Testing and Training Sets in R
Authors: Turner Stephen
Published: December 2024

I recently analyzed some data trying to find a model that would explain body fat distribution as predicted by several blood biomarkers. I had more predictors than samples (p>n), and I didn't have a clue which variables, interactions, or quadratic terms made biological sense to put into a model.
ROADTRIPS: Case-Control Association Testing with Partially or Completely Unknown Population and Pedigree Structure
Authors: Turner Stephen
Published: December 2024

A tip of the hat to @JVJAI for pointing out this interesting looking paper in AJHG. ROADTRIPS: Case-Control Association Testing with Partially or Completely Unknown Population and Pedigree Structure Timothy Thornton and Mary Sara McPeek Department of Biostatistics, University of Washington.

Abstract:

Genome-wide association studies are routinely conducted to identify genetic variants that influence complex disorders.
Accuracy of Individualized Risk Estimates for Personalized Medicine
Authors: Turner Stephen
Published: December 2024

Lucila Ohno-Machado, Professor of Medicine and Chief of the Division of Biomedical Informatics at UC-San Diego, will be giving a talk on "Accuracy of Individualized Risk Estimates for Personalized Medicine" next week, August 18, noon-1pm in 202 Light Hall. This should be an interesting perspective from a scientist with medical training on the utility of personal genomics tools in making healthcare decisions.
Make Pretty Regression Tables in Stata
Authors: Turner Stephen
Published: December 2024

The estout package for Stata is useful for quickly creating nicely formatted tables from a regression analysis for tables or papers. To install it, fire up Stata and type in this command:ssc install estout, replaceStata will automatically download and install the package. Run the regression as you normally would, then use the esttab command (part of the estout package) to create a table using those results.
For Today’s Graduate, Just One Word: Statistics
Authors: Turner Stephen
Published: December 2024

That's the title of a good article published yesterday in the New York Times about the emergence of statistics being in huge demand in the career market, becoming "the sexy job in the next 10 years" as Google's chief economist puts it. Now I just need to find one of these don't drink and derive t-shirts...For Today’s Graduate, Just One Word: StatisticsGetting Genetics Done by Stephen Turner is licensed under a Creative Commons Attribution (CC
Data Analysis for Genomics MOOC
Authors: Turner Stephen
Published: December 2024

Last month I told you about Coursera's specializations in data science, systems biology, and computing. Today I was reading Jeff Leek's blog post defending p-values and found a link to HarvardX's Data Analysis for Genomics course, taught by Rafael Irizarry and Mike Love. Here's the course description: If you've ever wanted to get started with data analysis in genomics and you'd learn R along the way, this looks like a great place to start.
Free Book: Elements of Statistical Learning
Authors: Turner Stephen
Published: December 2024

The Elements of Statistical Learning: Data Mining, Inference, and Prediction by Trevor Hastie, Robert Tibshirani, and Jerome Friedman, one of the best books on data mining and machine learning, is now available free in PDF format. Download it here or view it online here.Getting Genetics Done by Stephen Turner is licensed under a Creative Commons Attribution (CC BY) License.
Stepping Outside My Open-Source Comfort Zone: A First Look at Golden Helix SVS
Authors: Turner Stephen
Published: December 2024

I'm a huge supporter of the Free and Open Source Software movement. I've written more about R than anything else on this blog, all the code I post here is free and open-source, and a while back I invited you to steal this blog under a cc-by-sa license. Every now and then, however, something comes along that just might be worth paying for.
RStudio: New free IDE for R
Authors: Turner Stephen
Published: December 2024

Just saw the announcement of the availability of Rstudio, a new (free & open source) integrated development environment for R that works on Windows, Mac, and Linux. Judging from the screenshots, it looks like Rstudio supports syntax highlighting for Sweave &
Special Bioinformatics issue on next-gen sequencing
Authors: Turner Stephen
Published: December 2024

Bioinformatics is running a special issue on next generation sequencing, featuring lots of papers on alignment, assembly, Chip-Seq, RNA-Seq, and other related topics. This "virtual issue" will be continually updated as more developments are made. From the editors:Bioinformatics: Next generation sequencing issueGetting Genetics Done by Stephen Turner is licensed under a Creative Commons Attribution (CC BY) License.
Using the "Divide by 4 Rule" to Interpret Logistic Regression Coefficients
Authors: Turner Stephen
Published: December 2024

I was recently reading a bit about logistic regression in Gelman and Hill's book on hierarchical/multilevel modeling when I first learned about the "divide by 4 rule" for quickly interpreting coefficients in a logistic regression model in terms of the predicted probabilities of the outcome. The idea is pretty simple.
Galaxy Project Group on CiteULike and Mendeley
Authors: Turner Stephen
Published: December 2024

The Galaxy Project started using CiteULike to organize papers that are about, use, or reference Galaxy. The Galaxy CiteULike group is open to any CUL user, and once you join, you can add papers to the group, assign tags, and rate papers.
Check out the GGD poster at ASHG!
Authors: Turner Stephen
Published: December 2024

Aloha! If you're going to the American Society of Human Genetics meeting next week, come by our poster (poster #116, abstract #1567/T) and say hello! We would love to meet any of you who read GGD and hear what you think and what you'd like to see in the future.Getting Genetics Done by Stephen Turner is licensed under a Creative Commons Attribution (CC BY) License.
FreeMyPDF.com unlocks PDFs for submitting to PubMed Central
Authors: Turner Stephen
Published: December 2024

Do you submit manuscripts to journals that are not indexed in PubMed? This can make it difficult for others to find your publications, especially if they don't have a subscription to the journal. This often happens with us when we publish in computer science journals. Using the NIH manuscript submission system you can upload your manuscript to PubMed Central, which provides free open access, and is indexed in PubMed.
Moving to blog.stephenturner.us (Paired Ends)
Authors: Turner Stephen
Published: December 2024

My new blog/newsletter ("Paired Ends") is now at blog.stephenturner.us. I'll be posting semi-regular updates and literature highlights in bioinformatics, computational biology, and data science, along with the occasional post on programming.
GNU Screen
Authors: Turner Stephen
Published: December 2024

This is one of those things I picked up years ago while in graduate school that I just assumed everyone else already knew about. GNU screen is a great utility built-in to most Linux installations for remote session management. Typing 'screen' at the command line enters a new screen session.
find | xargs ... Like a Boss
Authors: Turner Stephen
Published: December 2024

*Edit March 12*

Be sure to look at the comments, especially the commentary on Hacker News - you can supercharge the find|xargs idea by using find|parallel instead. --- Do you ever discover a trick to do something better, faster, or easier, and wish you could reclaim all the wasted time and effort before your discovery?
Hadley Wickham: ggplot2 Webinar (Today!)
Authors: Turner Stephen
Published: December 2024

Title: A Backstage Tour of ggplot2 with Hadley Wickham

Date: Wednesday, February 8, 2012

Time: 11:00AM - 12:00PM Pacific

Presenter: Hadley Wickham, Professor of Statistics, Rice University

Register here.
Qualifying exam study guide phase I
Authors: Turner Stephen
Published: December 2024

Vanderbilt 2nd year grad students: Here is the study guide I made for studying for my general knowledge phase I qualifying exam. I'd recommend making your own, but this may help you with a place to start. You can download it at the link below.

Update January 25, 2013

: I've uploaded the link to Figshare for a more permanent home.
Translational Bioinformatics Year In Review
Authors:   Unknown
Published: December 2024

Per tradition, Russ Altman gave his "Translational Bioinformatics: The Year in Review" presentation at the close of the AMIA Joint Summit on Translational Bioinformatics in San Francisco on March 26th.  This year, papers came from six key areas (and a final Odds and Ends category).  His full slide deck is available here.
Machine Learning in R
Authors: Turner Stephen
Published: December 2024

Revolutions blog recently posted a link to R code by Joshua Reich with self-contained examples of using machine learning techniques in R, including various clustering methods (k-means, nearest neighbor, and kernel), recursive partitioning (CART), principle components analysis, linear discriminant analysis, and support vector machines.  This post also links to some slides that go over the basics of machine learning.
Archival, Analysis, and Visualization of #ISMBECCB 2013 Tweets
Authors: Turner Stephen
Published: December 2024

As the 2013 ISMB/ECCB meeting is winding down, I archived and analyzed the 2000+ tweets from the meeting using a set of bash and R scripts I previously blogged about. The archive of all the tweets tagged #ISMBECCB from July 19-24, 2013 is and will forever remain here on Github. You'll find some R code to parse through this text and run the analyses below in the same repository, explained in more detail in my previous blog post.
qqman: an R package for creating Q-Q and manhattan plots from GWAS results
Authors: Turner Stephen
Published: December 2024

Three years ago I wrote a blog post on how to create manhattan plots in R. After hundreds of comments pointing out bugs and other issues, I've finally cleaned up this code and turned it into an R package.
Seminar: Next-gen sequencing at VUMC: Our experience with RNA-, ChIP- and DNA-seq
Authors: Turner Stephen
Published: December 2024

The Vanderbilt Genome Technology Core is hosting a seminar/workshop on next-generation sequencing where Vanderbilt investigators will share their experiences with several types of next-gen technologies.  You can visit the Genome Technology Core at
Cancer Epidemiology, Biostatistics, and Bioinformatics Retreat
Authors: Turner Stephen
Published: December 2024

The 2009 Cancer Epidemiology, Biostatistics, and Bioinformatics Retreat will be held on Friday, December 4th, 2009, from 1:30 pm to 5:00 pm, on the eighth floor of the VICC building (898B PRB). The purpose of the retreat is to promote interactions among biostatisticians, bioinformaticians, epidemiologists, clinical investigators, and other translational researchers.
Copy Text to the Local Clipboard from a Remote SSH Session
Authors: Turner Stephen
Published: December 2024

This is an issue that has bugged me for years, and I've finally found a good solution on osxdaily and Stack Overflow.
R: Given column name in a Data Frame, Get the Index
Authors: Turner Stephen
Published: December 2024

Had a mental block today trying to figure out how to get the indices of columns in a data frame given their names. Simple task but difficult to search Google for an answer. Thanks to jashapiro, Matt, and Vince for giving me a heads up on the which() function. The which() function returns the indices of TRUE values in a logical vector. If you're looking at the iris data: data(iris) head(iris)
Tuesday Fun -- Epidemiological Dessert
Authors:   Unknown
Published: December 2024

Both useful and delicious, this two-by-two table pie by Sarah Lowry, Sarah McDougal (my 2nd cousin) and friends of the UW MPH program helps you get genetics done and satisfies the appetite! If only she could mail me the Odds Ratio...Getting Genetics Done by Stephen Turner is licensed under a Creative Commons Attribution (CC BY) License.
We're Hiring a Postdoc
Authors: Turner Stephen
Published: December 2024

Our lab is looking for a postdoc. See the ad here, reproduced below.

POST-DOCTORAL POSITION VANDERBILT CENTER FOR HUMAN GENETICS RESEARCH PROGRAM IN COMPUTATIONAL GENOMICS

The Program in Computational Genomics in the CHGR at Vanderbilt University has an immediate opening for a post-doctoral fellow to pursue new and exciting research in human genetics.
Using Volcano Plots in R to Visualize Microarray and RNA-seq Results
Authors: Turner Stephen
Published: December 2024

I've been asked a few times how to make a so-called volcano plot from gene expression results. A volcano plot typically plots some measure of effect on the x-axis (typically the fold change) and the statistical significance on the y-axis (typically the -log10 of the p-value). Genes that are highly dysregulated are farther to the left and right sides, while highly significant changes appear higher on the plot.
Havasupai Indians and the Ethical Use of Data
Authors:   Unknown
Published: December 2024

The recent settlement between Arizona State University and the Havasupai Indian tribe is calling attention to (and perhaps challenging) the ideas of informed consent. While I'm sure there are arguments to be made supporting both sides of this case, regardless of your position this is an excellent reminder that there are people's lives behind the alleles in our spreadsheets and PED files.
Ten Reasons Why Grad Students Should Blog
Authors: Turner Stephen
Published: December 2024

NYU PhD student Drew Conway has compiled a very nice list of 10 reasons why grad students should blog. I've been writing GGD for a little over a year now and it's been a great way to extend my own network past the Vanderbilt walls, participate in lively discussions with other scientists oceans away, and to write stuff that people actually read and find useful.
Use PuTTY and XMing to see Linux graphics via SSH on your Windows computer
Authors: Turner Stephen
Published: December 2024

Do you use SSH to connect to a remote Linux machine from your local Windows computer?  Ever needed to run a program on that Linux machine that displays graphical output, or uses a GUI? I was in this position last week trying to make figures using ggplot2 in R of results from an analysis of GWAS data which required using a 64-bit Linux machine with more RAM than my 32-bit windows machine can see.
NetGestalt for Data Visualization in the Context of Pathways
Authors:   Unknown
Published: December 2024

Many of you may be familiar with WebGestalt, a wonderful web utility developed by Bing Zhang at Vanderbilt for doing basic gene-set enrichment analyses. Last year, we invited Bing to speak at our annual retreat for the Vanderbilt Graduate Program in Human Genetics, and he did not disappoint! Bing walked us through his new tool called NetGestalt.
Professor Bush
Authors: Turner Stephen
Published: December 2024

A short announcement - my friend, colleague, running partner, and GGD contributor Will Bush is now an assistant professor in the Department of Biomedical Informatics, and investigator in the Center for Human Genetics Research here at Vanderbilt.Getting Genetics Done by Stephen Turner is licensed under a Creative Commons Attribution (CC BY) License.
Collaborative lesson development with GitHub
Authors: Turner Stephen
Published: December 2024

If you're doing any kind of scientific computing and not using version control, you're doing it wrong. The git version control system and GitHub, a web-based service for hosting and collaborating on git-controlled projects, have both become wildly popular over the last few years.
Checklist: Statistical Problems to Document and Avoid
Authors: Turner Stephen
Published: December 2024

Update 2010-04-21

: I forgot to post the link last time. That would have been helpful. Here you go: Vanderbilt Biostatistics: Statistical Problems to Document and to Avoid ..... At the Regression Modeling Strategies course I attended a few weeks ago, Frank Harrell pointed out the checklist on the biostatistics department's website of statistical problems to document and avoid.
Empowering Personal Genomics by Considering Regulatory Cis-Epistasis and Heterogeneity
Authors: Turner Stephen
Published: December 2024

Will Bush and I just heard that our paper "Multivariate Analysis of Regulatory SNPs: Empowering Personal Genomics by Considering Cis-Epistasis and Heterogeneity" was accepted for publication and a talk at the Personal Genomics session of the 2011 Pacific Symposium in Biocomputing.
Software Carpentry at UVA, Redux
Authors: Turner Stephen
Published: December 2024

Software Carpentry is an international collaboration backed by Mozilla and the Sloan Foundation comprising a team of volunteers that teach computational competence and basic programming skills to scientists.
PLINK/SEQ for Analyzing Large-Scale Genome Sequencing Data
Authors: Turner Stephen
Published: December 2024

PLINK/SEQ is an open source C/C++ library for analyzing large-scale genome sequencing data. The library can be accessed via the pseq command line tool, or through an R interface. The project is developed independently of PLINK but it's syntax will be familiar to PLINK users. PLINK/SEQ boasts an impressive feature set for a project still in the beta testing phase.
Arrange multiple ggplot2 plots in the same image window
Authors: Turner Stephen
Published: December 2024

In a previous tutorial I showed you how to create plots faceted by the level of a third variable using ggplot2. A commenter asked about using faceted plots and viewports and reminded me of this function I found in the ggplot2 Google group. The arrange function below is similar to using par(mfrow=c(r,c)) in base graphics to put more than one plot in the same image window.
Weekly Recap (Dec 2024, part 3)
Authors: Turner Stephen
Published: December 2024

This week’s recap highlights the Evo model for sequence modeling and design, biomedical discovery with AI agents, improving bioinformatics software quality through teamwork, a new tool from Brent Pedersen and Aaron Quinlan (vcfexpress) for filtering and formatting VCFs with Lua expressions, a new paper about the NHGRI-EBI GWAS Catalog, and a review paper on designing and engineering synthetic genomes.
R User Group Recap: Heatmaps and Using the caret Package
Authors: Turner Stephen
Published: December 2024

At our most recent R user group meeting we were delighted to have presentations from Mark Lawson and Steve Hoang, both bioinformaticians at Hemoshear. All of the code used in both demos is in our Meetup’s GitHub repo.
Success of GWAS Approach Demonstrated by Latest Lipids Meta-Analysis
Authors: Turner Stephen
Published: December 2024

Last year I linked to a series of perspectives in NEJM with contrasting views on the success or failure of GWAS - David Goldstein's paper and Nick Wade's synopsis that soon followed in the New York Times being particularly pessimistic. Earlier this year I was swayed by an essay in Cell by Jon McClellan and Mary-Claire King condemning the common disease common variant hypothesis and chalking up most GWAS hits to population stratification.
Capture system commands as R objects with system(..., intern=T)
Authors: Turner Stephen
Published: December 2024

Just discovered this very handy R command to capture the output from a system command as an R object.  I wanted to use R to read in the output from another program (PLINK) and do some processing on each output file. Of course if the files are named sequentially (plink1.out, plink2.out, plink3.out, etc.) this would be simple with a for loop.
Which Reference Management Software do you use? (Reader Poll)
Authors: Turner Stephen
Published: December 2024

When I started grad school I started using Reference Manager (RefMan), similar to EndNote, to manage my references and bibliographies. It's a real pain, and I often feel like I'm powering my computer with the endless pumping and clicking of the mouse that it takes to import a reference into my library. Recently I've started using Zotero because of how easy it is to import references, store PDFs, and sync between computers.
Getting Genetics Done 2012 In Review
Authors: Turner Stephen
Published: December 2024

Here are links to all of this year's posts (excluding seminar/webinar announcements), with the most visited posts in

bold italic

. As always, you can follow me on Twitter for more frequent updates. Happy new year!
Cell: Genetic Heterogeneity in Human Disease Review
Authors: Turner Stephen
Published: December 2024

Check out this review essay in Cell: Genetic Heterogeneity in Human Disease, by Jon McClellan and Mary-Claire King. (King's lab, incidentally, was the group who discovered via linkage analysis that the gene for early-onset breast and ovarian cancer on chromosome 17q21, nearly 5 years before Myriad Genetics filed for patent protection on the BRCA1/2 genes). Anyhow, looks like a great review on genetic heterogeneity and GWAS. Thanks @JVJAI.
Randomly Select Subsets of Individuals from a Binary Pedigree .fam File
Authors: Turner Stephen
Published: December 2024

I'm working on imputing GWAS data to the 1000 Genomes Project data using MaCH. For the model estimation phase you only need ~200 individuals. Here's a one-line unix command that will pull out 200 samples at random from a binary pedigree .fam file called myfamfile.fam: for i in `cut -d ' ' -f 1-2  myfamfile.fam | sed s/\ /,/g`; do echo "$RANDOM $i"; done | sort |
Common disorders are quantitative traits
Authors: Turner Stephen
Published: December 2024

There are no common disorders - only extremes of quantitative traits. --- That's the argument made by Plomin, Haworth, and Davis in a great review paper just published online in Nature Reviews Genetics.
Forest plots using R and ggplot2
Authors: Turner Stephen
Published: December 2024

Abhijit over at Stat Bandit posted some nice code for making forest plots using ggplot2 in R. You see these lots of times in meta-analyses, or as seen in the BioVU demonstration paper. The idea is simple - on the x-axis you have the odds ratio (or whatever stat you want to show), and each line is a different study, gene, SNP, phenotype, etc.
STAR: ultrafast universal RNA-seq aligner
Authors: Turner Stephen
Published: December 2024

There's a new kid on the block for RNA-seq alignment. Dobin, Alexander, et al. "STAR: ultrafast universal RNA-seq aligner." Bioinformatics (2012). Aligning RNA-seq data is challenging because reads can overlap splice junctions. Many other RNA-seq alignment algorithms (e.g. Tophat) are built on top of DNA sequence aligners.
Illumina Sequencing Seminar Series
Authors: Turner Stephen
Published: December 2024

Next week Brent Anderson with Illumina will be hosting a seminar series showcasing presentations from Vanderbilt scientists using Illumina technology to power their next-generation sequencing studies.
Computing for Data Analysis, and Other Free Courses
Authors: Turner Stephen
Published: December 2024

Coursera's free Computing for Data Analysis course starts today. It's a four week long course, requiring about 3-5 hours/week. A bit about the course: There are also hundreds of other free courses scheduled for this year. While the Computing for Data Analysis course is more about using R, the Data Analysis course is more about the methods and experimental designs you'll use, with a smaller emphasis on the R language.
Use SQL queries to manipulate data frames in R with sqldf package
Authors: Turner Stephen
Published: December 2024

I've covered a few topics in the past including the plyr package, which is kind of like "GROUP BY" for R, and the merge function for merging datasets. I only recently found the sqldf package for R, and it's already one of the most useful packages I've ever installed. The main function in the package is sqldf(), which takes a quoted string as an argument. You can treat data frames as tables as if they were in a relational database.
ggplot2: more wicked-cool plots in R
Authors: Turner Stephen
Published: December 2024

As far as I know there are 3 different systems for producing figures in R: (1) base graphics, included with R, (2) the lattice package, and (3) ggplot2, one of the newer plotting systems which is, according to the creator Hadley Wickham, "based on the grammar of graphics, which tries to take the good parts of base and lattice graphics and none of the bad parts.
Comparison of plots using Stata, R base, R lattice, and R ggplot2, Part I: Histograms
Authors: Turner Stephen
Published: December 2024

One of the nicer things about many statistics packages is the extremely granular control you get over your graphical output.  But I lack the patience to set dozens of command line flags in R, and I'd rather not power the computer by pumping the mouse trying to set all the clicky-box options in Stata's graphics editor.  I want something that just looks nice, using the out-of-the-box defaults.
Video and slides from ASHG 1000 Genomes tutorials
Authors: Turner Stephen
Published: December 2024

If you missed the tutorial on the 1000 genomes project data last week at ASHG, you can now watch the tutorials on youtube and download the slides online at http://genome.gov/27542240.
NYT: In Simulation Work, the Demand Is Real
Authors: Turner Stephen
Published: December 2024

The New York Times published this interesting article on how the ability to design and perform computer simulations is a highly marketable skill for careers across many disciplines.In methodology development we use simulation nearly every day.
I'm Starting a New Position at the University of Virginia
Authors: Turner Stephen
Published: December 2024

I just accepted an offer for a faculty position at the University of Virginia in the Center for Public Health Genomics / Department of Public Health Sciences. Starting in October I will be developing and directing a new centralized bioinformatics core in the UVA School of Medicine. Over the next few weeks I'm taking a much-needed vacation next door in Kauai and then packing up for the move to Charlottesville.
Deducer: R and ggplot2 GUI
Authors: Turner Stephen
Published: December 2024

Last Year I introduced you to R Commander, a nice graphical user interface (GUI) for R for those of you who are still hesitant to leave the clicky-box style research a la SPSS for the far more superior reproducible research using R. As most of you know I'm a huge fan of ggplot2. Many of you came to the short course Hadley Wickham gave here a few weeks ago on ggplot2 and plyr.
Create annotated GWAS manhattan plots using ggplot2 in R
Authors: Turner Stephen
Published: December 2024

***

Update April 25, 2011: This code has gone through a major revision. Please see the updated code and tutorial here. ***

A few months ago I showed you in this post how to use some code I wrote to produce manhattan plots in R using ggplot2. The qqman() function I described in the previous post actually calls another function, manhattan(), which has a few options you can set.
New GenABEL Website, and more *ABEL software
Authors: Turner Stephen
Published: December 2024

The *ABEL suite of R packages and software for genetic analysis has grown substantially since the appearance of GenABEL and the previously mentioned ProbABEL R packages. There are now a handful of useful R packages and other software utilities facilitating genome-wide association studies, analysis of imputed data, meta-analysis, efficient data storage, prediction, parallelization, and mixed model methods.
Sequencing technologies — the next generation
Authors: Turner Stephen
Published: December 2024

Following up on last week's coverage of the Genotyping Portal, check out this new review article on next-generation sequencing in Nature Reviews Genetics.  One major focus of this paper is that the next generation of sequencing platforms each use fundamentally different technologies.
Tutorial on the 1000 Genomes Project Data
Authors: Turner Stephen
Published: December 2024

There will be a (free) tutorial on the 1000 genomes project at this year's ASHG meeting on Wednesday, November 3, 7:00 – 9:30pm. You can register online at the link below.
Estimating Trait Heritability from GWAS Data
Authors:   Unknown
Published: December 2024

Peter Visscher and colleagues have recently published a flurry of papers employing a new software package called GCTA to estimate the heritability of traits using GWAS data (GCTA stands for Genome-wide Complex Trait Analysis -- clever acronymity!). The tool, supported (and presumably coded) by Jian Yang is remarkably easy to use, based in part on the familiar PLINK commandline interface.
Reproducible Research in the Omics Era: A Presentation and Panel Discussion
Authors: Turner Stephen
Published: December 2024

Seminar announcement for Vanderbilt folks:

Vanderbilt-Ingram Cancer Center

Quantitative Sciences Seminar Series

Presents

Reproducible Research in the Omics Era:

A Presentation and Panel Discussion

Kevin R. Coombes, PhD

Deputy Chair, Bioinformatics, and Professor of Bioinformatics and Computational BiologyM.D. Anderson Cancer Center and

Keith Baggerly, PhD

Associate Professor, Dept.
Twitter Roundup, January 4 2013
Authors: Turner Stephen
Published: December 2024

I've said it before: Twitter makes me a lazy blogger. Lots of stuff came across my radar this week that didn't make it into a full blog post.
PubMed Commons: One post-publication peer review forum to rule them all?
Authors: Turner Stephen
Published: December 2024

Several post-publication peer review forums already exist, such as Faculty of 1000 or PubPeer, that facilitate discussion of papers after they have already been published. F1000 only allows a small number of "faculty" to comment on articles, and access to read commentary requires a paid subscription. PubPeer and similar startup services lack a critical mass of participants to make such a community truly useful.
Pathway Analysis for High-Throughput Genomics Studies
Authors: Turner Stephen
Published: December 2024

I get a lot of requests in the core about running a "pathway analysis." Someone ran a handful of gene expression arrays, or better yet, ran an RNA-seq experiment (with replicates!). These, and many other kinds of high-throughput assays (GWAS, ChIP-seq, etc.) result in a list of genes and some associated p-value, fold change, or other statistic. Here's some R code to download public data from a study on susceptibility to colorectal cancer.
Friday Links: R, OpenHelix Bioinformatics Tips, 23andMe, Perl, Python, Next-Gen Sequencing
Authors: Turner Stephen
Published: December 2024

I haven't posted much here recently, but here is a roundup of a few of the links I've shared on Twitter (@genetics_blog) over the last two weeks.

Here is a nice tutorial on

accessing high-throughput public data

(from NCBI) using R and Bioconductor.

Cloudnumbers.com

, a startup that allows you to run high-performance computing (HPC) applications in the cloud, now supports the previously mentioned R IDE, RStudio.
Federal Courts Invalidate Myriad's Breast Cancer Gene Patents
Authors: Turner Stephen
Published: December 2024

A District Court handed down a summary judgment invalidating most of Myriad's claims to both the BRCA1 DNA sequence and the method of testing for early-onset familial breast and ovarian cancer. See Genetic Future and Genomics Law Report for analysis.Getting Genetics Done by Stephen Turner is licensed under a Creative Commons Attribution (CC BY) License.
Comparing Sequence Classification Algorithms for Metagenomics
Authors: Turner Stephen
Published: December 2024

Metagenomics

is the study of DNA collected from environmental samples (e.g., seawater, soil, acid mine drainage, the human gut, sputum, pus, etc.). While traditional microbial genomics typically means sequencing a pure cultured isolate, metagenomics involves taking a culture-free environmental sample and sequencing a single gene (e.g. the 16S rRNA gene), multiple marker genes, or shotgun sequencing everything in the sample in order to
Annotables: R data package for annotating/converting Gene IDs
Authors: Turner Stephen
Published: December 2024

I work with

gene lists

on a nearly daily basis. Lists of genes near ChIP-seq peaks, lists of genes closest to a GWAS hit, lists of differentially expressed genes or transcripts from an RNA-seq experiment, lists of genes involved in certain pathways, etc. And lots of times I’ll need to convert these gene IDs from one identifier to another. There’s no shortage of tools to do this. I use Ensembl Biomart.
The Impact of Workplace Inequality on Employee Performance: Moderating Role of Work Social Support and Workplace Resilience in Mitigating the Effect of Perceived Discrimination
Authors: Sana Mukhtar  , Dr. Muhammad Ibrahim
Published: December 2024

This paper aims to examine how workplace inequality effect employee performance of Academia of South Punjab, Pakistan; exploring the mediation role of perceived discrimination and moderating role of work social support and workplace resilience. The targeted population for this research comprised the 470 employees (faculty) in the academia of South Punjab in Pakistan. These participants included a diverse range of faculty members from numerous academic fields, offering a complete view of the impact of workplace inequality in the academic sector. As per the research, workplace inequality effects the employee performance. Workplace inequality is a serious and pervasive issue, affecting both employee productivity and ability to design job responsibilities. This study delves into intricate dynamics of workplace inequality, and analyzes the impact of workplace inequality on employee performance by examining the moderating role of work social support and resilience. The negative impacts of inequality are exacerbated by perceived discrimination, which causes disengagement and reduces desire for proactive efforts such as employee performance. Moreover, the study also examines how the impact of work social support and resilience can influence results. Receiving emotional and practical help from colleagues and supervisors at work, known as workplace social support, can decrease the negative effects of inequality and discrimination by lowering stress levels and fostering a more inclusive atmosphere. Resilience, as a characteristic of individuals, helpsemployees to recover from obstacles, reducing the impact of stress and encouraging a proactive approach to adapting work duties in challenging circumstances. This research highlights the importance of addressing workplace inequity and establishing supportive work atmosphere in order to enhance both employee performance and their efficiency
Entropy techniques for robust management decision making in high-dimensional data
Authors: Kalina Jan
Published: December 2024

Entropy, a key measure of chaos or diversity, has recently found intriguing applications in the realm of management science. Traditional entropy-based approaches for data analysis, however, prove inadequate when dealing with high-dimensional datasets. In this paper, a novel uncertainty coefficient based on entropy is proposed for categorical data, together with a pattern discovery method suitable for management applications. Furthermore, we present a robust fractal-inspired technique for estimating covariance matrices in multivariate data. The efficacy of this method is thoroughly examined using three real datasets with economic relevance. The results demonstrate the superior performance of our approach, even in scenarios involving a limited number of variables. This suggests that managerial decision-making processes should reflect the inherent fractal structure present in the given multivariate data. The work emphasizes the importance of considering fractal characteristics in managerial decision-making, thereby advancing the applicability and effectiveness of entropy-based methods in management science.
Understanding the attitudes towards climate change in the context of trust in selected countries of Central and Eastern Europe
Authors: Deák Zsuzsanna , Vaznonienė Gintarė , Wojewódzka-Wiewiórska Agnieszka
Published: December 2024

Although there is a growing trend in scientific and political discussions about how people feel about climate change in the context of trust, adequate research in this area is lacking in Central Eastern Europe (CEE). This article aims to determine whether trust is an important factor for the perception of climate change by the inhabitants of selected CEE countries. European Social Survey (ESS) Round 10 data were used, and a multivariable binary logistic regression method was applied. This paper considers three different dimensions of climate change, concern, personal norms, and attribution, as well as a composite indicator reflecting climate attitudes (skeptic or proponent). Four different models are presented that differ only in terms of their dependent variables, while the independent variable (trust) and the control variables (socio-demographic variables) are the same in all the cases. The results show that both personal and institutional trust are very low in the selected countries. Institutional trust was significant in all four models, while personal trust was significant in the environmental norm and skepticism models. Greater trust in institutions decreases the odds of being worried about climate change and increases the odds of having feelings of personal responsibility for climate change reduction. An increased level of personal or institutional trust increases one's chances of being in the climate proponent group. Of the socio-demographic variables examined only political left-right scale did not affect attitudes significantly.
Public debt management in Serbia during transition, Great Recession and COVID-19 pandemic
Authors: Andrić Vladimir
Published: December 2024

This paper examines the nonlinear asymmetric behaviour of the public debt/GDP ratio in Serbia in the first two decades of economic transition following the political and market reforms started at the beginning of the twenty-first century. Using quarterly data for the government debt-to-GDP ratio, a two-regime self-exciting threshold autoregressive (SETAR) model of order one finds a public debt/GDP ratio threshold of 66.2% above which fiscal policymakers in Serbia take corrective action in the form of increased fiscal prudence. The estimated government debt/GDP ratio threshold corresponds to a 60% threshold from the Maastricht fiscal criteria and shows how fiscal authorities in Serbia systematically ignore the 45% public debt/GDP limit set in the national fiscal rules. Such fiscal policy behaviour could jeopardize the credibility of fiscal institutions in Serbia and have a negative impact on fiscal discipline and the likelihood of sovereign default.
Status of Ornamental Plant Production in Iloilo: Problems and Prospects
Authors: Lopez Crisanto , Ballano Monica
Published: December 2024

This study was designed to survey the status and problems of ornamental plant production in Iloilo; specifically to determine the practices of the respondents regarding the use of inorganic and organic fertilizers and chemicals. It also aimed to possibly identify and quantify the commercial pesticides used by the commercial growers both in the ornamental and cutflower industry. A questionnaire validated by experts and pre-tested among plant growers was used to gather information from the respondents. Final phase of the study was to add more depth to their answers to the questionnaire
The survey revealed that commercial fertilizers (14-14-14 and 46-0-0) are still popular as 93% of the respondents use them using since they are easy to use, are readily available and have immediate effect on the growth of plants. Majority of the respondents (73%) were regularly spraying commercial pesticides once a month, such as Tamaron, Cymbush, and Malathion while the rest used crushed pepper mixed in water and lemon grass as organic pesticides sprayed monthly. Contrary to the fact that 74% of the growers favor the use of organic fertilizers such as cow, hog, and carabao manures, however, 16% are actually using these. It is recommended that a strong and vigorous campaign on awareness program should be undertaken by concerned agencies on the long-term benefits of using organic fertilizers for the sake of well-being and the environment.
Editorial
Authors: Barsky Osvaldo
Published: December 2024

En este n˙mero se incluyen an·lisis de distintos momentos del sistema universitario argentino vinculados a la evoluciÛn de la situaciÛn polÌtica del paÌs.
La Tragedia Silenciada. La Persecución de la Educación Superior Salesiana en Bahía Blanca
Authors: Tanos Padre  Guillermo
Published: December 2024

La noche del 21 de marzo de 1975 se inscribió en la memoria colectiva de la comunidad salesiana debido a la trágica invasión de una vivienda que albergaba a sacerdotes dedicados a la Educación Superior, quienes fueron injustamente acusados de subversivos. Este artículo se propone analizar los acontecimientos históricos que condujeron a este acto de violencia irracional, examinando las diversas causas históricas, políticas, eclesiales y sociales que catalizaron este episodio sangriento. La Educación Superior se establece como un eje central, resaltando cómo esta institución sufrió una severa represión y la pérdida de vidas. Gracias a la recopilación de documentos y escritos del archivo salesiano de Bahía Blanca, se logra abordar la escasez de información existente y el limitado testimonio de los sobrevivientes. La vida de cada uno de los afectados inspira a la comunidad académica a seguir sembrando paz y compromiso con aquellos que más lo necesitan, subrayando así la relevancia de la memoria colectiva en contextos que pueden reivindicar la violencia desde diversas ideologías.
PHONETICS IN DIGITAL MEDIA: IMPLICATIONS FOR SPEECH RECOGNITION TECHNOLOGY
Authors: Insyra Pasaribu Attala Rania , Al Khalili Muhammad Miftah
Published: December 2024

Phonetics, a branch of linguistics, examines the production, transmission, and perception of speech sounds, divided into articulatory, acoustic, and auditory subfields. Each area provides unique insights into how language sounds are generated, transmitted, and interpreted. This study explores the implications of phonetics in advancing digital speech recognition technology, particularly focusing on phoneme variation, intonation, and accent recognition. A research and development (R&D) methodology was employed, encompassing analysis, design, implementation, and evaluation stages to develop a prototype system integrating phonetic principles. The mixed-method approach combined qualitative and quantitative analyses to ensure a comprehensive evaluation of phonetics' integration in speech recognition technology. The research underscores the critical role of articulatory phonetics in modeling the production of diverse phonemes and accents, especially in complex languages like Arabic, which features unique phonemes such as pharyngeal sounds and emphatics. Findings reveal phonetics as foundational to developing inclusive and efficient Arabic speech recognition technology, with applications in language education, religious recitation, customer service, and linguistic research. This technology offers transformative potential for oral tradition preservation, inclusivity in services, and economic opportunities in the Arabic-speaking market, fostering accessibility and cultural preservation. The research highlights the interdisciplinary potential of phonetics to drive innovation, enhance social inclusion, and support the sustainable development of speech-based technologies in the digital era.