bluuebunny/crossref_metadata_2025 huggingface dataset:
Rekreasyon İşletmelerinde Stratejik Yönetim: Genel Bir Değerlendirme
Authors: Akdeniz Burcu
Published: December 2024

Teknolojik gelişmeler ve ekonomik koşulların değişmesi bireylerin boş zamanlarını artırmaktadır. Değişen sosyal hayat ve kültürel normlar ise toplumun her kesiminden insanların bu zamanı kişisel ilgilerine göre verimli bir şekilde değerlendirme ihtiyacını giderek daha fazla ön plana çıkarmaktadır. Rekreasyon insanların çalışmak ve zorunlu ihtiyaçlarını karşılamaktan arta kalan zamanda gönüllü olarak katıldıkları aktif veya pasif faaliyetlerin tümünü ifade etmektedir. Rekreatif faaliyetler turizm sektörü ile sınırlı olmayıp son derece çeşitlidir. Ayrıca toplumun sadece belirli bir gelir düzeyine sahip kesimine de hitap etmemektedir. Genç, yaşlı, çocuk, engelli toplumun her kesiminden bireylerin kendini gerçekleştirme ihtiyaçlarının karşılanması ve hayattan zevk almaları için hem kamu kurumları hem de özel sektör işletmelerinin çeşitli alternatifler sunarak topluma hizmet etmeleri mümkündür. Rekreatif işletmelerin varlığı ekonomiye katkısının yanı sıra toplumsal hayatı geliştirmeleri, bireylerin sosyalleşme ihtiyacını karşılamaları ve hem beden hem de ruh sağlıklarına katkıları nedeniyle de son derece gereklidir. Tüm özel sektör işletmelerinin olduğu gibi rekreasyon işletmelerinin de uzun vadeli sürdürülebilirlik ve rekabet avantajı sağlamak amacıyla stratejik yönetim konusunu ciddiyetle ele almaları gerekir. İnovasyon ve girişimcilik açısından son derece geniş seçenekler sunan ve çoğunlukla rekabetin üst düzeyde olduğu bu sektörde işletmelerin güçlü temel yetenekler üzerine kurulması, ürünlerinin taklit edilmemesi açısından patent ve ticari hakların hukuki açıdan korunması konularında bilinçli davranması, sosyal becerileri kuvvetli, eğitimli ve yetenekli personel çalıştırarak bu kişileri elde tutmaya yarayacak insan kaynakları yönetimi stratejileri uygulaması önerilmektedir. Sosyo-ekonomik değişikliklere karşı son derece hassas, yenilik, gelişim ve yaratıcı fikirlere açık böylesi bir iş alanında etkili bir stratejik yönetim yaklaşımı şüphesiz ki karlı işletmeler için bir ön koşuldur. Bu bölümde stratejik yönetim alanında kısıtlı bir şekilde ele alınmış olan rekreatif işletmelere değinilecek, daha ayrıntılı şekilde ele alınması gereken bu konuya sektörden örnekler ile genel bir giriş yapılacaktır.
Yeşil Pazarlama Bağlamında Yeşil Aklama Kavramına Genel Bir Bakış
Authors: Kavaslar Sare
Published: December 2024

Bu bölüm, çevre sorunlarının artışıyla birlikte işletmelerin sürdürülebilirlik sorumluluğunu ve yeşil pazarlamanın önemini vurgulamaktadır. Yeşil pazarlama, çevre dostu ürün ve hizmetlerin ötesine geçerek tüketici güvenini kazanmayı hedeflemektedir. Yeşil pazarlama faaliyetlerinin başlaması ile birlikte tanınabilirlik, yüksek kâr marjı beklentisi gibi çeşitli nedenlerle bazı işletmelerin yeşil aklama (greenwashing) uygulamalarına yöneldiği de bilinmektedir. Çalışmada öncelikle, yeşil pazarlamanın tanımı, tarihçesi ve kavramsal çerçevesini açıklanmaktadır bununla birlikte yeşil aklama ve tüketici algısına da yer verilmektedir. Bu bağlamda, yeşil aklamanın işletmelerin çevresel çabalarını nasıl olumsuz etkileyebileceği ve buna karşı geliştirilebilecek mücadele stratejileri incelenmektedir. Ayrıca, bazı işletmelerin yeşil aklama örneklerine yer verilerek, tüketiciye şeffaf bilgi sunmanın önemine değinilmektedir. Çalışma, yeşil pazarlamanın ve yeşil aklamayla mücadelenin, işletmelerin uzun vadeli sürdürülebilirlik hedeflerine katkıda bulunabilecek gelecekteki pazarlama stratejilerini nasıl şekillendirebileceğini teorik olarak ele almayı amaçlamaktadır.
Dünya’da ve Türkiye’de Turizmde Konaklama Vergisi Uygulamalarının Değerlendirilmesi
Authors: Bahçe Abdullah Burhan , Bahçe Ezgi
Published: December 2024

Turizm, insanların kişisel veya ticari/mesleki amaçlarla olağan çevrelerinin dışındaki yerlere veya ülkelere hareketini içeren yaygın, kültürel ve ekonomik bir faaliyettir. Turizm, uygulandığı yerin veya ülkenin gelirini artırmak, sağlanacak kamusal mal ve hizmetlerin maliyetlerini dengelemek ve turizm sektöründeki piyasa başarısızlıklarını veya olumsuz dışsallıkları gidermek amacıyla turistik faaliyetlerin başlangıcından itibaren vergilendirilen bir faaliyet olmuştur. Avrupa Birliği'nde ve dünyada popüler şehirler veya ülkeler, turizmden kaynaklanabilecek olumsuz etkileri azaltmak veya önlemek ve turizm sektöründen ekstra gelir elde etmek amacıyla çeşitli isimler altında konaklama vergisi uygulamaktadır. Dünya genelindeki konaklama vergisi uygulamalarına bakıldığında, bu vergilerin genellikle ülkeyi gündüz veya gece ziyaret eden ziyaretçilerden tahsil edildiği ve bölgenin veya mevsimin konumuna bağlı olarak değişebildiği görülmektedir. Bu çalışmada dünyada ve Türkiye'de turizme uygulanan konaklama vergisi türleri, sınıflandırılmaları, oranları ve vergi gelirlerinin nasıl kullanılacağı gibi temel bilgiler ülke ve şehir örnekleri üzerinden değerlendirilmektedir. Bu bağlamda, Türkiye'de uygulanan konaklama vergisine ek olarak, İstanbul ve Antalya gibi önemli turizm destinasyonları için ekstra şehir vergisi uygulamalarına ilişkin öneriler sunulmaktadır.
Dijital Hizmet Vergisi: Uygulama Örnekleri
Authors: Aleçakır Hasan Hüseyin , Altıok Gülistan
Published: December 2024

Bu çalışmanın amacı, Türkiye'de ve dünyada Dijital Hizmet Vergisi (DST) uygulamalarını incelemektir. Dijitalleşme, bilgi ve süreçlerin dijital teknolojiler aracılığıyla dönüştürülerek daha verimli, daha hızlı ve daha erişilebilir hale getirilmesidir. Bilgisayar ve internetin yaygınlaşmasıyla birlikte dijitalleşme süreci hızlanmakta ve yeni iş modellerinin ortaya çıkmasıyla birlikte ekonomik sistemler değişmektedir. Yeni iş modelleri, mallar ve hizmetler arasındaki ayrımı bulanıklaştırmaktadır. Şirketler, özellikle de çok uluslu şirketler, merkezlerini düşük vergi oranlarına sahip ülkelerde kurabilmekte ve dünyanın herhangi bir ülkesine hizmet sunabilmektedir. Sonuç olarak ülkeler vergi gelirlerini kaybetmektedir. Birçok ülke OECD'nin öncülüğünde bu vergi kayıplarını önlemek için DHV uygulamalarını benimsemektedir. DHV şu anda 26 ülkede uygulanmakta ve 8 ülkede de uygulanması beklenmektedir. DHV'nin konusu, oranı ve kapsamı ülkeden ülkeye değişmekle birlikte  amaç dijital hizmet sağlayan şirketleri vergilendirmek ve vergi kayıplarını önlemektir. Türkiye dijital hizmetlere nispeten yüksek bir vergi oranı uygulamaktadır (%7,5) ve vergi oranı yıllar içinde değişmese de dijital hizmetler vergisinin toplam vergi geliri içindeki payı artmaktadır.
Kuruluşundan Bugüne Türkiye Cumhuriyeti’nin Dış Borçlanma Serüveni
Authors: Gezer Tuba
Published: December 2024

Borçlanma, ülkelerin kendi kaynaklarının yeterli olmadığı durumlarda bir zorunluluk unsuru olmakla birlikte bazen de bir ekonomi politikası aracı olarak kullanılmaktadır. Ülkelerin borçlanırken dikkat etmesi gereken temel konu borçlanmanın Gayri Safi Milli Hasıla'ya oranıdır. Bu oran belli bir seviyeyi aştığında ülke ekonomisi borç yönetiminde sorunlar yaşar. Hem gelişmiş hem de gelişmekte olan ülkeler kalkınma için borçlanmaya başvurmaktadır. Ancak gelişmekte olan ülkeler iç kaynaklarının yetersizliği nedeniyle daha fazla dış borçlanmaya ihtiyaç duymaktadır. Dış borçlar ülkeleri ekonomik ve sosyal olarak etkilemektedir.
Çalışmanın amacı, kuruluşundan bu yana Türkiye Cumhuriyeti’nin dış borç politikasını ve sonuçlarını analiz etmektir. Bu doğrultuda çalışmada öncelikle devlet borçlanmasının teorik yönleri incelenmiş, ardından dış borç kavramı, türleri ve nedenlerine değinilmiştir. Son olarak, Türkiye'de dış borçların gelişimi Cumhuriyet dönemi (1923-1946), Planlı Kalkınma öncesi dönem (1946-1960), Planlı Kalkınma dönemi (1960-1980), 1980-2000 ve 2000'den günümüze ayrı ayrı analiz edilmiştir. Sonuç olarak, Türkiye özellikle kuruluş yıllarında dış borçlanmaya fazla başvurmamıştır. 1950 sonrası dönem ise dış borçlanmaya en çok başvurulan dönem olmuştur. Petrol Krizi ve Kıbrıs Barış Harekâtı gibi ekonomik ve siyasi durumlar dış borç stokunu artırmıştır. 1980 sonrasında sermaye hareketlerinin serbestleşmesiyle birlikte ülkedeki dış borç miktarı daha da artmıştır. Dış borçlardaki artış ülkenin 1994 yılında krize girmesine neden olmuştur. 2001 krizinden sonra güçlü ekonomiye geçiş programı ve 4749 sayılı Kamu Finansmanı ve Borç Yönetiminin Düzenlenmesi Hakkında Kanun ile borç yönetiminde kontrol sağlanmıştır. Türkiye'de borçlar sürdürülebilir hale gelmiştir. Ancak 2008 Küresel Ekonomik krizi sonrasında küresel piyasalarda yaşanan olumsuz gelişmeler, Türkiye'nin yeni borç almak yerine eski borçlarını ödemesine neden olmuştur. Son yıllarda yaşanan kur atakları ve Covid-19 krizi sonrasında özel sektörün borç miktarı azalmış, kamunun payı artmıştır. Bu çalışmada ele alınan çeşitli gösterge rasyolarına göre Türkiye'nin dış borç göstergeleri hala olumlu sinyaller vermemektedir.
Yapay Zekâ Destekli Geri Dönüşüm Sistemleri: İklim Değişikliğine Karşı Sürdürülebilir Çözümler
Authors: Saygılı Balcı Hilal , Erdem Tevfik
Published: December 2024

Bu çalışma, iklim krizinin küresel etkileri ile bu krize karşı gelişen yeni toplumsal hareketleri ve yeni dalga iklim aktivizmini ele almaktadır. İklim krizi, yalnızca çevresel değil, aynı zamanda sosyal ve sağlık alanında da derin etkiler yaratmakta; şehir merkezlerinde artan sıcaklıklar ve uygun olmayan iklim koşulları nedeniyle her yıl milyonlarca insan hayatını kaybetmektedir. Bu durum, iklim krizini yalnızca bir çevre sorunu değil, aynı zamanda bir halk sağlığı ve sosyal adalet meselesi haline getirmektedir. Fridays for Future, Extinction Rebellion ve Sunrise Movement gibi yeni dalga hareketler, iklim krizine karşı küresel bir farkındalık oluşturmayı ve sosyal değişim sağlamayı amaçlamaktadır. Çalışmada, bu hareketlerin çıkış nedenleri, stratejileri ve toplumsal etkileri analiz edilmiş; iklim krizine yönelik mücadelede daha geniş bir katılım sağlamak için siyasi ve ekonomik yapılarla olan ilişkileri değerlendirilmiştir. Aynı zamanda, yeni dalga iklim aktivizmine yönelik bazı noktalar eleştirel bir bakış açısı ile tahlil edilmiş ve geleceğe yönelik tavsiyelerde bulunulmuştur.
Artificial Intelligence and the Future of Digital Marketing
Authors: Juriah Siti , Susilastuty Darwati
Published: December 2024

This research aims to explore the use of artificial intelligence (AI) in digital marketing among MSME practitioners in Indonesia. In an increasingly evolving digital era, understanding and implementing AI technology becomes crucial for MSMEs to improve their competitiveness and marketing effectiveness. This study involved 50 respondents who are MSME actors and used a quantitative method with questionnaires to collect data. The results indicate that 72% of respondents have a basic understanding of AI; however, only 44% have implemented AI-based tools in their marketing strategies. Furthermore, linear regression analysis revealed a significant relationship between the use of AI and increased sales, with a regression coefficient of 0.75 (p < 0.01), demonstrating that the use of AI positively contributes to marketing outcomes. The study also found that the use of AI tools such as chatbots and automated copywriting can enhance customer engagement. Although MSME actors show awareness of AI's potential, there exists a gap between knowledge and practice. Therefore, this research recommends the need for greater training and support for MSMEs to maximize the use of AI in their digital marketing strategies. The findings are expected to provide insights for stakeholders and policymakers in designing initiatives that support the integration of AI technology in MSME businesses, allowing them to adapt to changes and improve marketing effectiveness.
Aziz Augustine’in Sevgi Kavramı Çerçevesinde Ümit Ünal’ın Sofra Sırları Filminde Aşk ve Adalet
Authors: Gençalp Hüseyin
Published: December 2024

Ortaçağ Felsefesinin başat düşünürlerinden biri olduğu ifade edilen Aziz Augustine’in sevgi etiği, bireyin eylemlerini yönlendiren temel unsurun aşk/sevgi olduğu fikri üzerine bina edilmiştir. Bu bağlamda bütün insanları sevgilerinin niteliği ve bu sevgilerin yöneldiği nesneler özelinde değerlendirerek, iyi ya da kötü, adil ya da adaletsiz olduklarına karar vermek mümkündür. Söz konusu bu durum sinemasal evrenler için de geçerlidir. Film dünyalardaki karakterlerin davranışlarını, bu davranışların eyleme dökülmesine kaynaklık eden irade ve sevgi nosyonu üzerinden irdelemek, karakterlerin edimlerini Augustine’in söylemleri kapsamında ahlaki bir bakış açısıyla ele alma imkânı sağlarken aynı zamanda izleyicilerin zihinlerinde adil ve adaletli eylemlere ilişkin etik sorgulamaları da tetikler. Bu çalışma, felsefe olarak film anlayışı çerçevesinde, Ümit Ünal’ın Sofra Sırları filminin sinematik evrenini, Augustine’in etik felsefesinin merkezinde yer alan sevgi ve adalet kavramları özelinde incelemeyi amaçlamaktadır. Bu kapsamda Gilles Deleuze ve Daniel Frampton’un düşüncelerinden hareketle, film-zihnin, kendi film-dünyasına ilişkin film-düşünmeleri karakterlerin eylem ve söylemleriyle ilgili ahlaki değerlendirmeler üzerinden ortaya konulmaya çalışılmıştır.
Male involvement and perception towards prevention of malnutrition of children less than 5 years in Ishaka division Bushenyi-district
Authors:   Department of Nursing, Kampala International University, Uganda, Anitah Asiimwe
Published: December 2024

This study was undertaken to assess male involvement and perception towards prevention of malnutrition of children less than 5 years in Ishaka Division Bushenyi district. The study design was a cross-sectional descriptive study, carried out in Ishaka division found in Bushenyi district involving 85 males with children below five years and residents of Ishaka Division, selected by simple random sampling. The study showed that there was poor male involvement 32(37%) towards prevention of malnutrition, with majority 28(52.8%) saying it was the duty of women to feed children. The study showed a poor perception of participants towards prevention of malnutrition, majority 29(54.7%) of those who had not been fully involved in child nutrition said it was not necessary to give children special attention for their nutrition needs, the study established that knowing signs of malnutrition in children was a significant factor for males to be involved in prevention of malnutrition for their children with an odds ratio of 0.22(0.09-11.0 and a p-value of 0.003. The result showed that culture was not a significant factor in influencing male involvement in child nutrition, with an odds ratio 3.47(0.14-12.10 and a p-value of 0.128. In conclusion, there was a poor male involvement and perception towards prevention of malnutrition in under five children.

Keywords: Male involvement, Child malnutrition prevention, Perception of child nutrition, Under-five nutrition, Ishaka Division study
Risks of Long-Term Steroid Use: Balancing Efficacy with Adverse Effects
Authors:   Faculty of Science and Technology Kampala International University Uganda, Muthoni L. Kibibi
Published: December 2024

Corticosteroids, synthetic analogs of cortisol, are pivotal in managing chronic inflammatory and autoimmune conditions due to their potent anti-inflammatory and immunosuppressive properties. While these medications significantly enhance patient quality of life by rapidly alleviating symptoms, their long-term use poses serious risks, including metabolic disorders, musculoskeletal issues, endocrine complications, gastrointestinal problems, psychiatric effects, and increased susceptibility to infections. This review explores the common adverse effects associated with prolonged corticosteroid therapy, elucidates the mechanisms behind these risks, and discusses strategies for risk mitigation. A multifaceted approach that includes individualized treatment plans, continuous monitoring, patient education, and a multidisciplinary care model is essential for optimizing therapeutic benefits while minimizing potential harms. By striking a balance between efficacy and safety, healthcare providers can enhance patient outcomes and quality of life in individuals requiring long-term corticosteroid therapy. This comprehensive understanding of the risks associated with corticosteroids aims to empower clinicians in making informed treatment decisions that prioritize patient safety without compromising therapeutic efficacy.

Keywords: corticosteroids, long-term use, adverse effects, chronic inflammatory conditions, risk mitigation.
Operate on the body of a file but not the header
Authors: Turner Stephen
Published: December 2024

Sometimes you need to run some UNIX command on a file but only want to operate on the body of the file, not the header. Create a file called body somewhere in your $PATH, make it executable, and add this to it: #!/bin/bash IFS= read -r header printf '%s\n' "$header" eval $@ Now, when you need to run something but ignore the header, use the body command first.
R: single plot with two different y-axes
Authors: Turner Stephen
Published: December 2024

I forgot where I originally found the code to do this, but I recently had to dig it out again to remind myself how to draw two different

y

axes on the same plot to show the values of two different features of the data. This is somewhat distinct from the typical use case of aesthetic mappings in ggplot2 where I want to have different lines/points/colors/etc. for the

same

feature across multiple subsets of data.
Identifying Pathogens in Sequencing Data
Authors: Turner Stephen
Published: December 2024

I just read an interesting paper on pathogen discovery using next-generation sequencing data, recommended to me by Nick Loman. A previously described algorithm (PathSeq, Kostic et al) for discovering microbes by deep-sequencing human tissue uses computational subtraction, whereby the initial collection of reads is depleted of human DNA by consecutive alignment to the human reference using MAQ and BLAST.
Embed R Code with Syntax Highlighting on your Blog
Authors: Turner Stephen
Published: December 2024

Note 2010-11-17: there's more than one way to do this.
My thoughts on ICHG 2011
Authors:   Unknown
Published: December 2024

I’m a bit exhausted from a week of excellent science at ICHG. First, let me say that Montreal is a truly remarkable city with fantastic food and a fascinating blend of architectural styles, all making the meeting a fun place to be…. Now on to the genomics – I’ll recap a few of the most exciting sessions I attended. You can find a live-stream of tweets from the meeting by searching the #ICHG2011 and #ICHG hashtags.
UVA / Charlottesville R Meetup
Authors: Turner Stephen
Published: December 2024

TL;DR? We started an R Users group, awesome community, huge turnout at first meeting, lots of potential. --- I've sat through many hours of meetings where faculty lament the fact that their trainees (and the faculty themselves!) are woefully ill-prepared for our brave new world of computing- and data-intensive science.
Fix Overplotting with Colored Contour Lines
Authors: Turner Stephen
Published: December 2024

I saw this plot in the supplement of a recent paper comparing microarray results to RNA-seq results. Nothing earth-shattering in the paper - you've probably seen a similar comparison many times before - but I liked how they solved the overplotting problem using heat-colored contour lines to indicate density. I asked how to reproduce this figure using R on Stack Exchange, and my question was quickly answered by Christophe Lalanne.
A New Dimension to Principal Components Analysis
Authors:   Unknown
Published: December 2024

In general, the standard practice for correcting for population stratification in genetic studies is to use principal components analysis (PCA) to categorize samples along different

ethnic axes

.  Price et al. published on this in 2006, and since then PCA plots are a common component of many published GWAS studies.
An example RNA-Seq Quality Control and Analysis Workflow
Authors: Turner Stephen
Published: December 2024

I found the slides below on the education page from Bioinformatics & Research Computing at the Whitehead Institute. The first set (PDF) gives an overview of the methods and software available for quality assessment of microarray and RNA-seq experiments using the FastX toolkit and FastQC. The second set (PDF)  gives an example RNA-seq workflow using TopHat, SAMtools, Python/HTseq, and R/DEseq.
The Sweeping Assumptions of GWAS
Authors:   Unknown
Published: December 2024

As a graduate student a few years ago, I learned about (and in some cases witnessed) the various phases, fads, and revolutions in the field of human genetics. The mid to late 90's saw a shift from family-based linkage analysis to a plethora of small candidate gene studies. The early 2000's saw the completion of the human genome project, the development of the HapMap project, and the birth of genome-wide association studies.
Using and Abusing Data Visualization: Anscombe's Quartet and Cheating Bonferroni
Authors: Turner Stephen
Published: December 2024

Anscombe’s quartet comprises four datasets that have nearly identical simple statistical properties, yet appear very different when graphed. Each dataset consists of eleven (

x

,

y

) points. They were constructed in 1973 by the statistician Francis Anscombe to demonstrate both the importance of graphing data before analyzing it and the effect of outliers on statistical properties. Let’s load and view the data.
Compiling RMarkdown from a Helper R Script
Authors: Turner Stephen
Published: December 2024

The problem I was looking for a way to compile an RMarkdown document and have the filename of the resulting PDF or HTML document contain the name of the input data that it processed. That is, if I compiled the analysis.Rmd file, where in that file it did some analysis and reporting on data001.txt, I’d want the resulting filename to look something like data001.txt.analysis.html.
Find the function you're looking for in R
Authors: Turner Stephen
Published: December 2024

Any R user no matter what level of experience has had trouble finding the package or the function to do what you want to do and then figuring out how to use it.  The sos package in R just made that a lot easier. First, fire up R, then install the sos package (don't omit the quotes): install.packages("sos") It'll ask you to choose a mirror.  Choose the closest one.
Free one-day R course at Vanderbilt
Authors: Turner Stephen
Published: December 2024

The Vanderbilt Kennedy Center is offering a free (repeat, free) one-day introductory course to the R statistical computing language on June 23, taught by Theresa Scott from the department of Biostatistics. You can find contact/registration info at the link below.Vanderbilt Kennedy Center - An Introduction to the Fundamentals &
Nucleic Acids Research Web Server Issue
Authors: Turner Stephen
Published: December 2024

Nucleic Acids Research just published its Web Server Issue, featuring new and updates to existing web servers and applications for genomics and proteomics research. In case you missed it, be sure to check out the Database Issue that came out earlier this year. This web server issue has lots of papers on tools for microRNA analysis, and protein/RNA secondary structure analysis and annotation.
Prune GWAS data in R
Authors: Turner Stephen
Published: December 2024

Hansong Wang, our biostats professor here at the Hawaii Cancer Center, generously gave me some R code that goes through a SNP annotation file (i.e. a mapfile) and selects SNPs that are at least a certain specified distance apart. You might want to do this if you're picking a subset of SNPs for PCA, for instance.
What happens when a consumer genetics company goes bankrupt?
Authors: Turner Stephen
Published: December 2024

Dan Vorhaus and Lawrence Moore recently put together this excellent three part series on Genomics Law Report.  Headlines about deCODE Genetics on the brink of insolvency and major shifts in the upper management of 23andMe inspired this series of posts on what would happen when a direct-to-consumer (DTC) genomics company goes declares bankruptcy.
Staying Current in Bioinformatics & Genomics: 2017 Edition
Authors: Turner Stephen
Published: December 2024

A while back I wrote this post about how I stay current in bioinformatics & genomics. That was

nearly five years ago

. A lot has changed since then. A few links are dead.
Parallelize IBD estimation with PLINK
Authors: Turner Stephen
Published: December 2024

Obtaining the probability that zero, one, or two alleles are shared identical by descent (IBD) is useful for many reasons in a GWAS analysis. A while back I showed you how to visualize sample relatedness using R and ggplot2, which requires IBD estimates. Using plink --genome uses IBS and allele frequencies to infer IBD.
Introductory statistics with R
Authors: Turner Stephen
Published: December 2024

I know that a lot of you are scrambling to spend your training grant money by next week. If you think you'll ever need to use R, I strongly recommend buying this book: Introductory Statistics with R, by Peter Dalgaard ($48, Amazon). I picked this up a while back and read through most of it in a day or two.
A Primer on Logistic Regression (using Stata)
Authors: Turner Stephen
Published: December 2024

This handy introduction comes from UCLA's Statistical Computing webbook on logistic regression. If you're familiar with linear regression but you've never used logistic regression before, this is a good place to start.
More on Exploring Correlations in R
Authors: Turner Stephen
Published: December 2024

About a year ago I wrote a post about producing scatterplot matrices in R. These are handy for quickly getting a sense of the correlations that exist in your data. Recently someone asked me to pull out some relevant statistics (correlation coefficient and p-value) into tabular format to publish beside a scatterplot matrix.
Importing Illumina BeadArray data into R
Authors: Turner Stephen
Published: December 2024

A colleague needed some help getting Illumina BeadArray gene expression data loaded into R for data analysis with limma. Hopefully whoever ran your arrays can export the data as text files formatted as described in the code below. If so, you can import those text files directly using the beadarray package.
Visualizing sample relatedness in a GWAS using PLINK and R
Authors: Turner Stephen
Published: December 2024

Strict quality control procedures are extremely important for any genome-wide association study.  One of the first steps you should take when running QC on your GWAS is to look for related samples in your dataset.  This does two things for you.
Biostar Tutorial: Cheat sheet for one-based vs zero-based coordinate systems
Authors: Turner Stephen
Published: December 2024

Obi Griffith over at Biostar put together this excellent cheat sheet for dealing with one-based and zero-based genomic coordinate systems. The cheat sheet visually explains the difference between zero and one-based coordinate systems, as well as how to indicate a position, SNP, range, or indel using both coordinate systems.
Stop Hosting Data and Code on your Lab Website
Authors: Turner Stephen
Published: December 2024

It's happened to all of us. You read about a new tool, database, webservice, software, or some interesting and useful data, but when you browse to http://instititution.edu/~home/professorX/lab/data, there's no trace of what you were looking for.

THE PROBLEM

This isn't an uncommon problem. See the following two articles: The first gives us some alarming statistics.
Seminar: Pathway-based analysis for genome-wide association studies
Authors: Turner Stephen
Published: December 2024

Vanderbilt Epidemiology Center, Institute for Medicine and Public Health presents: "Pathway-based analysis for genome-wide association studies" Steven Chen Ph.D Assistant Professor of Biostatistics Tuesday, March 16, 2010 9:00 AM - 10:00 AM 2525 West End Avenue 6th Floor BoardroomGetting Genetics Done by Stephen Turner is licensed under a Creative Commons Attribution (CC BY) License.
Get the full path to a file in Linux / Unix
Authors: Turner Stephen
Published: December 2024

In the last post I showed you how to point to a file in windows and get the full path copied to your clipboard.  I wanted to come up with something similar for a Linux environment.  This is helpful on Vampire/ACCRE because you have to fully qualify the path to every file you use when you submit jobs with PBS scripts.
RNA-seq Data Analysis Course Materials
Authors: Turner Stephen
Published: December 2024

Last week I ran a one-day workshop on RNA-seq data analysis in the UVA Health Sciences Library. I set up an AWS public EC2 image with all the necessary software installed.
An Annotated Online Bioinformatics / Computational Biology Curriculum
Authors: Turner Stephen
Published: December 2024

Two years ago David Searls published an article in PLoS Comp Bio describing a series of online courses in bioinformatics. Yesterday, the same author published an updated version, "A New Online Computational Biology Curriculum," (PLoS Comput Biol 10(6): e1003662.
Webinar: Applications of Next-Generation Sequencing in Clinical Care
Authors: Turner Stephen
Published: December 2024

I just got an email from Illumina about a webinar that looks interesting this Wednesday at 9am PST (noon EST) on clinical applications of next-gen sequencing. Date: Wednesday, December 7, 2011Time: 9:00 AM (PST)Speaker: Rick Dewey, MD, Stanford Center for Inherited Cardiovascular Disease Next-generation sequencing (NGS) presents both challenges and opportunities for clinical care.
How to Read a Genome-Wide Association Study (@GenomesUnzipped)
Authors: Turner Stephen
Published: December 2024

Jeff Barret (@jcbarret on Twitter) over at Genomes Unzipped (@GenomesUnzipped) has posted a nice guide for the uninitiated on how to read a GWAS paper. Barret outlines five critical areas that readers should pay attention to: sample size, quality control, confounding (including population substructure), the replication requirement, and biological significance.
Obama names Francis Collins NIH Director
Authors: Turner Stephen
Published: December 2024

Yesterday President Barack Obama announced his intent to appoint former leader of the Human Genome Project, discoverer of delta-F508, and all around science rockstar Francis Collins as the director of the National Institutes of Health.In his statement, Obama noted: "The National Institutes of Health stands as a model when it comes to science and research.
Merging data from different files using R
Authors: Turner Stephen
Published: December 2024

A reader asked yesterday how you would merge data from two different files. For example, let's say you have a ped file with genotypes for individuals, and another file that had some other data for some of the individuals in the pedfile, like clinical or environmental covariates.
Video Tip: Convert Gene IDs with Biomart
Authors: Turner Stephen
Published: December 2024

I get asked frequently how to convert from one gene identifier to another. This can be tricky, especially when relying on gene symbols, as Will pointed out in a previous post a few years ago. There are several tools that can do this, including DAVID and the previously mentioned new Biomart ID Converter, but I still prefer using the Ensembl Biomart for this because of its added flexibility and annotation.
JBrowse: a JavaScript Based Genome Browser
Authors: Turner Stephen
Published: December 2024

Genome Browsers are nothing new, but JBrowse is a new JavaScript based genome browser that uses information from the UCSC genome browser and has the look and feel of Google Maps.  It's extremely easy to zoom in and out and scroll around because all the "work" is being done by your computer rather than some server farm thousands of miles away.
Using NCBI E-Utilities
Authors:   Unknown
Published: December 2024

NCBI has put a lot of effort into unifying their data access and retrieval system -- whether you are searching for a gene, protein, or publication, the results are returned in a similar fashion.
Microbiome Digest Blog
Authors: Turner Stephen
Published: December 2024

I have a noteworthy blogs tag on this blog that I sort of forgot about, and haven't used in years. But I started reading one recently that's definitely qualified for the distinction. The Microbiome Digest is written by Elisabeth Bik, a scientist studying the microbiome at Stanford.
Mixed linear model approach adapted for genome-wide association studies
Authors: Turner Stephen
Published: December 2024

A few weeks ago I covered an R package for efficient mixed model regression that is capable of simultaneously accounting for both population stratification and relatedness to compute unbiased estimates of standard errors and p-values for genetic association studies.
Use plyr instead of _apply() in R
Authors: Turner Stephen
Published: December 2024

I've covered plyr once before, showing you how to get means and variances for two quantitative traits across multilocus genotypes. JD Long over at Cerebral Mastication recently posted a nice screencast illustrating how plyr "just works" as an alternative to R's family of apply commands.
Browsing dbGAP Results
Authors:   Unknown
Published: December 2024

Thanks to the excellent work of Lucia Hindorff and colleagues at NHGRI, the GWAS catalog provides a great reference for the cumulative results of GWAS for various phenotypes.  Anyone familiar with GWAS also likely knows about dbGaP – the NCBI repository for genotype-phenotype relationships – and the wealth of data it contains.
List of Bioinformatics Workshops and Training Resources
Authors: Turner Stephen
Published: December 2024

I frequently get asked to recommend workshops or online learning resources for bioinformatics, genomics, statistics, and programming. I compiled a list of both online learning resources and in-person workshops (preferentially highlighting those where workshop materials are freely available online):

List of Bioinformatics Workshops and Training Resources

I hope to keep the page above as up-to-date as possible.
There is no Such Thing as Biomedical "Big Data"
Authors:   Unknown
Published: December 2024

At the moment, the world is obsessed with “Big Data” yet it sometimes seems that people who use this phrase don’t have a good grasp of its meaning.  Like most good buzz-words, “Big Data” sparks the idea of something grand and complicated, while sounding ordinary enough that listeners feel like they have an intuitive understanding of the concept.
GGD Launches!
Authors: Turner Stephen
Published: December 2024

Welcome!You've reached the first official post of Getting Genetics Done. The idea for this blog was a spin off of the short courses and workshops that Vanderbilt's Computational Genomics Core has recently been offering. Our goal for writing this is to share anything we use or hear of that makes life easier in genetics research, or boosts productivity throughout the workday in general.
Seminar: Spectral Anonymization Data
Authors: Turner Stephen
Published: December 2024

Thomas Lasko, MD, PhD, from Google Inc., Mountain View CA, will be giving a seminar next week entitled: "Spectral Anonymization Data" March 3, 2010 12:00 - 1:00 p.m. 214 Light Hall Abstract: The great challenge of data anonymization is to condition a dataset for public release such that it remains scientifically useful, but it does not disclose sensitive information about the individuals it describes.
Jeff Leek's non-comprehensive list of awesome things other people did in 2013
Authors: Turner Stephen
Published: December 2024

Jeff Leek, biostats professor at Johns Hopkins and instructor of the Coursera Data Analysis course, recently posted on Simly Statistics this list of awesome things other people accomplished in 2013 in genomics, statistics, and data science. At risk of sounding too

meta

, I'll say that this list itself is one of the awesome things that was put together in 2013.
Review: The challenges of sequencing by synthesis
Authors: Turner Stephen
Published: December 2024

A tip of the hat to a commenter on my previous coverage of a next-gen sequencing paper for pointing out this detailed and perhaps more technically-oriented review on sequencing by synthesis recently published in Nature Biotechnology.  Thanks, Clive. Review: The challenges of sequencing by synthesis (Nature Biotechnology)Getting Genetics Done by Stephen Turner is licensed under a Creative Commons Attribution (CC BY) License.
A generative AI podcast dialogue exploring The Geneva Learning Foundation’s progress in 2024
Authors: Sadki Reda
Published: December 2024

This experimental podcast, created in collaboration with generative AI, demonstrates a novel approach to exploring complex learning concepts through a conversational framework that is intended to support dialogic learning. Based on TGLF’s 2024 end-of-year message and supplementary materials, the conversation examines their peer learning model through a combination of concrete examples and theoretical reflection.
R Snippet for Sampling from a Dataframe
Authors:   Unknown
Published: December 2024

It took me a while to figure this out, so I thought I'd share. I have a dataframe with millions of observations in it, and I want to estimate a density distribution, which is a memory intensive process. Running my kde2d function on the full dataframe throws and error -- R tries to allocate a vector that is gigabytes in size. A reasonable alternative is to run the function on a smaller subset of the data.
Advanced QQ Plots in R
Authors:   Unknown
Published: December 2024

***Update Monday, November 09, 2009: The

sma

package is no longer available on CRAN.  See this updated post for making QQ-plots in R using ggplot2.***

Nearly everyone who has read a paper on a genome-wide association study should now be familiar with the QQ-plot.
RegulomeDB: Identify DNA Features and Regulatory Elements in Non-Coding Regions
Authors:   Unknown
Published: December 2024

Many papers have noted the challenges associated with assigning function to non-coding genetic variation, and since the majority of GWAS hits for common traits are non-coding, resources for providing some mechanism for these associations are desperately needed.
Real-time streaming differential RNA-seq analysis with eXpress
Authors: Turner Stephen
Published: December 2024

RNA-seq has been performed routinely for at least 5+ years, yet there is no consensus on the best methodology for analyzing this data.
R + ggplot2 Graph Catalog
Authors: Turner Stephen
Published: December 2024

Joanna Zhao’s and Jenny Bryan’s R graph catalog is meant to be a complement to the physical book, Creating More Effective Graphs, but it’s a really nice gallery in its own right. The catalog shows a series of different data visualizations, all made with R and ggplot2. Click on any of the plots and you get the R code necessary to generate the data and produce the plot.
Steal This Blog!
Authors: Turner Stephen
Published: December 2024

I wanted to contribute any content and code I post here to the R Programming Wikibook so I made a slight change to the Creative Commons license on this blog. All the written content is now cc-by-sa and all the code here is still open source BSD.
R clinic this week: Regression Modeling Strategies in R
Authors: Turner Stephen
Published: December 2024

At this week's R clinic Frank Harrell will unveil the new rms (Regression Modeling Strategies) package that is a replacement for the R Design package.  He will demonstrate the differences with Design, especially related to enhanced graphics for displaying effects in regression models.  Frank will also discuss the implementation of quantile regression in rms.
Not just another MDR paper
Authors: Turner Stephen
Published: December 2024

Nature Reviews Genetics just published an excellent paper on interaction analysis by Heather Cordell. This masterfully written review starts by defining interaction, then delving into strategies to statistically model it in human genetics studies.
Journal club notes coming soon
Authors: Turner Stephen
Published: December 2024

The Program in Computational Genomics holds a journal club twice a month. Our technical writer Julia Wall will soon start posting here references to the articles we talked about. Keep an eye out here to see some of the latest research we're discussing!Getting Genetics Done by Stephen Turner is licensed under a Creative Commons Attribution (CC BY) License.
Understanding the ENSEMBL Schema
Authors:   Unknown
Published: December 2024

ENSEMBL is a frequently used resource for various genomics and transcriptomics tasks.  The ENSEMBL website and MART tools provide easy access to their rich database, but ENSEMBL also provides flat-file downloads of their entire database and a public MySQL portal.  You can access this using the MySQL Workbench using the following: Once inside, you can get a sense for what the ENSEMBL schema (or data model) is like.
Illumina Onmi
Authors: Turner Stephen
Published: December 2024

Illumina recently announced their latest chip for GWA studies - the HumanOmni1-Quad.
Get Started with Machine Learning in R
Authors: Turner Stephen
Published: December 2024

A Beautiful WWW

put together a great set of resources for getting started with machine learning in R.  First, they recommend the previously mentioned free book, The Elements of Statistical Learning.  Then there's a link to a list of dozens of machine learning and statistical learning packages for R.  Next, you'll need data.  Hundreds of free real datasets are available at the UCI machine learning repository.
The HaploREG Database for Functional Annotation of SNPs
Authors:   Unknown
Published: December 2024

The ENCODE project continues to generate massive numbers of data points on how genes are regulated.  This data will be of incredible use for understanding the role of genetic variation, both for altering low-level cellular phenotypes (like gene expression or splicing), but also for complex disease phenotypes.  While it is all deposited into the UCSC browser, ENCODE data is not always the easiest to access or manipulate.
Replication of >180 Genetic Associations with Self-Report Medical Data
Authors: Turner Stephen
Published: December 2024

DNA genotyping and sequencing are getting cheaper every day. As Oxford Nanopore CTO Clive Brown recently discussed at Genomes Unzipped, when the cost of a full DNA sequence begins to fall below $1000, the value of having that information far outweighs the cost of data generation.
ggplot2 Tutorial: Scatterplots in a Series of Small Multiples
Authors: Turner Stephen
Published: December 2024

It took several months after learning about ggplot2 before I gave it a try myself.  I was apprehensive about learning a new graphics system with a new set of commands.  Thing is, if you've ever used plot() in R, you already know how to use much of the functionality in ggplot2!  In this tutorial I want to show you just how easy it is to start producing high-quality graphics using ggplot2.
Accessing Databases From R
Authors: Turner Stephen
Published: December 2024

Jeffrey Breen put together a useful slideshow on accessing databases from R. I use RODBC

every single day

to access my own local MySQL server from R. I've had trouble with RMySQL, so I've always used RODBC instead after setting up my

localhost

MySQL server as a Windows data source. Once you get accustomed to accessing your data directly with SQL queries rather than dumping files you'll wonder why you waited so long.
Sync your home directories on ACCRE and the local Linux servers (a.k.a. "the cheeses")
Authors: Turner Stephen
Published: December 2024

Vanderbilt ACCRE users with PCs only... If you use ACCRE to run multi-processor jobs you'll be glad to know that they now allow you to map your home directory to your local desktop using Samba (so you can access your files through My Computer as you normally would with local files).
Joint Techs Netcast: Enhancing Infrastructure Support for Data Intensive Science
Authors: Turner Stephen
Published: December 2024

The winter Joint Techs meeting is next week in Baton Rouge. I'm not going, but I plan on participating via a netcast to see what's going on. Jim Bottum, Clemson's CIO, is moderating an entire day devoted to the topic Enhancing Infrastructure Support for Data Intensive Science. Of particular interest to me are the talks from 9:30-11am Tuesday January 24 from researchers and those supporting climatology, genomics, and the XSEDE projects.
Side by side analyses in Stata, SPSS, SAS, and R
Authors: Turner Stephen
Published: December 2024

I've linked to UCLA's stat computing resources once before on a previous post about choosing the right analysis for the questions your asking and the data types you have.
Coming to R from SQL, Python, SAS, Matlab, or Lisp
Authors: Turner Stephen
Published: December 2024

Head over to Revolutions Blog for a list of PDF and powerpoint resources for making the transition to R from other programming or stats languages.  All of these notes come from the New York R meetup. I enjoyed browsing the meetup's files - lots of powerpoints, PDFs, and example R data files for various topics, including several slideshows on ggplot2.
Introduction to R for Life Scientists: Course Materials
Authors: Turner Stephen
Published: December 2024

Last week I taught a three-hour introduction to R workshop for life scientists at UVA's Health Sciences Library. I broke the workshop into three sections: In the first half hour or so I presented slides giving an overview of R and why R is so awesome. During this session I emphasized reproducible research and gave a demonstration of using knitr + rmarkdown in RStudio to produce a PDF that can easily be recompiled when data updates.
SNPper: quickly get info about a list of SNPs
Authors: Turner Stephen
Published: December 2024

Many of you have used this before, but for those who haven't, SNPper is a convenient little web application for quickly annotating results. So you've done your association analysis and have a list of rs-numbers you'd like to quickly get more information about.
BioMart Gene ID Converter
Authors: Turner Stephen
Published: December 2024

BioMart recently got a facelift. I'm not sure if this was always available in the old BioMart, but there's now a link to a gene ID converter that worked pretty well for me for converting S. cerevisiae gene IDs to standard gene names. It looks like the tool will convert nearly any ID you could imagine. Looks like it will also map Affy probe IDs to gene, transcript, or protein IDs and names.
Differential Isoform Expression With RNA-Seq: Are We Really There Yet?
Authors: Turner Stephen
Published: December 2024

In case you missed it, a new paper was published in Nature Biotechnology on a method for detecting isoform-level differential expression with RNA-seq Data: Trapnell, Cole, et al. "Differential analysis of gene regulation at transcript resolution with RNA-seq." Nature Biotechnology (2012).

THE PROBLEM

RNA-seq enables transcript-level resolution of gene expression, but there is no proven methodology for simultaneously accounting for
Install and load R package "Rcmdr" to quickly install lots of other packages
Authors: Turner Stephen
Published: December 2024

I recently reformatted my laptop and needed to reinstall R and all the packages that I regularly use. In a previous post I covered R Commander, a nice GUI for R that includes a decent data editor and menus for graphics and basic statistical analysis.
gcol == awk++
Authors: Turner Stephen
Published: December 2024

A while back Will showed you how to ditch Excel for awk, a handy Unix command line tool for extracting certain rows and columns from a text file. While I was browsing the documentation on the previously mentioned PLINK/SEQ library, I came across gcol, another utility for extracting columns from a tab-delimited text file. It can't do anything that awk can't, but it's easier and more intuitive to use for simple text munging tasks.
Papers from Feb 8 2010 Journal Club
Authors: Turner Stephen
Published: December 2024

Here are the papers we talked about in yesterday's Journal Club: PLoS Biol. 2010 Jan 26;8(1):e1000294. Rare variants create synthetic genome-wide associations. See my previous coverage of this paper and the comments. Dickson SP, Wang K, Krantz I, Hakonarson H, Goldstein DB. PLoS Genet. 2010 Jan;6(1):e1000798.