Publications by R on Guangchuang Yu
Case sensitive R in sp_execute_external_script
R Language is case sensitive! Any R-coder can tell you this and share the experience. Case sensitive in R can be a challenge as with any case sensitive language. This also applies to SP_EXECUTE_EXTERNAL_SCRIPT stored procedure in T-SQL. This is a simple demo that will support this. This script will return normal result. EXECUTE sp_execute_externa...
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First thoughs on R integration in SQL Server 2016
This blog post is a very personal confession, might be delicate but it must be understood as a proposal or plan for improvement. Update #1: Typing error in title: correct title is First thoughts on R integration in SQL Server 2016 (update: June 24, 2016) Before the start, let me put some background and context. I have been working with statist...
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Running multiple correlations with R and T-SQL
Getting to know the data is always an interesting part of data science. With R integration into SQL Server, the exploration part is still part of the game. Usual way to get some statistics out of the dataset is to run some frequencies, descriptive statistics and nevertheless correlations. Running correlations against a set of variables in T-SQL m...
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identify method for ggtree
We are happy to announce that ggtree supports interactive tree annotation/manipulation by implementing an identify method. Users can click on a node to highlight a clade, to label or rotate it etc. Here is an example of highlighting clades using geom_hilight with identify: Here is another example of using emojifont to label clades. Interactive ...
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How to bug author
As an author of several Bioconductor packages. I found many questions from users are quite annoying. Some of them never use google and they are reluctant to read vignettes. Step 1: make sure you are using the latest release I found many peoples are using out-of-date packages. When they got an issue of an out-dated package, they never check whethe...
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leading edge analysis
leading edge and core enrichment Leading edge analysis reports Tags to indicate the percentage of genes contributing to the enrichment score, List to indicate where in the list the enrichment score is attained and Signal for enrichment signal strength. It would also be very interesting to get the core enriched genes that contribute to the enrichm...
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using meshes for MeSH Enrichment Analysis
MeSH (Medical Subject Headings) is the NLM (U.S. National Library of Medicine) controlled vocabulary used to manually index articles for MEDLINE/PubMed. MeSH is comprehensive life science vocabulary. MeSH has 19 categories and MeSH.db contains 16 of them. That is: Abbreviation Category A Anatomy B Organisms C Diseases D Chemicals and Drugs ...
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using clusterProfiler for MeSH Enrichment Analysis
MeSH (Medical Subject Headings) is the NLM (U.S. National Library of Medicine) controlled vocabulary used to manually index articles for MEDLINE/PubMed. MeSH is comprehensive life science vocabulary. MeSH has 19 categories and MeSH.db contains 16 of them. That is: Abbreviation Category A Anatomy B Organisms C Diseases D Chemicals and Drugs ...
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ggtree paper published
Today ggtree received 100 stars on and I found the paper was online at the same day by the tweet: ggtree, Methods in Ecology and Evolutionに掲載されたのか。オープンアクセスっぽいな。https://t.co/JlET18BSZv— ホクソピペット (@siero5335) August 16, 2016 I am quite exciting about it. Now ggtree is citable by doi:10.111...
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ggtree for microbiome data
ggtree can parse many software outputs and the evolution evidences inferred by these software can be used directly for tree annotation. ggtree not only works as an infrastructure that enables evolutionary data that inferred by commonly used software packages to be used in R, but also serves as a general tree visualization and annotation tool for ...
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