When we work with data, we usually find with an obstacle: repeated values. This type of values don’t represent a critical problem if we have the ability to identify. Once we have that list of repeated values, it is very easy to discard, eliminate or simply extract. We are ... [Read more...]

This is the third set of exercises on networks in which we practice the functions for graph structure, using package igraph. The first and second part are available here: Part 1 Part 2 If you don’t have package already installed, install it using the following code: install.packages("igraph") and load ... [Read more...]

Motivation This is the result of trial and error until I got RStudio Server working in my network I have a powerful Mac Pro server and I wanted to use that computing from my "old" iMac (i.e. to do my calculations in a fraction of the time that it ... [Read more...]

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I love the work of @beesandbombs and while some of his creations are a poor fit for redoing in R, one of his latest got me wondering how I would recreate it in the venerable statistics language… The gif in question can be seen here (I don’t know ... [Read more...]

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R Tools for Visual Studio, the open-source Visual Studio add-in for R programmers, has a new update available for download. RTVS 0.5 makes it easier to run R within SQL Server 2016 as a stored procedure, and supports multiple windows for R graphics. RTVS 0.5 makes use of Visual Studio's polyglot nature so ... [Read more...]

Last Friday’s “The Riddler” column on FiveThirtyEight presents an interesting probabilistic puzzle: While traveling in the Kingdom of Arbitraria, you are accused of a heinous crime. Arbitraria decides who’s guilty or innocent not through a court system, but a board game. It’s played on a simple board: ... [Read more...]

Our new Financial Trading in R course is here! Learn from Ilya Kipnis, a professional quantitative analyst and co-author of Introduction to Quantitative Trading With R.  Master the basics of financial trading, and learn how to use quantstrat to build ... [Read more...]

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This is the first chapter of our new web book, Raccoon - Statistical Models with R: it's an introduction to Linear models, with theoratical explanation and lots of examples + two summary tables with linear model formulae and functions in R The post Raccoon | Ch. 1 – Introduction to Linear Models with R ... [Read more...]

Descriptive Analytics is the examination of data or content, usually manually performed, to answer the question “What happened?”. This is the first set of exercise of a series of exercises that aims to provide a descriptive analytics solution to the ‘2008’ data set from here. Download it and save it as ... [Read more...]

I have 7 packages published within the Bioconductor project. ChIPseeker clusterProfiler DOSE ggtree GOSemSim meshes ReactomePA A new package meshes was included in BioC 3.4 release. ChIPseeker For ChIPseeker, this release fixed several minor bugs. GEO data was updated, now ChIPseeker contains 20947 bed file information.

CHANGES IN VERSION 1.9.8
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 o plotAvgProf/plotAvgProf2 order of panel by names of input tagMatrix List <2016-09-25, Sun>
 o test ENSEMBL ID using '^ENS' instead of '^ENSG' <2016-09-20, Tue>
   + https://github.com/GuangchuangYu/ChIPseeker/issues/41

CHANGES IN VERSION 1.9.7
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 o unit test <2016-08-16, Tue>

CHANGES IN VERSION 1.9.6
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 o update vignette <2016-08-16, Tue>

CHANGES IN VERSION 1.9.5
------------------------
 o when TxDb doesn't have gene_id information, converting gene ID (ensembl/entrez and symbol) will be omitted instead of throw error. <2016-08-02, Tue>
   + https://www.biostars.org/p/204142
 o bug fixed if testing targetPeak is a list of GRanges objects in enrichPeakOverlap function <2016-07-20, Wed>
   + https://github.com/GuangchuangYu/ChIPseeker/issues/37
   + https://github.com/GuangchuangYu/ChIPseeker/issues/36
 o fixed typo in determine gene ID type <2016-06-21, Tue>
   + https://github.com/GuangchuangYu/ChIPseeker/issues/28#issuecomment-227212519
 o move upsetplot generics to DOSE and import from DOSE to prevent function name conflict <2016-06-14, Tue>

CHANGES IN VERSION 1.9.4
------------------------
 o bug fixed <2016-06-08, Wed>
   + https://github.com/GuangchuangYu/ChIPseeker/issues/17#issuecomment-224407402
   + https://github.com/GuangchuangYu/ChIPseeker/pull/24/files

CHANGES IN VERSION 1.9.3
------------------------
 o use byte compiler <2016-05-18, Wed>
 o https://github.com/Bioconductor-mirror/ChIPseeker/commit/f1ada57b9c66a1a44355bbbbdaf5b0a88e10cf7d

CHANGES IN VERSION 1.9.2
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 o name tagMatrix in plotAvgProf automatically if missing <2016-05-12, Thu>
 o https://github.com/Bioconductor-mirror/ChIPseeker/commit/d5f16b2bc01725e30282c3acb33007ef521a514c

CHANGES IN VERSION 1.9.1
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 o bug fixed in getNearestFeatureIndicesAndDistances <2016-05-11, Wed>
   + correct metadata in dummy NA feature

clusterProfiler Thanks to the update of ... [Read more...]

Last Friday together with Przemysław Szufel and Wit Jakuczun we were giving a live demo on introduction to deep learning at Digital Champions conference.The objective of the workshop was to show how to build a simple predictive model using MXNet library in a few minutes. In the example, ... [Read more...]

A new package gpg has appeared on CRAN. From the package description: Bindings to GnuPG for working with OpenGPG (RFC4880) cryptographic methods. Includes utilities for public key encryption, creating and verifying digital signatures, and managing your local keyring. Note that some functionality depends on the version of GnuPG that is ... [Read more...]