Blog Archives

fastqcr: An R Package Facilitating Quality Controls of Sequencing Data for Large Numbers of Samples

April 11, 2017
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fastqcr: An R Package Facilitating Quality Controls of Sequencing Data for Large Numbers of Samples

Introduction High throughput sequencing data can contain hundreds of millions of sequences (also known as reads). The raw sequencing reads may contain PCR primers, adaptors, low quality bases, duplicates and other contaminants coming from the experimental protocols. As these may affect the...

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Survminer Cheatsheet to Create Easily Survival Plots

March 23, 2017
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Survminer Cheatsheet to Create Easily Survival Plots

We recently released the survminer verion 0.3, which includes many new features to help in visualizing and sumarizing survival analysis results. In this article, we present a cheatsheet for...

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survminer 0.3.0

March 20, 2017
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survminer 0.3.0

I’m very pleased to announce that survminer 0.3.0 is now available on CRAN. survminer makes it easy to create elegant and informative survival curves. It includes also functions for summarizing and inspecting graphically the Cox proportional hazards model assumptions. This is a big release...

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Factoextra R Package: Easy Multivariate Data Analyses and Elegant Visualization

February 19, 2017
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Factoextra R Package: Easy Multivariate Data Analyses and Elegant Visualization

factoextra is an R package making easy to extract and visualize the output of exploratory multivariate data analyses, including: Principal Component Analysis (PCA), which is used to summarize the information contained in a continuous (i.e, quantitative) multivariate data by reducing the dimensionality of...

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Text mining and word cloud fundamentals in R : 5 simple steps you should know

February 11, 2017
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Text mining and word cloud fundamentals in R : 5 simple steps you should know

Text mining methods allow us to highlight the most frequently used keywords in a paragraph of texts. One can create a word cloud, also referred as text cloud or tag cloud, which is a visual representation of text data. The procedure of creating...

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Practical Guide to Cluster Analysis in R – Book

February 7, 2017
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Practical Guide to Cluster Analysis in R – Book

Introduction Large amounts of data are collected every day from satellite images, bio-medical, security, marketing, web search, geo-spatial or other automatic equipment. Mining knowledge from these big data far exceeds human’s abilities. Clustering is one of the important data mining methods for...

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Survival Analysis

December 12, 2016
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Survival Analysis

Survival analysis corresponds to a set of statistical methods for investigating the time it takes for an event of interest to occur. In this chapter, we start by describing how to fit survival curves and how to perform logrank tests comparing the...

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survminer 0.2.4

December 12, 2016
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survminer 0.2.4

I’m very pleased to announce survminer 0.2.4. It comes with many new features and minor changes. Install survminer with: install.packages("survminer") To load the package, type this: library(survminer) ContentsNew features Minor changes Bug fixes Summary of survival curves Plot survival curves Determine...

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R packages

December 12, 2016
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In this section, you’ll find R packages developed by STHDA for easy data analyses. factoextra factoextra let you extract and create ggplot2-based elegant visualizations of multivariate data analyse results, including PCA, CA, MCA, MFA, HMFA and clustering methods.

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Cox Model Assumptions

December 12, 2016
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Cox Model Assumptions

Previously, we described the basic methods for analyzing survival data, as well as, the Cox proportional hazards methods to deal with the situation where several factors impact on the survival process. In the current article, we continue the series by describing...

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