BOL: Related items

One page R survival guide !!

Rahul Nayak — Thu, 28 May 2015 21:10:12 -0500

There any many of the documents have been developed and tested by scientist around the world. I found this one really useful. The data used is available for download as data.zip.

Reference@http://www.datasciencecentral.com/profiles/blogs/one-page-r-a-survival-guide-to-data-science-with-r

Templates for the Data Scientist
1. A Template for Preparing Data: *OnePageR - *R
2. A Template for Building Models: *OnePageR - *R
Getting Started as a Data Scientist
1. Getting Started with R and Rattle: *Lecture - *Laboratory
2. Introducing and Interacting with R: *Lecture - *Laboratory
3. BasicR - OnePage(R) - Writing R scripts
Dealing With Data
1. Read Data into R: *OnePageR - *R
2. Explore and Summarise Data: *OnePageR - *R
3. Transform Data: *OnePageR - *R
4. Dealing with Dates and Time: (PDF, R) Dates and Time
5. Visualising Data with GGPlot2: *OnePageR - *R
6. Visualising Data with Maps *OnePageR - *R
7. Spatial (R) Spatial Analysis
8. Handling Big Data *OnePageR - *R
Descriptive Analytics
1. Cluster Analysis: *Lecture - *OnePageR - *R
2. Association Analysis: *Lecture
Predictive Analytics
1. Decision Trees: *Lecture - *OnePageR - *R - *Rattle
2. Ensembles of Decision Trees: *Lecture - *OnePageR - *R
3. SVM (R)
4. KernLab (R)
5. NeuralNetworks (R)
6. NNet (R)
Model Delivery
1. Evaluating Models: *OnePageR - *R
2. Evaluation (R)
3. Scoring (R)
4. PMML (R) Exporting Models for Deployment
Advanced Topics
1. Text Mining: *OnePageR - *R
Advanced R Topics
1. Plots (PDF, R) Miscellaneous Plots
2. Functions (PDF, R) Writing Functions in R
3. Parallel (PDF, R) Parallel Execution
4. Packaging (R) Pulling it Together into a Package
5. Doing R with Style: *OnePageR - *R
6. Literate Data Mining with KnitR: *Lecture - *OnePageR - *

Efficient genome searching with Biostrings and the BSgenome data package

Aasha — Mon, 07 Mar 2016 05:18:06 -0600

Address of the bookmark: https://www.bioconductor.org/packages/3.3/bioc/vignettes/BSgenome/inst/doc/GenomeSearching.pdf

RCircos: an R package for Circos 2D track plots

Jit — Fri, 20 May 2016 11:01:13 -0500

RCircos package provides a simple and flexible way to make Circos 2D track plots with R and could be easily integrated into other R data processing and graphic manipulation pipelines for presenting large-scale multi-sample genomic research data. It can also serve as a base tool to generate complex Circos images.

More at https://bitbucket.org/henryhzhang/rcircos/src

Address of the bookmark: https://bitbucket.org/henryhzhang/rcircos/src

Sushi: An R/Bioconductor package for visualizing genomic data

Jit — Wed, 31 Aug 2016 08:29:12 -0500

Sushi: An R/Bioconductor package for visualizing genomic data

Address of the bookmark: https://www.bioconductor.org/packages/devel/bioc/vignettes/Sushi/inst/doc/Sushi.pdf

R Graphical Cookbook by Winston Chang

Abhimanyu Singh — Fri, 04 Nov 2016 12:50:30 -0500

R Graphical Cookbook by Winston Chang

A very nice book by Winston Chang for R ethusiast. The R code presented in these pages is the R code actually used to produce the Figures in the book. There will be differences compared to the code chunks shown in the text of the book, but in most cases the differences will be that these pages contain additional code to lay out multiple plots on a single "page".

The code presented for each figure is self-contained, i.e., all code required to produce the figure is included. This means that there is sometimes considerable overlap of code between several figures In some cases, it may be necessary to install an add-on package from CRAN to get the code to run.

More books at http://www.e-reading.club/bookreader.php/137370/C486x_APPb.pdf

UpSetR Shiny App!

Jit — Fri, 14 Apr 2017 06:19:54 -0500

UpSetR generates static UpSet plots. The UpSet technique visualizes set intersections in a matrix layout and introduces aggregates based on groupings and queries. The matrix layout enables the effective representation of associated data, such as the number of elements in the aggregates and intersections, as well as additional summary statistics derived from subset or element attributes.

To begin, input your data using one of the three input styles.

"File" takes a correctly formatted.csv file.
"List" takes up to 6 different lists that contain unique elements, similar to that used in the web applications BioVenn (Hulsen et al., 2008) and jvenn (Bardou et al., 2014)
"Expression" takes the input used by the venneuler R package (Wilkinson, 2015)

Address of the bookmark: https://gehlenborglab.shinyapps.io/upsetr/

poRe: an R package for the visualization and analysis of nanopore sequencing data

Jit — Thu, 23 Nov 2017 09:55:57 -0600

Motivation: The Oxford Nanopore MinION device represents a unique sequencing technology. As a mobile sequencing device powered by the USB port of a laptop, the MinION has huge potential applications. To enable these applications, the bioinformatics community will need to design and build a suite of tools specifically for MinION data.

Results: Here we present poRe, a package for R that enables users to manipulate, organize, summarize and visualize MinION nanopore sequencing data. As a package for R, poRe has been tested on Windows, Linux and MacOSX. Crucially, the Windows version allows users to analyse MinION data on the Windows laptop attached to the device.

Availability and implementation: poRe is released as a package for R at http://sourceforge.net/projects/rpore/ . A tutorial and further information are available at https://sourceforge.net/p/rpore/wiki/Home/

Contact:mick.watson@roslin.ed.ac.uk

Address of the bookmark: https://academic.oup.com/bioinformatics/article/31/1/114/2365693

dupRadar package

Jit — Sun, 04 Feb 2018 14:28:57 -0600

The dupRadar package gives an insight into the duplication problem by graphically relating the gene expression level and the duplication rate present on it. Thus, failed experiments can be easily identified at a glance

Address of the bookmark: https://bioconductor.org/packages/3.7/bioc/vignettes/dupRadar/inst/doc/dupRadar.html

chromoMap-An R package for Interactive visualization and mapping of human chromosomes

Rahul Nayak — Mon, 25 Jun 2018 17:22:24 -0500

chromoMap is an R package that provides interactive, configurable and elegant graphics visualization of the human chromosomes allowing users to map chromosome elements (like genes, SNPs etc.) on the chromosome plot. It introduces a special plot viz. the "chromosome heatmap" that, in addition to mapping elements, can visualize the data associated with chromosome elements (like gene expression) in the form of heat colors which can be highly advantageous in the scientific interpretations and research work. Because of the enormous size of the chromosomes, it is impractical to visualize each element on the same plot. But chromoMap plots provide a magnified view for each of chromosome location to render additional information and visualization specific for that location. You can map thousands of genes and can view all mappings easily. Users can investigate the detailed information about the mappings (like gene names or total genes mapped on a location) or can view the magnified single or double stranded view of the chromosome at a location showing each mapped element in sequential order (You will see in the demos below). Not ony that, the plots can be saved as HTML documents that can be customized and shared easily. In addition, you can include them in R Markdown or in R Shiny applications.

https://cran.r-project.org/web/packages/chromoMap/index.html

Applied Statistics for Bioinformatics using R

Neel — Thu, 30 Aug 2018 03:45:39 -0500

The purpose of this book is to give an introduction into statistics in order to solve some problems of bioinformatics. Statistics provides procedures to explore and visualize data as well as to test biological hypotheses. The book intends to be introductory in explaining and programming elementary statistical concepts, thereby bridging the gap between high school levels and the specialized statistical literature