BOL: Related items

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

regioneR: an R package for the management and comparison of genomic regions

Jit — Tue, 11 Dec 2018 08:43:51 -0600

Regioner is an R package for the management and comparison of genomic regions. It offers a set of function for basic manipulation of region sets extending the functionality of GenomicRanges and a powerful and customizable permutation test framework. With it, it's possible to study the association of a set of regions with other sets of regions, functions defined over the genome or essentially any user defined function.

http://gattaca.imppc.org/regioner/

Address of the bookmark: http://gattaca.imppc.org/regioner/

chromoMap-An R package for Interactive Visualization and Annotation of Chromosomes

Neel — Fri, 12 Apr 2019 05:30:41 -0500

Provides interactive, configurable and elegant graphics visualization of the chromosomes or chromosome regions of any living organism 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. The package provide multiple features like visualizing multiple sets, chromosome heat-maps, group annotations, adding hyperlinks, and labelling. 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.

Address of the bookmark: https://cran.r-project.org/web/packages/chromoMap/vignettes/chromoMap.html

Platypus – R package for object detection and image segmentation.

BioStar — Mon, 09 Nov 2020 02:56:25 -0600

platypus is an R package for object detection and semantic segmentation. Currently using

platypus you can perform:

multi-class semantic segmentation using U-Net architecture
multi-class object detection using YOLOv3 architecture

You can install the latest version of platypus with remotes package:

remotes::install_github("maju116/platypus")

Note that in order to install platypus you need to install keras and tensorflow packages and Tensorflow version >= 2.0.0 ( Tensorflow 1.x will not be supported!)

Address of the bookmark: https://github.com/maju116/platypus

GrapheR !!!

John Parker — Thu, 14 Aug 2014 14:02:17 -0500

What a wonderful gem GrapheR is.... Oh yes it is. GrapheR is a GUI for base graphics in R by http://www.maximeherve.com/. The package provides a graphical user interface for creating base charts in R. It is ideal for beginners in R, as the user interface is very clear and the code is written along side into a text file, allowing users to recreate the charts directly in the console.

Adding and changing legends? Messing around with the plotting window settings? It is much easier/quicker with this GUI than reading the help file and trying to understand the various parameters.
Here is a little example using the iris data set.

library(GrapheR)
data(iris)
run.GrapheR()

This will bring up a window that helps me to create the chart and tweak the various parameters.

Finally, I find the underlying R code in a file created by GrapheR. For more details read also the package vignette, which is available in English, French and German!

RStudio

Jitendra Narayan — Sat, 27 Dec 2014 06:50:58 -0600

RStudio IDE is a powerful and productive user interface for R. It’s free and open source, and works great on Windows, Mac, and Linux.

The developers and expert trainers are the authors of several popular R packages, including ggplot2, plyr, lubridate, and others.

More at http://www.rstudio.com/

http://www.rstudio.com/products/RStudio/

Address of the bookmark: http://www.rstudio.com/

R for Microsoft Excel

Jitendra Narayan — Wed, 18 Feb 2015 00:43:27 -0600

If you currently use a spreadsheet like Microsoft Excel for data analysis, you might be interested in taking a look at this tutorial on how to transition from Excel to R by Tony Ojeda. The tutorial explains how to use R functions in place of Excel formulas, including tools like =AVERAGE and =VLOOKUP. For the most part, it uses modern R packages to keep the R code clear and concise.

You'll likely still be using Excel as a data source, though, so you'll also want to check out this guide to importing data from Excel to R from MilanoR.

Reference http://www.r-bloggers.com/an-r-tutorial-for-microsoft-excel-users/

A guide for complete R beginners :- R Syntax

Archana Malhotra — Fri, 20 Feb 2015 23:41:03 -0600

R is a functional based language, the inputs to a function, including options, are in brackets. Note that all dat and options are separated by a comma

Function(data, options)

Even quit is a function

So is help

help(read.table)

Provides the help page for the FUNCTION ‘read.table’

help.search(“t test”)

Searches for help pages that might relate to the phrase ‘t test’

NOTE: quotes are needed for search strings, they are not needed when referring to data objects or function names.

There is a short cut for help,

? shows the help page on a function name, same as help(function)

?read.table

?? searches for help pages on functions, same as help.search(‘phrase’)

??“t test”

Information is usually returned from a function, by default this is printed to screen

read.table(‘data.tsv’)

This can always be stored, we call what it is stored in an ‘object’

mydata

here mydata is an object of type dataframe

Reminder:

Vector: a list of numbers, equivalent to a column in a table
Data Frame = a collection of vectors. Equivalent to a table

Hint:

Up/Down arrow keys can be use to cycle through previous commands

Kamaleshwar Singh Lab

Fri, 25 Mar 2016 10:46:49 -0500

The focus of Dr. Singh’s research and teaching is on the molecular mechanistic basis for environmental carcinogen-induced genetic (DNA damage) and epigenetic changes, and susceptibility to human cancer development

More at http://www.tiehh.ttu.edu/dr.-kamaleshwar-singh.html

SLURM

Jit — Wed, 04 May 2016 05:13:21 -0500

SLURM workload manager software, a free open-source workload manager designed specifically to satisfy the demanding needs of high performance computing.

This page is a HOWTO guide for setting up a SLURM installation, currently focused on a CentOS 7 Linux OS. Please send feedback to Ole.H.Nielsen /at/ fysik.dtu.dk.

See the SLURM homepage (also https://computing.llnl.gov/linux/slurm/).

Address of the bookmark: https://wiki.fysik.dtu.dk/niflheim/SLURM