blairdrummond / scbursts

R-package for analysis of single channel bursts

Available on CRAN

SCBursts - Single Channel Bursts Analysis

This R Package was originally designed for use by the daCosta lab, but is being provided to the wider Single Ion-Channel analysis community (or whoever else might find use in the package).

The package contains the following features:

• Transform data between formats generated by TAC, QUB, Clampfit, SCAN, etc.
• Correct for effects of the Gaussian filter on the time-series data.
• Identify bursts in time series, and isolate those bursts.
• Provide toolkit for sorting, filtering, and studying individual bursts.

If any features seem wrongfully absent, or if any methods can be improved upon, feel free to either create an issue or (even better) submit a pull request.

Installation

From CRAN

To install the package from CRAN, in R you can run

install.packages("scbursts")

and then, as usual, just run

library(scbursts)

to get started.

From a tarball

Get the scbursts_*.*.tar.gz file from releases. You should then be able to install from this file within R-Commander, R-Studio, or from the command-line with

R CMD INSTALL scbursts_*.*.tar.gz

From R (with pdf documentation)

If you have LaTeX and pandoc installed, you can install the package and generate some documentation for it (this is optional. If you don't have those see the next section).

Open an R console, and run the following lines

install.packages("devtools",  repos="http://cran.rstudio.com")
install.packages("knitr",     repos="http://cran.rstudio.com")
install.packages("rmarkdown", repos="http://cran.rstudio.com")
install.packages("roxygen2",  repos="http://cran.rstudio.com")
install.packages("readxl",    repos="http://cran.rstudio.com")
install.packages("tibble",    repos="http://cran.rstudio.com")
install.packages("tinytex",   repos="http://cran.rstudio.com")
library(devtools)
install_github("dacostalab/scbursts", build_vignettes = TRUE)

# to update install run
# install_github("dacostalab/scbursts", build_vignettes = TRUE, force=TRUE)

You should then be able to call

library(scbursts)

and to see documentation run

vignette("scbursts")

From R

If you have LaTeX and pandoc installed, you can install the package and generate some documentation for it (this is optional. If you don't have those see the next section).

Open an R console, and run the following lines

install.packages("devtools")
library(devtools)
install_github("dacostalab/scbursts", build_vignettes = TRUE)

# to update install run
# install_github("dacostalab/scbursts", force=TRUE)

You should then be able to call

library(scbursts)

From Source

You only want to do this if you plan to modify the package. Otherwise use another option

1. Start by installing the dependencies. On Ubuntu

# apt-get install texlive-full pandoc pandoc-citeproc make r-base pkg-config libcurl4-openssl-dev libxml2-dev

With those installed, you can install this from source with make. You will need to make sure that you have this installed. Once you have it, the steps are:

2. Get a copy of this repository, either by downloading a zip or by git clone-ing.

3. Open a terminal in the directory

4. You will also need some R packages. If you have write access to your R library path, then you can run make deps. Otherwise in an R terminal run

install.packages("devtools")
install.packages("knitr")
install.packages("rmarkdown")
install.packages("roxygen2")
install.packages("readxl")
install.packages("tibble")
install.packages("tinytex")

5. Now, back in the shell, you can run make (or make export) and make install.

And then the package should be installed. Note that you won't be able to create any manuals unless you have LaTeX and pandoc installed.

Manual

You can view the soft-documentation for this package by calling

vignette("scbursts")

from an R console.