Sojourner: Statistical Analysis of Single Molecule Trajectories

Single molecule tracking has evolved as a novel new approach complementing genomic sequencing, it reports live biophysical properties of molecules being investigated besides properties relating their coding sequence. Here we provided “sojourner” package, to address statistical and bioinformatic needs related to the analysis and comprehension of high throughput single molecule tracking data (https://bioconductor.org/packages/release/bioc/html/sojourner.html).

Maintainer:

sojourner developer <sojourner.developer at outlook.com>

Citation:

Liu S, Yoo S, Tang X, Sung Y, Wu C (2020). Sojourner: statistical analysis of single molecule trajectories. R package version 1.0.2, https://github.com/sheng-liu/sojourner. DOI: 10.18129/B9.bioc.sojourner.

Installation

You can install sojourner as a Bioconductor package:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("sojourner")

Alternatively, you can also install sojourner directly from github.

# install.packages("devtools")
devtools::install_github("sheng-liu/sojourner", build_vignettes = TRUE, ref = "master")

Documentation

Sojourner has a vignette contained in the package. You can view the documentation by

browseVignettes("sojourner")

Alternatively, you can also access the the vignette on sojourner’s website

https://sheng-liu.github.io/sojourner/articles/sojourner-vignette.html

Dependencies

These are packages that sojourner uses in case they are not installed automatically.

# plotting
install.packages('ggplot2')
install.packages('reshape2')
install.packages('dplyr')
install.packages('scales')
install.packages('gridExtra')

# curve fitting and clustering
install.packages('mixtools')
install.packages('fitdistrplus')
install.packages('nls2')
install.packages('minpack.lm')
install.packages('truncnorm')
install.packages('mclust')

# image processing - CRAN
install.packages('rtiff')
install.packages('jpeg')
install.packages('tiff')
install.packages('png')
install.packages('pixmap')

# image processing- Bioconductor
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install()
BiocManager::install(c("EBImage"))

# interfacing
install.packages('R.matlab')
install.packages('Rcpp')
install.packages("reticulate")

# GUI
install.packages('shiny')
install.packages('shinyjs')

# others
install.packages('mltools')
install.packages('sampSurf')
install.packages('sp')
install.packages('rlang')