README.Rmd

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output: github_document
---
# <img src="vignettes/sojourner_logo.png" align="right" alt="" width="180" />

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```
# _Sojourner_: Statistical Analysis of Single Molecule Trajectories

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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/sojourner/).

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 1.3.0,  https://github.com/sheng-liu/sojourner. DOI: 10.18129/B9.bioc.sojourner.


## Installation

You can install _sojourner_ as a Bioconductor package:

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

BiocManager::install("sojourner")
```

Alternatively, you can also install _sojourner_ directly from github. 

``` r
# 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

``` r
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.

``` r
# 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('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')


```