README.md 813 Bytes
Newer Older
Jean-Karim Heriche's avatar
Jean-Karim Heriche committed
1
2
# SMLM.data.analysis

3
4
5
6
An R package to deal with data from single molecule localization microscopy.
This package provides three sets of functionalities:
  - data input: read SMLM data as point sets either from csv files or from TIFF images
  - registration: pairwise point sets registration using the iterative closest point algorithm or the coherent point drift algorithm
Jean-Karim Heriche's avatar
Jean-Karim Heriche committed
7
  - topological data analysis: compute similarity between point sets using persistent homology
8
9
10
11
12
13
14

# Installation

To install this package, run (from within R):

``` R
library(devtools)
15
git_install('https://git.embl.de/heriche/smlm.data.analysis')
16
17
18
19
20
21
```

This package depends on these other packages:
  * TDA
  * foreach
  * doSNOW
22
  
23
24
25
26
27
For some functions, these packages are also required:
  * EBImage (from Bioconductor)
  * dbscan
  * Morpho