forked from drieslab/Giotto
-
Notifications
You must be signed in to change notification settings - Fork 0
/
README.Rmd
100 lines (59 loc) · 5.01 KB
/
README.Rmd
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
<!-- This line is from RStudio -->
# Giotto
<!-- badges: start -->
<!-- badges: end -->
The Giotto package consists of two modules, Giotto Analyzer and Viewer (see [www.spatialgiotto.com](http://www.spatialgiotto.com)), which provide tools to process, analyze and visualize **single-cell spatial expression** data. The underlying framework is generalizable to virtually all currently available spatial datasets. We recently demonstrated the general applicability on 10 different datasets created by 9 different state-of-the-art spatial technologies, including *in situ* hybridization (seqFISH+, merFISH, osmFISH), sequencing (Slide-seq, Visium, STARmap) and imaging-based multiplexing/proteomics (CyCIF, MIBI, CODEX). These technologies differ in terms of resolution (single cell vs multiple cells), spatial dimension (2D vs 3D), molecular modality (protein vs RNA), and throughput (number of cells and genes). More information and documentation about the latest version of Giotto Analyzer can be found at https://rubd.github.io/Giotto_site/ (**URL change !!**).
<img src="inst/images/general_figs/overview_datasets.png" />
## Requirements
- R (>= 3.5.1)
- Python (>= 3.0)
- Windows, MacOS or Linux specific installation tools. See [link](https://support.rstudio.com/hc/en-us/articles/200486498-Package-Development-Prerequisites).
\
## Installation
See [FAQs](https://rubd.github.io/Giotto_site/articles/faqs.html) for additional information.
#### R installation
You can install Giotto with (~1-5 mins):
``` r
library(devtools) # if not installed: install.packages('devtools')
library(remotes) # if not installed: install.packages('remotes')
remotes::install_github("RubD/Giotto")
```
#### Required python modules
These are necessary to run all available analyses, but can be installed automatically.
Required python modules:
- pandas
- python-igraph (igraph)
- networkx
- leidenalg
- python-louvain (community)
- smfishHmrf
- python.app (OSX only)
- scikit-learn
##### Automatic installation
The python modules will be installed automatically in a miniconda environment when installing Giotto. However, it will ask you whether you want to install them and you can opt out and select your preferred python path. In that case you need to do a manual installation of the python modules.
##### Manual installation
See [python installation](https://rubd.github.io/Giotto_site/articles/installation_issues.html#python-manual-installation)
#### Giotto Viewer
See [link](http://spatial.rc.fas.harvard.edu/spatialgiotto/giotto.install.native.html)
\
## Examples
- see https://github.com/RubD/spatial-datasets to find raw and pre-processed input data and Giotto scripts (in progress).
- typical run time range for the different datasets on a personal computer is around 10~45 mins.
- click on the image and try them out yourself.
- all examples are gradually updated to the latest Giotto version [work in progress]
[{width=10cm}](https://rubd.github.io/Giotto_site/articles/mouse_seqFISH_cortex_200517.html)
[{width=10cm}](https://rubd.github.io/Giotto_site/articles/mouse_merFISH_preoptic_region_200601.html)
[{width=10cm}](https://rubd.github.io/Giotto_site/articles/mouse_starmap_cortex.html)
[{width=10cm}](https://rubd.github.io/Giotto_site/articles/mouse_visium_brain_200601.html)
[{width=10cm}](https://rubd.github.io/Giotto_site/articles/mouse_visium_kidney_200601.html)
[{width=10cm}](https://rubd.github.io/Giotto_site/articles/human_cycif_PDAC_200601.html)
[{width=10cm}](https://rubd.github.io/Giotto_site/articles/mouse_osmFISH_SScortex_200518.html)
[{width=10cm}](https://rubd.github.io/Giotto_site/articles/mouse_CODEX_spleen.html)
## References
- [Dries, R. et al. Giotto, a toolbox for integrative analysis and visualization of spatial expression data. bioRxiv 701680 (2019).](https://www.biorxiv.org/content/10.1101/701680v2) doi:10.1101/701680
- [Eng, C.-H. L. et al. Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+. Nature 1 (2019).](https://www.nature.com/articles/s41586-019-1049-y) doi:10.1038/s41586-019-1049-y
- [Zhu, Q., Shah, S., Dries, R., Cai, L. & Yuan, G.-C. Identification of spatially associated subpopulations by combining scRNAseq and sequential fluorescence in situ hybridization data. Nature Biotechnology (2018).](https://www.nature.com/articles/nbt.4260) doi:10.1038/nbt.4260