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https://github.com/robertaboukhalil/ginkgo
Cloud-based single-cell copy-number variation analysis tool
https://github.com/robertaboukhalil/ginkgo
bioinformatics sequencing single-cell-genomics
Last synced: 23 days ago
JSON representation
Cloud-based single-cell copy-number variation analysis tool
- Host: GitHub
- URL: https://github.com/robertaboukhalil/ginkgo
- Owner: robertaboukhalil
- License: bsd-2-clause
- Created: 2013-05-01T03:54:53.000Z (about 11 years ago)
- Default Branch: master
- Last Pushed: 2023-03-21T02:12:22.000Z (over 1 year ago)
- Last Synced: 2024-02-24T16:36:28.249Z (4 months ago)
- Topics: bioinformatics, sequencing, single-cell-genomics
- Language: PHP
- Homepage: qb.cshl.edu/ginkgo
- Size: 101 MB
- Stars: 46
- Watchers: 11
- Forks: 26
- Open Issues: 7
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Lists
- awesome_single_cell - Ginkgo - [R, C] - Ginkgo is a web application for single-cell copy-number variation analysis. (Software packages / Copy number analysis)
- awesome-single-cell - Ginkgo - [R, C] - Ginkgo is a web application for single-cell copy-number variation analysis. (Software packages / Copy number analysis)
- awesome-single-cell - Ginkgo - [R, C] - Ginkgo is a web application for single-cell copy-number variation analysis. (Software packages / Copy number analysis)
README
Ginkgo
=========
#### Ginkgo is a cloud-based single-cell copy-number variation analysis tool.
#### Launch Ginkgo: [qb.cshl.edu/ginkgo](http://qb.cshl.edu/ginkgo)
Usage
=========
* Step 0: Upload .bed files
* Step 1: Choose analysis parameters
* Step 2: Compute Copy Number Profiles, and a Phylogenetic Tree
* Step 3: Analyze Individual Cells
Setup Ginkgo on your own server
=========
**Requirements:**
- PHP >=5.2
- R >= 3.0.0
- R Packages:
- ctc
- DNAcopy
- inline
- gplots
- scales
- plyr
- ggplot2
- gridExtra
- fastcluster
- heatmap3
**WARNING** Version 3.0.0 (Mar 28, 2016) of gplots introduced a bug in heatmap.2 that makes it calculate dendrograms even when Rowv or Colv is set to FALSE so that Ginkgo will run for a very long time. The solution is to use an older version of gplots or use fixed version from: https://github.com/ChristophH/gplots. This can be installed using the commands below
```
remove.packages('gplots');
library('devtools');
install_github("ChristophH/gplots")
```
**Install Ginkgo:**
Type ```make``` in the ginkgo/ directory
**Server Configuration:**
- /etc/php.ini
- ```upload_tmp_dir```: make sure this directory has write permission
- ```upload_max_filesize```: set to >2G since .bam files can be large
- ginkgo/includes/fileupload/server/php/UploadHandler.php
- In constructor, on line 43 and 44:
- ```upload_dir = [FULL_PATH_TO_UPLOADS_DIR] . $_SESSION["user_id"] . '/'```
- ```upload_url = [FULL_URL_TO_UPLOADS_DIR] . $_SESSION["user_id"] . '/'```
- ginkgo/bootstrap.php
- Change ```DIR_ROOT```, ```DIR_UPLOADS``` and ```URL_ROOT```
- ginkgo/scripts/analyze.sh
- Change ```home``` variable to where the ginkgo/ folder is located
- ginkgo/scripts/process.R
- Change ```main_dir``` variable to the folder where ginkgo/scripts is located
- ginkgo/scripts/reclust.R
- Change ```main_dir``` variable to the folder where ginkgo/scripts is located
- ginkgo/scripts/analyze-subset.R
- Set the folder to where ginkgo/scripts is located
- Set the folder to where ginkgo/genomes is located (warning: test this carefully if your ginkgo/uploads folder is a symlink)
- Make sure the uploads directory has the correct write permissions
**Download data files:**
- Download binning data for hg19 at https://labshare.cshl.edu/shares/schatzlab/www-data/ginkgo/genomes/hg19.tgz
- untar into ginkgo/genomes/hg19 (which needs to be created)
- Other genomes, including hg18, hg19, mm9, mm10, rheMac7, rheMac8, rn5 and dm3 can be found at http://labshare.cshl.edu/shares/schatzlab/www-data/ginkgo/genomes/