This repository contains a docker image with the main R packages used in Single-Cell RNA-Seq data analysis in a Rstudio interface.
In this image we have some R packages installed:
- CRAN repository:
| Package | Version |
|---|---|
| BiocManager | 1.30.4 |
| bookdown | 0.9 |
| caret | 6.0-81 |
| circlize | 0.4.5 |
| cluster | 2.0.7-1 |
| clustree | 0.2.2 |
| corrplot | 0.84 |
| cowplot | 0.9.4 |
| crayon | 1.3.4 |
| data.table | 1.12.0 |
| devtools | 2.0.1 |
| doParallel | 1.0.14 |
| dplyr | 0.7.8 |
| energy | 1.7-5 |
| Formula | 1.2-3 |
| ggbeeswarm | 0.6.0 |
| ggforce | 0.1.3 |
| ggplot2 | 3.1.0 |
| ggraph | 1.0.2 |
| ggrepel | 0.8.0 |
| ggthemes | 4.0.1 |
| git2r | 0.24.0 |
| googleVis | 0.6.3 |
| KernSmooth | 2.23-15 |
| knitr | 1.21 |
| lle | 1.1 |
| matrixStats | 0.54.0 |
| mclust | 5.4.2 |
| mgcv | 1.8-26 |
| mvoutlier | 2.0.9 |
| pathfindR | 1.3.0 |
| penalized | 0.9-51 |
| phateR | 0.2.9 |
| pheatmap | 1.0.12 |
| png | 0.1-7 |
| psych | 1.8.12 |
| rARPACK | 0.11-0 |
| RColorBrewer | 1.1-2 |
| RCurl | 1.95-4.11 |
| Rmagic | 1.4.0 |
| RMySQL | 0.10.16 |
| ROCR | 1.0-7 |
| Rtsne | 0.15 |
| scales | 1.0.0 |
| seqinr | 3.4-5 |
| Seurat | 2.3.4 |
| statmod | 1.4.30 |
| stringr | 1.3.1 |
| tidyverse | 1.2.1 |
| XML | 3.98-1.16 |
- Bioconductor:
| Package | Version |
|---|---|
| annotate | 1.60.1 |
| AUCell | 1.4.1 |
| beachmat | 1.4.0 |
| Biobase | 2.42.0 |
| BiocParallel | 1.16.6 |
| biomaRt | 2.38.0 |
| CEMiTool | 1.6.11 |
| clusterExperiment | 2.2.0 |
| clusterProfiler | 3.10.1 |
| ComplexHeatmap | 1.20.0 |
| DESeq2 | 1.22.2 |
| destiny | 2.12.0 |
| DOSE | 3.8.2 |
| EDASeq | 2.16.3 |
| edgeR | 3.24.3 |
| fgsea | 1.8.0 |
| genefilter | 1.64.0 |
| geneplotter | 1.60.0 |
| GenomicFeatures | 1.34.4 |
| GSEABase | 1.44.0 |
| GSVA | 1.30.0 |
| iCOBRA | 1.10.0 |
| limma | 3.38.3 |
| MAST | 1.8.2 |
| monocle | 2.10.1 |
| MultiAssayExperiment | 1.8.3 |
| org.Hs.eg.db | 3.7.0 |
| pathview | 1.22.3 |
| pcaMethods | 1.74.0 |
| PGSEA | 1.56.0 |
| Rhdf5lib | 1.4.2 |
| rtracklayer | 1.42.2 |
| RUVSeq | 1.16.1 |
| SC3 | 1.10.1 |
| scater | 1.10.1 |
| scde | 2.10.1 |
| scfind | 1.4.1 |
| scmap | 1.4.1 |
| scran | 1.10.2 |
| SingleCellExperiment | 1.4.1 |
| slingshot | 1.0.0 |
| SummarizedExperiment | 1.12.0 |
| sva | 3.30.1 |
| TSCAN | 1.20.0 |
- GitHub:
| Package | Version |
|---|---|
| BPSC | 0.99.2 |
| ggbiplot | 0.55 |
| ggfortify | 0.4.6 |
| kBET | 0.99.5 |
| M3Drop | 3.10.3 |
| ouija | 0.99.0 |
| pcaReduce | 1.0 |
| scImpute | 0.0.9 |
| scRNA.seq.funcs | 0.1.0 |
| SingleR | 0.2.2 |
| SLICER | 0.2.0 |
| xCell | 1.1.0 |
| zinbwave | 1.5.2 |
| zingeR | 0.1.0 |
To install docker follow the instructions in the links below depending on your operating system:
- CentOS: https://docs.docker.com/install/linux/docker-ce/centos/
- Debian: https://docs.docker.com/install/linux/docker-ce/debian/
- Fedora: https://docs.docker.com/install/linux/docker-ce/fedora/
- Ubuntu: https://docs.docker.com/install/linux/docker-ce/ubuntu/
- MacOS: https://docs.docker.com/docker-for-mac/install/
- Windows: https://docs.docker.com/docker-for-windows/install/
Once docker is installed, the next step is pull the scrnaseq-bit image from dockerhub using the following command:
docker pull biagii/scrnaseq-bit
There are several differents parameters to run the downloaded image. The most commom way is executing the following command:
docker run -d -P -e PASSWORD=password --rm --name [ANY_NAME] -v /server/path/:/docker/path/ -e USERID=$UID biagii/scrnaseq-bit
Next step is necessary to check the port that is running our image:
docker ps
Knowing the port that the image is running, just open the browser and type:
http://localhost:[PORT]
Any questions contact the developer by email: [email protected]