bioinfo-hub / shortcake

A docker image for singlecell analysis

ShortCake🍰

A docker image for single-cell analysis. It's on docker-hub and GitHub. This repository is an update of singlecell_jupyter.

0. Changelog

See Changelog

1. Included tools (latest)

• Pipeline: Seurat (and Seurat wrappers), scater, scran, Scanpy, scvi-tools (previous scVI), monet, Pagoda2, kallisto-bustools

• Quality check: DropletQC

• Doublet finding: Scrublet, DoubletFinder

• Batch correction and data integration: Harmony, scmap, scBio, SingleCellNet

• Clustering: SC3, metacell, SCCAF, Constclust, bigSCale2, scTriangulate

• Cell-type annotation: RCA, garnett, scCatch, SingleR, ikarus

• Trajectory (pseudo-time) analysis: Monocle2/3, slingshot, Palantir, FROWMAP

• RNA velocity: velocyto, scVelo, CellRank, Dynamo, MultiVelo

• Spatial transcriptome: STELLAR

• Cell-cycle prediction: tricycle

• Gene network: WGCNA, SCENIC (pySCENIC), CellOracle, EEISP, RENGE

• Cell-cell interaction: CellPhoneDB, SingleCellSignalR, scTensor, cell2cell, CellChat, Scriabin

• Data imputation: MAGIC, SAVER, scImpute, SCRABBLE, RECODE

• Multi-modal analysis: LIGER, scAI, MOFA2, scMoMaT, MARIO, SATURN

• Bulk deconvolution: SCDC, MuSiC, BayesPrism, AutoGeneS

• Gene perturbation prediction: GEARS

• Simulation: Splatter, dyngen, scGen, scReadSim, scDesign3

• Others: Sleepwalk, singleCellHaystack, SignatuR, ComplexHeatmap

• scATAC-seq: Cicero, chromVAR, ArchR, Signac, cisTopic, EpiScanpy

• Database (genome): BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Dmelanogaster.UCSC.dm6

• Database (gene): EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v79, EnsDb.Hsapiens.v86, EnsDb.Mmusculus.v79

• Database (motif): JASPAR2016, JASPAR2018, JASPAR2020, JASPAR2022

• SeuratData: ifnb_3.1.0, panc8_3.0.2, pbmcsca_3.0.0, pbmc3k_3.1.4, celegans.embryo_0.1.0, cbmc_3.1.4, hcabm40k_3.0.0, thp1.eccite_3.1.5, stxBrain_0.1.1, stxKidney_0.1.0, bmcite_0.3.0, pbmcMultiome_0.1.2, ssHippo_3.1.4

2. Run

For Docker:

# pull docker image
docker pull rnakato/shortcake

# container login
docker run [--gpus all] --rm -it rnakato/shortcake /bin/bash
# jupyter notebook (see 'mnt/' directory in the notebook )
docker run [--gpus all] --rm -p 8888:8888 -v (your directory):/work/mnt rnakato/shortcake jupyternotebook.sh

For Singularity:

# build image
singularity build -F shortcake.sif docker://rnakato/shortcake
# jupyter notebook
singularity exec [--nv] shortcake.sif jupyternotebook.sh
# execute R directory
singularity exec [--nv] shortcake.sif R

3. Usage

3.1 Jupyter

We recommend using Jupyter notebook to use ShortCake:

singularity exec shortcake.sif jupyternotebook.sh

To isolate the environment, ShortCake prepares virtual environments for several tools. Specify the appropriate kernel to use them. In addition, the R command and all R tools are usable in the R kernel.

3.2 Rstudio

ShortCake also provides the Rstudio environment:

singularity exec shortcake.sif rstudio

3.2 Command line

Of course, you can also use ShortCake with command line tools. For example:

singularity exec shortcake.sif velocyto run10x -m repeat_msk.gtf <10Xdir> <gtf>

If you want to use a virtual Python environment from the command line, use run_env.sh to activate it:

singularity exec shortcake.sif run_env.sh <environment> <command>
# Example to activate "celloracle" environment
singularity exec shortcake.sif run_env.sh celloracle python -c "import celloracle"

4. Build image from Dockerfile

First clone and move to the repository

git clone https://github.com/rnakato/ShortCake
cd ShortCake

• Since the Dockerfile installs many packages from GitHub, first get a GitHub token from your own repository and add it to Docker_R/docker-compose.Seurat.yml, Docker_R/docker-compose.R.yml, and Docker_Python/docker-compose.yml.
• Before building, download the SeuratData dataset using wget.sh in the Docker_R/SeuratData directory.

Then build packages:

# build R packages
cd Docker_R
docker compose -f docker-compose.R_Seurat.yml build 
docker-compose -f docker-compose.R.yml build
# Then build Python packages
cd ../Docker_Python/
docker-compose -f docker-compose.yml build

Contact

Ryuichiro Nakato: rnakato AT iqb.u-tokyo.ac.jp