bioconductor-sc3-scripts

In order to wrap SC3's internal workflow in any given workflow language, it's important to have scripts to call each of those steps, which is what this package provides

Install

The recommended method for script installation is via a Bioconda recipe called bioconductor-sc3-scripts.

With the Bioconda channels configured the latest release version of the package can be installed via the regular conda install command:

conda install bioconductor-sc3-scripts

Test installation

There is a test script included:

bioconductor-sc3-scripts-post-install-tests.sh

This downloads a well-known test 10X dataset and executes all of the scripts described below.

Commands

The available wrapped SC3 functions are described below. Each script has usage instructions available via --help, consult function documentation in SC3 for further details. Wrappers are currently written for SC3 version 1.8.

sc3_prepare(): prepare a SingleCellExperiment for SC3

See ?sc3_prepare for argument meanings.

sc3-sc3-prepare.R -i <SingleCellExperiment object as .rds> -f <gene_filter> -p <pct_dropout_min> \
    -q <pct_dropout_max> -d <d_region_min> -e <d_region_max> -n <svm_num_cells> -m <svm_max> \
    -t <n_cores> -s <rand_seed> -k <kmeans_nstart> -a <kmeans_iter_max> \
    -o <path to file where .rds output file will be stored>

sc3_estimate_k(): Calculate k size for SC3 clustering

sc3-sc3-estimate-k.R -i <SC3 prepared SingleCellExperiment object as .rds> \
    -t <path to file where estimated k will be stored> \
    -o <path to file where .rds output file will be stored>

sc3_calc_dists(): Calculate distances

sc3-sc3-calc-dists.R -i <SingleCellExperiment object from sc3_estimate_k() as .rds> \
    -o <path to file where .rds output file will be stored>

sc3_calc_transfs(): Calculate transformations of the distance matrices

sc3-sc3-calc-transfs.R -i <SingleCellExperiment object from sc3_calc_dists() as .rds> \
    -o <path to file where .rds output file will be stored>

sc3_kmeans(): Cluster transform matrix using k-means

sc3-sc3-kmeans.R -i <SingleCellExperiment object from sc3_calc_transfs() as .rds> \
    -k <k values to try, comma-separated> -o <path to file where .rds output file will be stored>

sc3_calc_consens(): Calculate consensus clustering

sc3-calc-consens.R -i <SingleCellExperiment object from sc3_kmeans() as .rds> \
     -t <path to file where text output file will be stored> \
     -o <path to file where .rds output file will be stored>

jlchang/bioconductor-sc3-scripts