diff --git a/README.md b/README.md index c95f864..d4c1134 100644 --- a/README.md +++ b/README.md @@ -68,8 +68,7 @@ For a comprehensive decription of each Analytical Step please visit scRNAbox's [ ## Installation -`scrnabox.slurm` is written in the bash and, therefoe, can be used with any slurm system. To download the latest version of -`scrnabox.slurm` (v0.1.35) run the following command: +`scrnabox.slurm` is written in bash and can be used with any Slurm system. To download the latest version of `scrnabox.slurm` (v0.1.35) run the following command: ``` wget https://github.com/neurobioinfo/scrnabox/releases/download/v0.1.35/scrnabox.slurm.zip unzip scrnabox.slurm.zip @@ -80,13 +79,19 @@ For a description of the options for running `scrnabox.slurm` run the following bash ./scrnabox.slurm/launch_scrnabox.sh -h ``` -`scrnabox.slurm` needs `R` and `cellranger`. For the R, you need to install -`'Seurat','ggplot2', 'dplyr', 'foreach', 'doParallel', 'Matrix', 'DoubletFinder','cowplot','clustree'`. Then install `'scrnaboxR'`: +`scrnabox.slurm` requires that `R` and `cellranger` are also installed on the HPC system. In addition, the following R packages must be loaded: `'Seurat','ggplot2', 'dplyr', 'foreach', 'doParallel', 'Matrix', 'DoubletFinder','cowplot','clustree'`. Then users must install the `'scrnaboxR'` R package by running the following command: ``` devtools::install_github("neurobioinfo/scrnabox/scrnaboxR") ``` -The `'scrnaboxR'` is an R package that provides a collection of functions for conducting enrichment analysis and other analyses associated with single-cell RNA sequencing (scRNA-seq) data. It serves as a companion to scrnabox, offering a range of tools and functionalities to enhance scRNA-seq data analysis. You need to add the R info in `scrnabox_config.ini`, you can define the path of R library in `R_LIB_PATH=`, version of R in `R_VERSION`, you can add the path of `cell ranger`in `MODULECELLRANGER` +`'scrnaboxR'` provides a collection of functions for conducting enrichment analysis and other analyses associated with scRNAseq data. It serves as a companion to scRNAbox, offering a range of tools and functionalities to enhance scRNA-seq data analysis. +Please note that all R packages must be loaded into a common R library. For further instructions regarding the preparation of an R library please visit scRNAbox's [documentation](https://neurobioinfo.github.io/scrnabox/site/). Users must then define the location of their R library (`R_LIB_PATH=`), their version of R (`R_VERSION`), and the location of CellRanger (`MODULECELLRANGER`) in the `scrnabox_config.ini` file which is deposited into the working directory upon running the pipeline initation step: +``` +bash ./scrnabox.slurm/launch_scrnabox.sh \ +-d ./working_directory \ +--steps 0 \ +--method SCRNA +``` ## Tutorial You can find the details of how to use the pipeline in the