CReSCENT: CanceR Single Cell ExpressioN Toolkit (CReSCENT) v2.0 Example PBMC infiles and parameters (c) Pugh Lab. Under GNU General Public License v3.0 ############## ## CONTENTS ############## A) File crescent_v2.0_pbmc_example_infiles_and_commands.tar.bz2, folder INPUT_MTX contains four scRNA-seq PBMC datasets obtained from 10X https://www.10xgenomics.com/resources/datasets/ Two of them originally had ~8,000 and ~10,000 cells, and were downsampled to 1,000 B) File crescent_v2.0_pbmc_example_infiles_and_commands.tar.bz2, folder LISTS_AND_COMMANDS contains the tables with input parameters for the integration of the four datasets above, using the four CReSCENT scRNA-seq one-line-command R scripts: 1) Runs_Seurat_v3_MultiDatasets_QC_Normalization.R 2) Runs_Seurat_v3_MultiDatasets_Integration.R 3) Runs_Seurat_v3_MultiDatasets_PCA_Clustering_DimReduction.R 4) Runs_Seurat_v3_MultiDatasets_DGE.R Which can be obtained from: https://github.com/pughlab/crescent/tree/master/bin/in_use For help on how to run these scripts, in a Console/Terminal type: `Rscript Runs_Seurat_v3_MultiDatasets_QC_Normalization.R -h` Each script code has a section 'Required libraries' For Bug Reports and Feature Requests, please fill out a GitHub ticket: https://github.com/pughlab/crescent/issues C) File crescent_v2.0_pbmc_example_infiles_and_commands.tar.bz2, folder METADATA contains two tables with cell-level metadata to colour UMAP/TSNE plots and to compare class_1 vs. class_2 for Differential Gene Expression detection D) File crescent_v2.0_pbmc_example_outfiles.tar.bz2, folder SEURAT contains the results obtained by running the scripts using CReSCENT scripts GitHub version 5a78fe9. See sub-folder 'SEURAT/LOG_FILES' for R library versions and commands used for each script E) File crescent_gsva_pbmcs_example_infiles_and_commands.tar.bz2, folder INFILES contains example infiles to run Runs_GSVA.R F) File crescent_gsva_pbmcs_example_outfiles_and_commands.tar.bz2, folder GSVA contains the results obtained by running script Runs_GSVA.R folder LOG_FILES contains log files, including commands used for the run G) File crescent_infercnv_glio_example_infiles_and_commands.tar.bz2, folder INPUTS contains example infiles to run Runs_InferCNV.R H) File crescent_infercnv_glio_example_outfiles_and_commands.tar.bz2, folder INFERCNV contains the results obtained by running script Runs_InferCNV.R folder LOG_FILES contains log files, including commands used for the run