CReSCENT: CanceR Single Cell ExpressioN Toolkit (CReSCENT) v2.0 PBMC example infiles and commands

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