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

CReSCENT: CanceR Single Cell ExpressioN Toolkit (CReSCENT) v2.0
Example PBMC infiles and parameters

(c) Pugh Lab. Under GNU General Public License v3.0

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## CONTENTS
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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