stpipeline.Rd
Create count matrix from spatial transcriptomics fasta
stpipeline( group = c("sudo", "docker"), scratch.folder, data.folder, genome.folder, fastqPathFolder, ID, imgNameAndPath, slide = NULL, area = NULL )
group, | a character string. Two options: sudo or docker, depending to which group the user belongs |
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scratch.folder, | a character string indicating the path of the scratch folder |
data.folder, | a character string indicating the path of the result folder. |
genome.folder, | a character string indicating the path of the genome folder. |
fastqPathFolder, | a character string indicating the path of fastq folder |
ID, | a character string indicating the name of the project |
imgNameAndPath, | path and name of tiff image file required for analysis. |
slide, | identificative number from dataset download |
area, | identificative value from dataset download |
count matrix from spatial transcriptomics
Luca Alessandri , alessandri [dot] luca1991 [at] gmail [dot] com, University of Torino
if (FALSE) { Dataset="curl -O http://s3-us-west-2.amazonaws.com/10x.files/samples/spatial-exp/1.0.0/V1_Mouse_Kidney/V1_Mouse_Kidney_fastqs.tar" DatasetImage="curl -O http://cf.10xgenomics.com/samples/spatial-exp/1.0.0/V1_Mouse_Kidney/V1_Mouse_Kidney_image.tif" referenceGenomeHG38="curl -O http://cf.10xgenomics.com/supp/spatial-exp/refdata-cellranger-GRCh38-3.0.0.tar.gz" referenceGenomeMM10="curl -O http://cf.10xgenomics.com/supp/spatial-exp/refdata-cellranger-mm10-3.0.0.tar.gz" stpipeline(group="docker", scratch.folder="/run/media/user/Maxtor4/scratch", data.folder="/run/media/user/Maxtor4/prova2", genome.folder="/home/user/spatial/refdata-cellranger-mm10-3.0.0", fastqPathFolder="/home/user/spatial/V1_Mouse_Kidney_fastqs", ID="hey",imgNameAndPath="/home/user/spatial/V1_Mouse_Kidney_image.tif",slide="V19L29-096",area="B1") }