stpipeline: Spatial transcriptomics pipeline

In kendomaniac/rCASC: rCASC reproducible Classification Analysis of Single Cell Sequencing Data

Spatial transcriptomics pipeline

Description

Create count matrix from spatial transcriptomics fasta

Usage

stpipeline(
  group = c("sudo", "docker"),
  scratch.folder,
  data.folder,
  genome.folder,
  fastqPathFolder,
  ID,
  imgNameAndPath,
  slide = NULL,
  area = NULL
)

Arguments

group	a character string. Two options: sudo or docker, depending to which group the user belongs
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

Value

count matrix from spatial transcriptomics

Author(s)

Luca Alessandri , alessandri [dot] luca1991 [at] gmail [dot] com, University of Torino

Examples

## Not run: 
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")

## End(Not run)

kendomaniac/rCASC documentation built on July 3, 2024, 6:05 a.m.