HomosapienDEE2CellScore data package

Dataset downloaded from dee2.io for hsapiens, and processed for use with the new version of CellScore that uses SummarizedExperiment to contain the data. Data was generated by running (in R 4.2.0):

BiocManager::install()

BiocManager::install("getDEE2")

library(Biobase)

library(SummarizedExperiment)

library(getDEE2)

library(devtools)

devtools::install_github(repo="flaviusb/CellScore")

library(CellScore)

library(DESeq2)

devtools::install_github(repo="flaviusb/homosapienDEE2CellScore", force=TRUE)

library(homosapienDEE2CellScore)

BiocManager::install("AnnotationHub")

BiocManager::install("ExperimentHub")

library(AnnotationHub)

library(AnnotationHubData)

library(ExperimentHub)

library(ExperimentHubData)

homosapienDEE2CellScoreData <- buildData(build_tsne=FALSE, build_raw=TRUE, build_srx_agg=TRUE)

writeOutSEZip(homosapienDEE2CellScoreData$qc_pass_raw, filename_base="hsDEE2cs_qc_pass_raw")

writeOutSEZip(homosapienDEE2CellScoreData$qc_warn_raw, filename_base="hsDEE2cs_qc_warn_raw")

writeOutSEZip(homosapienDEE2CellScoreData$qc_pass_agg, filename_base="hsDEE2cs_qc_pass_agg")

writeOutSEZip(homosapienDEE2CellScoreData$qc_warn_agg, filename_base="hsDEE2cs_qc_warn_agg")

writeOutSEZip(homosapienDEE2CellScoreData$qc_pass_deseq2, filename_base="hsDEE2cs_qc_pass_deseq2")

writeOutSEZip(homosapienDEE2CellScoreData$qc_warn_deseq2, filename_base="hsDEE2cs_qc_warn_deseq2")

writeOutSEZip(homosapienDEE2CellScoreData$qc_pass_rank, filename_base="hsDEE2cs_qc_pass_rank")

writeOutSEZip(homosapienDEE2CellScoreData$qc_warn_rank, filename_base="hsDEE2cs_qc_warn_rank")