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HomosapienDEE2CellScore data package

dataset
posted on 11.08.2022, 01:49 authored by Justin MarshJustin Marsh

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")


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University of Auckland

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