R/data.R

In markowetzlab/SCperturb: Data package for various single cell perturbation experiments

################################################################################
# crop-seq
################################################################################

#' @name counts.datlinger2017_stim
#' @title Counts matrix from crop-seq datlinger2017 stimulated experiments
#' @format A mtx matrix with rows and columns corresponding to rowdata and coldata
"counts.datlinger2017_stim"


#' @name rowmetadata.datlinger2017_stim
#' @title metadata about the rows (transcriptional readout) from crop-seq datlinger2017 stimulated experiments
#' @format A data frame with variables:
#' 
"rowmetadata.datlinger2017_stim"


#' @name colmetadata.dalinger2017_stim
#' @title metadata about the columns (experiments) from crop-seq datlinger2017 stimulated experiments
#' @format A data frame with variables:
#' 
"colmetadata.datlinger2017_stim"

#' @name counts.datlinger2017_unstim
#' @title Counts matrix from crop-seq datlinger2017 unstimulated experiments
#' @format A mtx matrix with rows and columns corresponding to rowdata and coldata
"counts.datlinger2017_unstim"


#' @name rowmetadata.datlinger2017_unstim
#' @title metadata about the rows (transcriptional readout) from crop-seq datlinger2017 unstimulated experiments
#' @format A data frame with variables:
#' 
"rowmetadata.datlinger2017_unstim"


#' @name colmetadata.dalinger2017_unstim
#' @title metadata about the columns (experiments) from crop-seq datlinger2017 unstimulated experiments
#' @format A data frame with variables:
#' 
"colmetadata.datlinger2017_unstim"

################################################################################
# perturb-seq
################################################################################

#' @name counts.dixit2016_K562_highmoi
#' @title Counts matrix from pertub-seq dixit2016 K562 experiments
#' @format A mtx matrix with rows and columns corresponding to rowdata and coldata
"counts.dixit2016_K562_highmoi"


#' @name rowmetadata.dixit2016_K562_highmoi
#' @title metadata about the rows (transcriptional readout) from pertub-seq dixit2016 K562 experiments
#' @format A data frame with variables:
#' 
"rowmetadata.dixit2016_K562_highmoi"


#' @name colmetadata.dixit2016_K562_highmoi
#' @title metadata about the columns (experiments) from perturb-seq dixit2016 K562 experiments
#' @format A data frame with variables:
#' 
"colmetadata.dixit2016_K562_highmoi"


#' @name counts.dixit2016_K562_lowmoi
#' @title Counts matrix from pertub-seq dixit2016 K562 experiments
#' @format A mtx matrix with rows and columns corresponding to rowdata and coldata
"counts.dixit2016_K562_lowmoi"


#' @name rowmetadata.dixit2016_K562_lowmoi
#' @title metadata about the rows (transcriptional readout) from pertub-seq dixit2016 K562 experiments
#' @format A data frame with variables:
#' 
"rowmetadata.dixit2016_K562_lowmoi"


#' @name colmetadata.dixit2016_K562_lowmoi
#' @title metadata about the columns (experiments) from perturb-seq dixit2016 K562 experiments
#' @format A data frame with variables:
#' 
"colmetadata.dixit2016_K562_lowmoi"


################################################################################
# crisp-seq
################################################################################

#' @name counts.jaitin2016
#' @title Counts matrix from pertub-seq dixit2016 K562 experiments
#' @format A mtx matrix with rows and columns corresponding to rowdata and coldata
"counts.jaitin2016"


#' @name rowmetadata.jaitin2016
#' @title metadata about the rows (transcriptional readout) from pertub-seq dixit2016 K562 experiments
#' @format A data frame with variables:
#' 
"rowmetadata.jaitin2016"


#' @name colmetadata.jaitin2016
#' @title metadata about the columns (experiments) from perturb-seq dixit2016 K562 experiments
#' @format A data frame with variables:
#' 
"colmetadata.jaitin2016"


################################################################################
# jackson2019
################################################################################

#' @name rowmetadata.jackson2019
#' @title metadata about the rows (transcriptional readout) from all experiments in jackson2019 in yeast
#' @format A data frame with variables:
#' 
"rowmetadata.jackson2019"

#' @name counts.jackson2019_YPD
#' @title Counts matrix from jackson2019 YPD - Yeast Extract, Peptone, Glucose
#' @format A mtx matrix with rows and columns corresponding to rowdata and coldata
"counts.jackson2019_YPD"

#' @name colmetadata.jackson2019_YPD
#' @title metadata about the columns (experiments) from jackson2019 YPD
#' @format A data frame with variables:
#' 
"colmetadata.jackson2019_YPD"

#' @name counts.jackson2019_DIAUXY
#' @title Counts matrix from jackson2019 DIAUXY - YPD (Harvested after Post-Diauxic Shift)
#' @format A mtx matrix with rows and columns corresponding to rowdata and coldata
"counts.jackson2019_DIAUXY"

#' @name colmetadata.jackson2019_DIAUXY
#' @title metadata about the columns (experiments) from jackson2019 DIAUXY
#' @format A data frame with variables:
#' 
"colmetadata.jackson2019_DIAUXY"

#' @name counts.jackson2019_RAPA
#' @title Counts matrix from jackson2019 RAPA - YPD + 200 ng/mL Rapamycin
#' @format A mtx matrix with rows and columns corresponding to rowdata and coldata
"counts.jackson2019_RAPA"

#' @name colmetadata.jackson2019_RAPA
#' @title metadata about the columns (experiments) from jackson2019 RAPA
#' @format A data frame with variables:
#' 
"colmetadata.jackson2019_RAPA"

#' @name counts.jackson2019_YPEtOH
#' @title Counts matrix from jackson2019 YPEtOH - Yeast Extract, Peptone, Ethanol
#' @format A mtx matrix with rows and columns corresponding to rowdata and coldata
"counts.jackson2019_YPEtOH"

#' @name colmetadata.jackson2019_YPEtOH
#' @title metadata about the columns (experiments) from jackson2019 YPEtOH
#' @format A data frame with variables:
#' 
"colmetadata.jackson2019_YPEtOH"

#' @name counts.jackson2019_MMD
#' @title Counts matrix from jackson2019 MMD - Minimal Media (Glucose)
#' @format A mtx matrix with rows and columns corresponding to rowdata and coldata
"counts.jackson2019_MMD"

#' @name colmetadata.jackson2019_MMD
#' @title metadata about the columns (experiments) from jackson2019 MMD
#' @format A data frame with variables:
#' 
"colmetadata.jackson2019_MMD"

#' @name counts.jackson2019_MMEtOH
#' @title Counts matrix from jackson2019 MMEtOH - Minimal Media (Ethanol)
#' @format A mtx matrix with rows and columns corresponding to rowdata and coldata
"counts.jackson2019_MMEtOH"

#' @name colmetadata.jackson2019_MMEtOH
#' @title metadata about the columns (experiments) from jackson2019 MMEtOH
#' @format A data frame with variables:
#' 
"colmetadata.jackson2019_MMEtOH"

#' @name counts.jackson2019_NLIM-GLN
#' @title Counts matrix from jackson2019 NLIM-GLN - Nitrogen Limited Minimal Media (with Glutamine)
#' @format A mtx matrix with rows and columns corresponding to rowdata and coldata
"counts.jackson2019_NLIM-GLN"

#' @name colmetadata.jackson2019_NLIM-GLN
#' @title metadata about the columns (experiments) from jackson2019 NLIM-GLN
#' @format A data frame with variables:
#' 
"colmetadata.jackson2019_NLIM-GLN"

#' @name counts.jackson2019_NLIM-PRO
#' @title Counts matrix from jackson2019 NLIM-PRO - Nitrogen Limited Minimal Media (with Proline)
#' @format A mtx matrix with rows and columns corresponding to rowdata and coldata
"counts.jackson2019_NLIM-PRO"

#' @name colmetadata.jackson2019_NLIM-PRO
#' @title metadata about the columns (experiments) from jackson2019 NLIM-PRO
#' @format A data frame with variables:
#' 
"colmetadata.jackson2019_NLIM-PRO"

#' @name counts.jackson2019_NLIM-NH4
#' @title Counts matrix from jackson2019 NLIM-NH4 - Nitrogen Limited Minimal Media (with NH4)
#' @format A mtx matrix with rows and columns corresponding to rowdata and coldata
"counts.jackson2019_NLIM-NH4"

#' @name colmetadata.jackson2019_NLIM-NH4
#' @title metadata about the columns (experiments) from jackson2019 NLIM-NH4
#' @format A data frame with variables:
#' 
"colmetadata.jackson2019_NLIM-NH4"

#' @name counts.jackson2019_NLIM-UREA
#' @title Counts matrix from jackson2019 NLIM-UREA - Nitrogen Limited Minimal Media (with Urea)
#' @format A mtx matrix with rows and columns corresponding to rowdata and coldata
"counts.jackson2019_NLIM-UREA"

#' @name colmetadata.jackson2019_NLIM-UREA
#' @title metadata about the columns (experiments) from jackson2019 NLIM-UREA
#' @format A data frame with variables:
#' 
"colmetadata.jackson2019_NLIM-UREA"

#' @name counts.jackson2019_CSTARVE
#' @title Counts matrix from jackson2019 CSTARVE - 
#' @format A mtx matrix with rows and columns corresponding to rowdata and coldata
"counts.jackson2019_CSTARVE"

#' @name colmetadata.jackson2019_CSTARVE - Carbon Starvation
#' @title metadata about the columns (experiments) from jackson2019 CSTARVE
#' @format A data frame with variables:
#' 
"colmetadata.jackson2019_CSTARVE"