Files in rkawalerski/pdacR
Obtains and analyzes PDAC transcriptomics data
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/Convert_GUI_data.R
R/ICGC_PARSE_Nones.R
R/ICGC_cluster_based_subtyping.R
R/convert_kmeans_to_dendrogram.R
R/convert_order_to_dendrogram.R
R/convert_to_SummarizedExperiment.R
R/create.classif.R
R/demoPdac.R
R/generate_data_set_list.R
R/generate_mouse_data_set_list.R
R/getSideColors.R
R/heatmap.3.R
R/implement_PAMG.R
R/install.dependencies.R
R/other_cluster_based_subtyping.R
R/parse_ICGC.R
R/parse_Moffitt_supplement.R
R/parse_Puleo_array.R
R/parse_TCGA_PAAD.R
R/parse_gene_lists.R
R/parse_moffitt_classifier.R
R/parse_scOh_atlas.R
R/pdacShiny.R
R/pull_CPTAC_seq.R
R/pull_Chen_from_GEO.R
R/pull_Moffitt_from_GEO.R
R/pull_Olive_from_GEO.R
R/pull_Seino_from_GEO.R
README.md
data/Bailey_readable_list.tsv
data/CPTAC_exp.rds
data/Chen_GEO_array.rds
data/MoffittTumorClassifier_Tue_Jun_9_2015_cv.ktsp.500.100.RData
data/Moffitt_GEO_array.rds
data/Moffitt_S2.Hs.rds
data/Moffitt_S2.Mm.rds
data/Moffitt_classifier_2015.RData
data/Moffitt_classifier_2019.RData
data/Nones_GEO_array.rds
data/Olive_2019.rds
data/PACA_AU_array.rds
data/PACA_AU_seq.rds
data/PACA_CA_seq.rds
data/Puleo_array.rds
data/Puleo_readable_list.tsv
data/Seino_GEO_array.RDS
data/Seino_GEO_array.rds
data/TCGA_PAAD.rds
data/classifier_list.RData
data/data_set_list.RData
data/data_set_list.rds
data/gene_lists.RData
data/gene_lists.rds
data/mouse_data_set_list.RData
data/mouse_data_set_list.rds
data/mouse_gene_lists.RData
data/scAtlas.pseudobulked.rds
images/Cartesian_selection.png
images/DE_output.png
images/DE_selection.png
images/Heatmap.png
images/Survival_selection.png
images/TCGA_filtering.png
images/gene_and_track_selection.png
images/tabs.png
images/tsne_with_dotplot.png
inst/analysis/Analysis_ADEX.Rmd
inst/analysis/Analysis_ADEX.pdf
inst/analysis/Analysis_Moffitt_array.Rmd
inst/analysis/Analysis_Moffitt_array.pdf
inst/analysis/Analysis_PACA_CA_MoffittS2_clusters.Rmd
inst/analysis/Analysis_PACA_CA_MoffittS2_clusters.pdf
inst/analysis/Analysis_PAMG.pdf
inst/analysis/Analysis_PAMG.rmd
inst/analysis/Analysis_Puleo.Rmd
inst/analysis/Analysis_Puleo.pdf
inst/analysis/Analysis_TCGA.Rmd
inst/analysis/Analysis_TCGA.pdf
inst/analysis/Analysis_paired_ICGC.Rmd
inst/analysis/Analysis_paired_ICGC.pdf
inst/shiny/.gitignore
inst/shiny/app.R
inst/shiny/webApp.R
man/Convert_GUI_data.Rd
man/ICGC_PARSE_Nones.Rd
man/ICGC_cluster_based_subtyping.Rd
man/convert_kmeans_to_dendrogram.Rd
man/convert_order_to_dendrogram.Rd
man/convert_to_SummarizedExperiment.Rd
man/create.classif.Rd
man/demoPdac.Rd
man/generate_data_set_list.Rd
man/generate_mouse_data_set_list.Rd
man/getSideColors.Rd
man/heatmap.3.Rd
man/implement_PAMG.Rd
man/other_cluster_based_subtyping.Rd
man/parse_ICGC.Rd
man/parse_Moffitt_supplement.Rd
man/parse_Puleo_Array.Rd
man/parse_TCGA_PAAD.Rd
man/parse_gene_lists.Rd
man/parse_moffitt_classifier.Rd
man/parse_scOh_atlas.Rd
man/pdacShiny.Rd
man/pull_Chen_from_GEO.Rd
man/pull_Moffitt_from_GEO.Rd
man/pull_Olive_from_GEO.Rd
man/pull_Seino_from_GEO.Rd
pdacR.Rproj
