Files in AlexGa/GraftingScripts
Reproducible scripts for studying the graft formation
.Rbuildignore
.gitignore
DESCRIPTION
GraftingScripts.Rproj
LICENSE
NAMESPACE
R/analyses.R
R/data.R
R/plots.R
README.Rmd
README.md
README_files/figure-markdown_github-ascii_identifiers/barplot_up_down_example.png
README_files/figure-markdown_github-ascii_identifiers/unnamed-chunk-1-1.png
README_files/figure-markdown_github-ascii_identifiers/unnamed-chunk-2-1.png
README_files/figure-markdown_github-ascii_identifiers/unnamed-chunk-4-1.png
README_files/figure-markdown_github-ascii_identifiers/unnamed-chunk-5-1.png
README_files/figure-markdown_github/unnamed-chunk-1-1.png
README_files/figure-markdown_github/unnamed-chunk-2-1.png
README_files/figure-markdown_github/unnamed-chunk-4-1.png
data/baySeq_grafting_lists.rda
data/exp.data.rda
data/fc.list.rda
data/gene_lists.rda
data/go_result_lists.rda
data/graft_gene_lists.rda
data/groupS.rda
data/intersect_lists_graft_formation.rda
data/ml.list.down.rda
data/ml.list.up.rda
data/sym_asym_bS.rda
data/sym_asym_table_list.rda
data/treatments.rda
inst/extdata/Timepoints_overlap/gene_sets_time_points_1uM_3h_down_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_1uM_3h_down_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_1uM_3h_up_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_1uM_3h_up_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_250_random_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_250_random_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_500_random_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_500_random_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_A 3h Glucose repressed_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_A 3h Glucose repressed_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_ABAdown_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_ABAdown_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_ABAup_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_ABAup_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_ACCdown_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_ACCdown_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_ACCup_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_ACCup_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_APL_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_APL_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Asahina_3DAC_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Asahina_3DAC_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_B 3h Glucose induced_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_B 3h Glucose induced_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_BLdown_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_BLdown_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_BLup_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_BLup_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_CKdown_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_CKdown_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_CKup_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_CKup_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Efroni_cortex_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Efroni_cortex_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Efroni_epidermis+LRC_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Efroni_epidermis+LRC_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Efroni_pericycle_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Efroni_pericycle_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Efroni_phloem_APL_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Efroni_phloem_APL_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Efroni_protoxylem_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Efroni_protoxylem_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Efroni_stele_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Efroni_stele_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Efroni_trichoblast_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Efroni_trichoblast_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Goda_S5_down_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Goda_S5_down_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Goda_S5_up_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Goda_S5_up_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_IAAdown_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_IAAdown_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_IAAup_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_IAAup_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Ikeuchi_Cluster1_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Ikeuchi_Cluster1_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Ikeuchi_Cluster2_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Ikeuchi_Cluster2_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Ikeuchi_Cluster3_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Ikeuchi_Cluster3_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Ikeuchi_Cluster4_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Ikeuchi_Cluster4_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Ikeuchi_Cluster5_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Ikeuchi_Cluster5_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Iwase_S1_T87_up_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Iwase_S1_T87_up_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Iwase_S2_T87_down_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Iwase_S2_T87_down_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_K 3h mannitol repressed_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_K 3h mannitol repressed_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Kondo_S1_2014_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Kondo_S1_2014_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Kondo_VISUAL_4X_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Kondo_VISUAL_4X_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_L 3h mannitol induced_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_L 3h mannitol induced_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Libault_up_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Libault_up_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Long_10_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Long_10_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Long_11_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Long_11_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Long_12_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Long_12_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Long_1_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Long_1_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Long_2_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Long_2_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Long_3R_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Long_3R_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Long_4_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Long_4_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Long_5_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Long_5_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Long_6_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Long_6_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Long_7_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Long_7_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Long_8_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Long_8_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Long_9_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Long_9_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Long_Colum_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Long_Colum_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_MJdown_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_MJdown_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_MJup_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_MJup_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Price sugar down_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Price sugar down_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Price sugar up_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Price sugar up_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Ramonell_S3_up_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Ramonell_S3_up_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_S18_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_S18_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_S2_S3h_CSt3h_down_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_S2_S3h_CSt3h_down_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_S2_S3h_CSt3h_up_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_S2_S3h_CSt3h_up_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_SCR5_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_SCR5_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Yin_down_S2_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Yin_down_S2_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Yin_up_S2_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Yin_up_S2_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Zhao S3 X_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Zhao S3 X_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Zhao S4 PC_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Zhao S4 PC_fg_up.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Zhao S5 NV_fg_down.xlsx
inst/extdata/Timepoints_overlap/gene_sets_time_points_Zhao S5 NV_fg_up.xlsx
inst/extdata/all_gene_subsets_from_manuscript.xlsx
inst/extdata/all_gene_subsets_from_manuscript_original.xlsx
inst/extdata/overlap_gene_sets_logFC_1_ml_09.xlsx
man/Compute_GO_Enrichment.Rd
man/adjust_and_split.Rd
man/barplot_graft_formation.Rd
man/barplot_up_down.Rd
man/do_fisher_up_down.Rd
man/exp.data.Rd
man/fc.list.Rd
man/groupS.Rd
man/intersect.analysis.Rd
man/ml.list.down.Rd
man/ml.list.up.Rd
man/plotPCA.Rd
man/plot_colored_dendrogram.Rd
man/test_sym_asym.Rd
