kalganem/creedenzymatic
creedenzymatic

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creedenzymatic

.Rbuildignore
.Rprofile
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.github/workflows/pkgdown.yaml
.gitignore
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
R/combine_tools.R R/creedenzymatic.R R/data.R R/extract_top_kinases.R R/ptm_io.R R/ptm_utils.R R/quartile_figure.R R/rank_kinases.R R/read_kea.R R/read_krsa.R R/read_ptmsea.R R/read_uka.R R/run_kea.R R/run_ptmsea.R R/ssGSEA2.0_ce_version.R
R/sysdata.rda
R/utils.R README.Rmd README.md
_pkgdown.yml
creedenzymatic.Rproj
data-raw/KinomeMapping/2021_01_18-Justin-MasterExcel.xlsx
data-raw/KinomeMapping/2021_05_20-creedenzymatic_map.txt
data-raw/KinomeMapping/2021_06_11-creedenzymatic_map.txt
data-raw/KinomeMapping/2021_07_09-creedenzymatic_map.txt
data-raw/KinomeMapping/2021_07_09-creedenzymatic_map_KA_edits.txt
data-raw/KinomeMapping/2024_03_07-creedenzymatic_map_AH-ASI_edits.txt
data-raw/KinomeMapping/kinase_mapping.txt
data-raw/PTM_SEA_DB/PDCL15vsWT_input_PTM-SEA.gct_n1x167.gct
data-raw/PTM_SEA_DB/PDCL15vsWT_input_table.txt
data-raw/PTM_SEA_DB/parse_yaml_ssgsea.R
data-raw/PTM_SEA_DB/ptk_pamchip_86402_onlyChipPeps_dbs.gmt
data-raw/PTM_SEA_DB/ptm.sig.db.all.flanking.human.v1.8.1.gmt.txt
data-raw/PTM_SEA_DB/ptm.sig.db.all.uniprot.human.v1.9.0.gmt
data-raw/PTM_SEA_DB/ptm_sea_iptmnet_mapping_ptk.gmt
data-raw/PTM_SEA_DB/ptm_sea_iptmnet_mapping_stk.gmt
data-raw/PTM_SEA_DB/ptm_utils.R data-raw/PTM_SEA_DB/ssGSEA2.0.R data-raw/PTM_SEA_DB/ssGSEA2.0_ce_version.R
data-raw/PTM_SEA_DB/stk_pamchip_87102_onlyChipPeps_dbs.gmt
data-raw/PTM_SEA_DB/test_ptmsea.R
data-raw/Pamchips_Layout/2021_10_13-JFC_complete-ptk_peptides_mapping.txt
data-raw/Pamchips_Layout/2021_10_13-JFC_complete-stk_peptides_mapping-KA_edit.txt
data-raw/Pamchips_Layout/2021_10_13-JFC_complete-stk_peptides_mapping.txt
data-raw/Pamchips_Layout/86402_ArrayLayout.xlsx
data-raw/Pamchips_Layout/87102_ArrayLayout.xlsx
data-raw/Pamchips_Layout/PTK-196-PamChip-86402.pdf data-raw/Pamchips_Layout/STK-144-PamChip-87102.pdf
data-raw/iptm_net_input_ptk_chip.csv
data-raw/iptm_net_input_stk_chip.csv
data-raw/process_data.R
data-raw/runData.RData
data-raw/runDb.RData
data-raw/runDb_stk.RData
data/kinome_mp_file.rda
data/kinome_mp_file_v1.rda
data/kinome_mp_file_v2.rda
data/kinome_mp_file_v3.rda
data/kinome_mp_file_v4.rda
data/kinome_mp_file_v5.rda
data/kinome_mp_file_v6.rda
data/ptk_pamchip_86402_array_layout_ptmsea.rda
data/ptk_pamchip_86402_mapping.rda
data/ptk_pamchip_86402_onlyChipPeps_dbs.rda
data/ptm_sea_iptmnet_mapping_ptk.rda
data/ptm_sea_iptmnet_mapping_stk.rda
data/ptmsea_all_dbs.rda
data/stk_pamchip_87102_array_layout_ptmsea.rda
data/stk_pamchip_87102_mapping.rda
data/stk_pamchip_87102_onlyChipPeps_dbs.rda
data/uka_db_full.rda
data/uka_map_db.RDS
docs/404.html
docs/LICENSE-text.html
docs/LICENSE.html
docs/articles/creedenzymatic.html
docs/articles/creedenzymatic_files/figure-html/unnamed-chunk-4-1.png
docs/articles/creedenzymatic_files/figure-html/unnamed-chunk-5-1.png
docs/articles/creedenzymatic_files/figure-html/unnamed-chunk-5-2.png
docs/articles/creedenzymatic_files/figure-html/unnamed-chunk-6-1.png
docs/articles/creedenzymatic_files/header-attrs-2.11/header-attrs.js
docs/articles/creedenzymatic_files/header-attrs-2.6/header-attrs.js
docs/articles/creedenzymatic_files/header-attrs-2.9/header-attrs.js
docs/articles/index.html
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/GCT-class.html
docs/reference/Rplot001.png
docs/reference/annotate.gct.html
docs/reference/combine_tools.html
docs/reference/creedenzymatic.html
docs/reference/dot-align_matrices.html
docs/reference/dot-append.dim.html
docs/reference/dot-check_colnames.html
docs/reference/dot-check_dups.html
docs/reference/dot-extract.gct.html
docs/reference/dot-fix.datatypes.html
docs/reference/dot-is.wholenumber.html
docs/reference/dot-merge_with_precedence.html
docs/reference/dot-na_pad_matrix.html
docs/reference/dot-parse.gctx.html
docs/reference/dot-parse.gmt.html
docs/reference/dot-parse.gmx.html
docs/reference/dot-parse.grp.html
docs/reference/dot-process_ids.html
docs/reference/dot-read.gctx.ids.html
docs/reference/dot-read.gctx.meta.html
docs/reference/dot-subset_to_ids.html
docs/reference/dot-update.gctx.html
docs/reference/dot-write.gct.html
docs/reference/dot-write.gctx.html
docs/reference/dot-write.gctx.meta.html
docs/reference/dot-write.gmt.html
docs/reference/dot-write.grp.html
docs/reference/dot-write.tbl.html
docs/reference/extract_top_kinases.html
docs/reference/index.html
docs/reference/kinome_mp_file.html
docs/reference/kinome_mp_file_v1.html
docs/reference/kinome_mp_file_v2.html
docs/reference/kinome_mp_file_v3.html
docs/reference/kinome_mp_file_v4.html
docs/reference/melt.gct.html
docs/reference/merge.gct.html
docs/reference/ptk_pamchip_86402_array_layout_ptmsea.html
docs/reference/ptk_pamchip_86402_mapping.html
docs/reference/quartile_figure.html
docs/reference/rank.gct.html
docs/reference/rank_kinases.html
docs/reference/read_kea.html
docs/reference/read_krsa.html
docs/reference/read_ptmsea.html
docs/reference/read_uka.html
docs/reference/reexports.html
docs/reference/run_kea.html
docs/reference/run_ptmsea.html
docs/reference/stk_pamchip_87102_array_layout_ptmsea.html
docs/reference/stk_pamchip_87102_mapping.html
docs/reference/subset.gct.html
docs/reference/transpose.gct.html
docs/reference/uka_db_full.html
docs/sitemap.xml
inst/extdata/KRSA_example.txt
inst/extdata/UKA_example.txt
man/GCT-class.Rd man/annotate.gct.Rd man/combine_tools.Rd man/creedenzymatic.Rd man/dot-align_matrices.Rd man/dot-append.dim.Rd man/dot-check_colnames.Rd man/dot-check_dups.Rd man/dot-extract.gct.Rd man/dot-fix.datatypes.Rd man/dot-is.wholenumber.Rd man/dot-merge_with_precedence.Rd man/dot-na_pad_matrix.Rd man/dot-parse.gctx.Rd man/dot-parse.gmt.Rd man/dot-parse.gmx.Rd man/dot-parse.grp.Rd man/dot-process_ids.Rd man/dot-read.gctx.ids.Rd man/dot-read.gctx.meta.Rd man/dot-subset_to_ids.Rd man/dot-update.gctx.Rd man/dot-write.gct.Rd man/dot-write.gctx.Rd man/dot-write.gctx.meta.Rd man/dot-write.gmt.Rd man/dot-write.grp.Rd man/dot-write.tbl.Rd man/extract_top_kinases.Rd man/kinome_mp_file.Rd man/kinome_mp_file_v1.Rd man/kinome_mp_file_v2.Rd man/kinome_mp_file_v3.Rd man/kinome_mp_file_v4.Rd man/melt.gct.Rd man/merge.gct.Rd man/ptk_pamchip_86402_array_layout_ptmsea.Rd man/ptk_pamchip_86402_mapping.Rd man/quartile_figure.Rd man/rank.gct.Rd man/rank_kinases.Rd man/read_kea.Rd man/read_krsa.Rd man/read_ptmsea.Rd man/read_uka.Rd man/reexports.Rd man/run_kea.Rd man/run_ptmsea.Rd man/stk_pamchip_87102_array_layout_ptmsea.Rd man/stk_pamchip_87102_mapping.Rd man/subset.gct.Rd man/transpose.gct.Rd man/uka_db_full.Rd
renv.lock
renv/.gitignore
renv/activate.R
renv/settings.dcf
renv/settings.json
vignettes/.gitignore
vignettes/creedenzymatic.Rmd
vignettes/data_files/KEA3_2021-05-22-nick-stk-ad_v_ctrl-females-KRSA-LFC_df.txt
vignettes/data_files/KEA3_ex.txt
vignettes/data_files/KRSA_ex.txt
vignettes/data_files/UKA_ex.txt
vignettes/data_files/runData.RData
vignettes/data_files/runDb.RData
kalganem/creedenzymatic documentation built on March 31, 2024, 11:58 a.m.

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