Files in oldhamlab/Copeland.2021.hypoxia.flux
What the Package Does (One Line, Title Case)
.Rbuildignore
.gitignore
Copeland.2021.hypoxia.flux.Rproj
DESCRIPTION
NAMESPACE
R/1_expression.R
R/1_extracellular-fluxes.R
R/1_figures.R
R/1_flux-figures.R
R/1_matlab.R
R/1_metabolomics.R
R/1_mid-figures.R
R/1_mid.R
R/1_myc.R
R/1_nad.R
R/1_network-figures.R
R/1_rnaseq.R
R/1_two-factor-fluxes.R
R/1_utils.R
R/Copeland.2021.hypoxia.flux-package.R
R/cells_per_dna.R
R/correction_factors.R
R/flux_measurements.R
R/fluxes.R
R/growth_rates.R
R/k.R
R/mids.R
R/model_reactions.R
R/sysdata.rda
_packages.R
_targets.R
_targets_packages.R
analysis/biomass.Rmd
analysis/dna-per-cell.Rmd
analysis/extracellular-fluxes.Rmd
analysis/flux-differences.Rmd
analysis/mass-isotope-distributions.Rmd
analysis/metabolomics-targeted.Rmd
analysis/metabolomics-untargeted.Rmd
analysis/modeling/lf_05.m
analysis/modeling/lf_05/lf_05_2021-03-31_pc.mat
analysis/modeling/lf_21.m
analysis/modeling/lf_21/lf_21_2020-11-12_pc.mat
analysis/modeling/lf_BAY/lf_BAY_2020-12-31_pc.mat
analysis/modeling/lf_DMSO/lf_DMSO_2020-12-21_pc.mat
analysis/modeling/lf_bay.m
analysis/modeling/lf_dmso.m
analysis/modeling/matlab-input/lf_biomass.csv
analysis/modeling/matlab-input/lf_fluxes.csv
analysis/modeling/matlab-input/lf_mids.csv
analysis/modeling/matlab-input/pasmc_biomass.csv
analysis/modeling/matlab-input/pasmc_fluxes.csv
analysis/modeling/matlab-input/pasmc_mids.csv
analysis/modeling/matlab-input/reactions.csv
analysis/modeling/notes.Rmd
analysis/modeling/pasmc_05.m
analysis/modeling/pasmc_05/2021-05-07_pc.mat
analysis/modeling/pasmc_21.m
analysis/modeling/pasmc_21/2021-04-29_pc.mat
analysis/qbias-correction-factors.Rmd
analysis/rnaseq.Rmd
data-raw/cell-mass.csv
data-raw/cell-viability.csv
data-raw/dna-count-hypoxia.csv
data-raw/dna-per-cell-number.xlsx
data-raw/fluxes/lf_02/lf_02_a_2018-01-30.xlsx
data-raw/fluxes/lf_02/lf_02_a_2018-02-04.xlsx
data-raw/fluxes/lf_02/lf_02_a_2018-02-08.xlsx
data-raw/fluxes/lf_02/lf_02_a_2018-02-12.xlsx
data-raw/fluxes/lf_02/lf_02_meta.csv
data-raw/fluxes/lf_05-bay/lf_05-bay_d_2020-01-24.xlsx
data-raw/fluxes/lf_05-bay/lf_05-bay_d_2020-01-29.xlsx
data-raw/fluxes/lf_05-bay/lf_05-bay_d_2020-02-03.xlsx
data-raw/fluxes/lf_05-bay/lf_05-bay_d_2020-02-08.xlsx
data-raw/fluxes/lf_05-bay/lf_05-bay_meta.csv
data-raw/fluxes/lf_05-simyc/lf_05-simyc_d_2021-01-06.xlsx
data-raw/fluxes/lf_05-simyc/lf_05-simyc_d_2021-01-09.xlsx
data-raw/fluxes/lf_05-simyc/lf_05-simyc_d_2021-01-11.xlsx
data-raw/fluxes/lf_05-simyc/lf_05-simyc_d_2021-01-13.xlsx
data-raw/fluxes/lf_05-simyc/lf_05-simyc_meta.csv
data-raw/fluxes/lf_05/lf_05_a_2017-11-02.xlsx
data-raw/fluxes/lf_05/lf_05_a_2017-11-06.xlsx
data-raw/fluxes/lf_05/lf_05_a_2017-11-15.xlsx
data-raw/fluxes/lf_05/lf_05_a_2017-11-20.xlsx
data-raw/fluxes/lf_05/lf_05_b_2018-11-15.xlsx
data-raw/fluxes/lf_05/lf_05_b_2018-11-20.xlsx
data-raw/fluxes/lf_05/lf_05_b_2018-11-25.xlsx
data-raw/fluxes/lf_05/lf_05_b_2018-12-16.xlsx
data-raw/fluxes/lf_05/lf_05_meta.csv
data-raw/fluxes/lf_bay-myc/lf_bay-myc_d_2021-09-14.xlsx
data-raw/fluxes/lf_bay-myc/lf_bay-myc_d_2021-09-15.xlsx
data-raw/fluxes/lf_bay-myc/lf_bay-myc_d_2021-09-21.xlsx
data-raw/fluxes/lf_bay-myc/lf_bay-myc_d_2021-10-05.xlsx
data-raw/fluxes/lf_bay-myc/lf_bay-myc_d_2021-10-12.xlsx
data-raw/fluxes/lf_bay-myc/lf_bay-myc_d_2021-10-30.xlsx
data-raw/fluxes/lf_bay-myc/lf_bay-myc_d_2021-11-01.xlsx
data-raw/fluxes/lf_bay-myc/lf_bay-myc_meta.csv
data-raw/fluxes/lf_bay/lf_bay_a_2018-05-25.xlsx
data-raw/fluxes/lf_bay/lf_bay_a_2018-05-29.xlsx
data-raw/fluxes/lf_bay/lf_bay_a_2018-06-02.xlsx
data-raw/fluxes/lf_bay/lf_bay_a_2018-06-08.xlsx
data-raw/fluxes/lf_bay/lf_bay_b_2018-11-02.xlsx
data-raw/fluxes/lf_bay/lf_bay_b_2018-11-06.xlsx
data-raw/fluxes/lf_bay/lf_bay_b_2018-11-11.xlsx
data-raw/fluxes/lf_bay/lf_bay_b_2018-11-16.xlsx
data-raw/fluxes/lf_bay/lf_bay_meta.csv
data-raw/fluxes/pasmc_05/pasmc_05_c_2020-06-06.xlsx
data-raw/fluxes/pasmc_05/pasmc_05_c_2020-06-11.xlsx
data-raw/fluxes/pasmc_05/pasmc_05_c_2020-06-16.xlsx
data-raw/fluxes/pasmc_05/pasmc_05_c_2020-06-21.xlsx
data-raw/fluxes/pasmc_05/pasmc_05_meta.csv
data-raw/internal-data.R
data-raw/lf_05-bay_metabolomics-targeted.xlsx
data-raw/metabolomics/lf_05-bay/sample-sheet.csv
data-raw/mids/a_fs_lf_bay_2018-05-25.csv
data-raw/mids/a_fs_lf_bay_2018-05-29.csv
data-raw/mids/a_fs_lf_bay_2018-06-02.csv
data-raw/mids/a_fs_lf_bay_2018-06-08.csv
data-raw/mids/a_sim_lf_02_2018-01-30.csv
data-raw/mids/a_sim_lf_02_2018-02-04.csv
data-raw/mids/a_sim_lf_02_2018-02-08.csv
data-raw/mids/a_sim_lf_02_2018-02-12.csv
data-raw/mids/a_sim_lf_05_2017-11-02.csv
data-raw/mids/a_sim_lf_05_2017-11-06.csv
data-raw/mids/a_sim_lf_05_2017-11-15.csv
data-raw/mids/a_sim_lf_05_2017-11-20.csv
data-raw/mids/b_fs_lf_05_2018-11-15.csv
data-raw/mids/b_fs_lf_05_2018-11-20.csv
data-raw/mids/b_fs_lf_05_2018-11-25.csv
data-raw/mids/b_fs_lf_05_2018-12-16.csv
data-raw/mids/b_fs_lf_bay_2018-11-11.csv
data-raw/mids/b_fs_lf_bay_2018-11-16.csv
data-raw/mids/b_fs_lf_both_glc6_2019-05-06.csv
data-raw/mids/b_fs_lf_both_glc6_2019-05-10.csv
data-raw/mids/b_fs_lf_both_glc6_2019-05-14.csv
data-raw/mids/b_fs_lf_both_lac3_2019-05-06.csv
data-raw/mids/b_fs_lf_both_lac3_2019-05-10.csv
data-raw/mids/b_fs_lf_both_lac3_2019-05-14.csv
data-raw/mids/b_fs_pasmc_05_2020-06-06.csv
data-raw/mids/b_fs_pasmc_05_2020-06-11.csv
data-raw/mids/b_fs_pasmc_05_2020-06-16.csv
data-raw/mids/b_fs_pasmc_05_2020-06-21.csv
data-raw/mids/b_sim_lf_05_2018-11-15.csv
data-raw/mids/b_sim_lf_05_2018-11-20.csv
data-raw/mids/b_sim_lf_05_2018-11-25.csv
data-raw/mids/b_sim_lf_05_2018-12-16.csv
data-raw/mids/b_sim_lf_05_2019-03-10.csv
data-raw/mids/b_sim_lf_bay_2018-11-11.csv
data-raw/mids/b_sim_lf_bay_2018-11-16.csv
data-raw/mids/b_sim_lf_both_glc6_2019-05-06.csv
data-raw/mids/b_sim_lf_both_glc6_2019-05-10.csv
data-raw/mids/b_sim_lf_both_glc6_2019-05-14.csv
data-raw/mids/b_sim_lf_both_lac3_2019-05-06.csv
data-raw/mids/b_sim_lf_both_lac3_2019-05-10.csv
data-raw/mids/b_sim_lf_both_lac3_2019-05-14.csv
data-raw/mids/b_sim_pasmc_05_2020-06-06.csv
data-raw/mids/b_sim_pasmc_05_2020-06-11.csv
data-raw/mids/b_sim_pasmc_05_2020-06-16.csv
data-raw/mids/b_sim_pasmc_05_2020-06-21.csv
data-raw/model/lf_05_model.csv
data-raw/model/lf_21_model.csv
data-raw/model/lf_bay_model.csv
data-raw/model/lf_dmso_model.csv
data-raw/model/nodes.csv
data-raw/model/pasmc_05_model.csv
data-raw/model/pasmc_21_model.csv
data-raw/mrna/lf_02_glut1_ldha_serpine1_mrna_2018-04-11.csv
data-raw/mrna/lf_05_glut1_ldha_mrna_2018-04-11.csv
data-raw/mrna/lf_bay_glut1_ldha_mrna_2018-09-24.csv
data-raw/mrna/pasmc_05_glut1_ldha_mrna_2020-09-24.csv
data-raw/nad-assay/nad-assay_2020-07-24.xlsx
data-raw/nad-assay/nad-assay_2020-07-29.xlsx
data-raw/nad-assay/nad-assay_2020-08-04.xlsx
data-raw/nad-assay/nad-assay_2020-08-10.xlsx
data-raw/nad-assay/nad-assay_2020-08-14.xlsx
data-raw/q-bias-correction/q-bias-correction_a.csv
data-raw/q-bias-correction/q-bias-correction_b.csv
data/cells_per_dna.rda
data/correction_factors.rda
data/flux_differences.rda
data/flux_measurements.rda
data/fluxes.rda
data/growth_rates.rda
data/k.rda
data/mids.rda
data/model_fluxes.rda
data/model_reactions.rda
man/Copeland.2021.hypoxia.flux-package.Rd
man/cells_per_dna.Rd
man/correction_factors.Rd
man/flux_measurements.Rd
man/fluxes.Rd
man/grapes-nin-grapes.Rd
man/growth_rates.Rd
man/k.Rd
man/mids.Rd
man/model_reactions.Rd
manuscript/2021-12-07_wmo_hypoxia-flux_manuscript.docx
manuscript/2021-12-07_wmo_hypoxia-flux_supplement.docx
manuscript/2021-12-14_cover-letter.docx
manuscript/2021-12-14_wmo_hypoxia-flux_manuscript.docx
manuscript/2021-12-14_wmo_hypoxia-flux_supplement.docx
manuscript/2021-12-20_cover-letter.docx
manuscript/2021-12-20_wmo_hypoxia-flux_manuscript.docx
manuscript/2021-12-20_wmo_hypoxia-flux_supplement.docx
manuscript/2022-01-11_cover-letter.docx
manuscript/2022-01-11_wmo_hypoxia-flux_manuscript.docx
manuscript/2022-01-11_wmo_hypoxia-flux_supplement.docx
manuscript/author-info-blocks.lua
manuscript/cell-metabolism.csl
manuscript/figures/images/lf_02_hif1a-ldha-blots.ai
manuscript/figures/images/lf_05-bay_myc-blots.ai
manuscript/figures/images/lf_05-simyc_myc-blots.ai
manuscript/figures/images/lf_05_hif1a-ldha-blots.ai
manuscript/figures/images/lf_bay-myc_myc-blots.ai
manuscript/figures/images/lf_bay_hif1a-ldha-blots.ai
manuscript/figures/images/pasmc_05_hif1a-ldha-blots.ai
manuscript/library.bib
manuscript/manuscript.Rmd
manuscript/manuscript.docx
manuscript/multiple-bibliographies.lua
manuscript/nature-communications.csl
manuscript/packages.bib
manuscript/pagebreak.lua
manuscript/scholarly-metadata.lua
manuscript/supplement.Rmd
manuscript/supplement.docx
manuscript/template.docx
manuscript/template.tex
renv.lock
renv/.gitignore
renv/activate.R
renv/settings.dcf
