Files in mikeod38/ProvidenciaChemo

.Rbuildignore

.drake/.gitignore

.gitignore

CODE_OF_CONDUCT.md

DESCRIPTION

Figure_1A.html

Figure_1A.rmd

Figure_1B.html

Figure_1B.rmd

Figure_1C.html

Figure_1C.rmd Figure_1E_cfu.Rmd

Figure_1E_cfu.html

Figure_1F_mcherry.Rmd

Figure_1F_mcherry.html

Figure_2B.html

Figure_2D_30pct.Rmd

Figure_2D_30pct.html

Figure_2E_3D_TASuccinate.Rmd

Figure_2E_3D_TASuccinate.html

Figure_2G_Ext7b_tbh1rescue_cat1.Rmd

Figure_2G_Ext7b_tbh1rescue_cat1.html

Figure_2G_tbhSOS.Rmd

Figure_2G_tbhSOS.html

Figure_2b.Rmd Figure_3C_SOSJUKO.Rmd

Figure_3C_SOSJUKO.html

Figure_3D_TA_succinate_2KO.Rmd

Figure_3D_TA_succinate_2KO.html

Figure_3E_metabolites.Rmd

Figure_3E_metabolites.html

Figure_3F_TArescue.html

Figure_3f_TArescue.Rmd

Figure_4A_files/figure-html/dataload GPCRS-1.png

Figure_4A_files/figure-html/frequentist stats exp1-1.png

Figure_4A_octr1rescue.Rmd

Figure_4A_octr1rescue.html

Figure_4B_octr-1TA.Rmd

Figure_4B_octr-1TA.html

Figure_4D_2KOchoice.Rmd

Figure_4D_2KOchoice.html

Figure_4E_octr1_Choice.Rmd

Figure_4E_octr1_Choice.html

Figure_Ext10_eggLaying.Rmd

Figure_Ext10_eggLaying.html

Figure_Ext1a_attractants.Rmd

Figure_Ext1a_attractants.html

Figure_Ext1b_osm.Rmd

Figure_Ext1b_osm.html

Figure_Ext1d_tphGFP.Rmd

Figure_Ext1d_tphGFP.html

Figure_Ext1e_lid.Rmd

Figure_Ext1e_lid.html

Figure_Ext1f_supe.Rmd

Figure_Ext1f_supe.html

Figure_Ext1g_lifespan.Rmd

Figure_Ext1g_lifespan.html

Figure_Ext4c_Ext5c_Ext6.Rmd

Figure_Ext4c_Ext5c_Ext6.html

Figure_Ext7a_LTyr.Rmd

Figure_Ext7a_LTyr.html

Figure_Ext9A_receptors.html

Figure_Ext9a_mCherry.Rmd

Figure_Ext9a_mCherry.html

Figure_Ext9b_receptors.Rmd

Figure_Ext9b_receptors.html

Figure_n_Legends/.DS_Store

NAMESPACE

ProvidenciaChemo.Rproj

R/.DS_Store

R/ProvidenciaChemo-package.R R/exp.fit.all.log.R R/exp.fit.all.log.lin.R R/flag_outliers.R R/format_AttractData.R R/format_AvoidData.R R/format_AvoidData_median.R R/format_SOS.R R/ggplot_layers.R R/max_delta.R R/max_negdelta.R R/plot_ChemoIndex.R R/plot_color_themes.R R/plot_cooksD.R R/plot_outlier.resids.R R/plot_plasticityIndex.R R/recenter_fittedValues.R README.md

_site.yml

brms_uneq.rds

data/Bac_choice.csv

data/Chemotaxis-avoidance.csv

data/Figure1A_attractants.csv

data/Figure1A_attractants_B.csv

data/Figure1A_avoidance.csv

data/Figure_4A.csv

data/Figure_S1d_Supe_wcontrol.csv

data/Fruc_ring.csv

data/Fruc_ring.xlsx

data/SOS_OP50_JUb39.csv

data/egg_laying.numbers

data/egg_laying.xlsx

data/lifespan.csv

data/tph-1GFP.csv

data/wormpost_strains.csv

extdata/.DS_Store

extdata/Figure_1A_avoidance.csv

extdata/Figure_1B_PYb007.csv

extdata/Figure_1C_antibiotic.csv

extdata/Figure_1E_cfu.csv

extdata/Figure_1F_mcherry_oct_correlation.csv

extdata/Figure_2B_amines.csv

extdata/Figure_2D_30pct.csv

extdata/Figure_2E_3D_TAsucc.csv

extdata/Figure_2G_tbhSOS.csv

extdata/Figure_2g_tbh1rescue.csv

extdata/Figure_3A_NEEDSHOME.csv

extdata/Figure_3C_SOSJUKO.csv

extdata/Figure_3E_metabolites.csv

extdata/Figure_3f_TArescue.csv

extdata/Figure_4A_octr1Rescue.csv

extdata/Figure_4B_octr1TA.csv

extdata/Figure_4D_2KOchoice.csv

extdata/Figure_4E_octr1_Choice.csv

extdata/Figure_Ext10_eggLaying.csv

extdata/Figure_Ext1a_attractants.csv

extdata/Figure_Ext1b_osm.csv

extdata/Figure_Ext1d_tph1GFP.csv

extdata/Figure_Ext1e_lidAvoidance.csv

extdata/Figure_Ext1f_Supe.csv

extdata/Figure_Ext1g_lifespan.csv

extdata/Figure_Ext4-6Quant_metabo.csv

extdata/Figure_Ext7a_LTyr.csv

extdata/Figure_Ext7b_cat1.csv

extdata/Figure_Ext9a_mCherry.csv

extdata/Figure_Ext9b_receptors.csv

extdata/Figure_S1d_Supe.xlsx

extdata/Figure_S1e_Supe.csv

extdata/Figure_S2A.csv

extdata/Nonanone_SOS.csv

extdata/SOS_OP50_JUb39.csv

extdata/imaging.xlsx

extdata/lifespan.Rmd

extdata/lifespan.numbers

extdata/tdcKO_plateChemo.csv

extdata/tyra2_chemo/tyra2_chemo.csv

figures/Fig_ext1a.pdf figures/Figure1A.pdf

figures/Figure_1.ai

man/.DS_Store

man/ProvidenciaChemo-package.Rd man/exp.fit.all.log.Rd man/exp.fit.all.log.lin.Rd man/flag_outliers.Rd man/format_AttractData.Rd man/format_AvoidData.Rd man/format_AvoidData_median.Rd man/format_SOS.Rd man/ggplot_layers.Rd man/hello.Rd man/max_delta.Rd man/max_negdelta.Rd man/plot_ChemoIndex.Rd man/plot_color_themes.Rd man/plot_cooksD.Rd man/plot_outlier.resids.Rd man/plot_plasticityIndex.Rd man/recenter_fittedValues.Rd preprint.Rmd preprint/Figure1.pdf preprint/Figure2.pdf preprint/Figure3.pdf preprint/Figure4.pdf preprint/Figure_1v5.pdf preprint/Figure_2vB6.pdf

preprint/O'Donnell_MP.docx

preprint/Supplemental_Figs.pdf preprint/preprint.Rmd preprint/preprint.pdf

preprint/preprint.tex

preview.pdf

references.bib

scripts/AHS_Ca_Tyrosien.R scripts/ASH_glycerol_OPJU.R scripts/ASH_octanol_Ca.R scripts/Dilute_vConcOct_responses.R scripts/Figure1.R scripts/Figure1_drake.R scripts/Figure_Ext1f_lifespan.Rmd.Rmd scripts/Nonanone_SOS.Rmd scripts/PCA.R scripts/RingAssay_analysis.R scripts/SImulate_binary_power.R scripts/SImulate_binary_power.Rmd scripts/SOS_analysis.R scripts/bacterial_choce.R

scripts/brms_Gompertz.rds

scripts/brms_Gompertz_G_byStrain.rds

scripts/brms_Gompertz_G_gamma_byStrain.rds

scripts/brms_Gompertz_GbyStrain.rds

scripts/brms_Gompertz_RE.G.rds

scripts/brms_Gompertz_gamma_byStrain.rds

scripts/brms_eq.rds

scripts/brms_uneq.rds

scripts/cfu_data.R scripts/contig_lengths.R scripts/egg-laying.Rmd scripts/expfit_script.R scripts/plot_amines.R scripts/plot_tdcKO_plateChemo.R scripts/rel_log.R scripts/simulate_patch.R

mikeod38/ProvidenciaChemo documentation built on April 6, 2020, 11:57 p.m.

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