Files in mikeod38/dauergut
Scripts for rict-1 dauer paper
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DESCRIPTION
Figure_1.Rmd
Figure_1.html
Figure_1_files/figure-html/gut resc plot-1.png
Figure_1_files/figure-html/plot TORC2-1.png
Figure_2.Rmd
Figure_2.aux
Figure_2.fdb_latexmk
Figure_2.fls
Figure_2.html
Figure_2.log
Figure_2.out
Figure_2.tex
Figure_2_files/figure-html/2A daf-7 stats-1.png
Figure_2_files/figure-html/daf7 FISH-1.png
Figure_2_files/figure-html/daf7 pheromone response-1.png
Figure_2_files/figure-html/plot daf-16-1.png
Figure_2_files/figure-html/rict-1 food plot-1.png
Figure_2_files/figure-html/rict-1 pheromone response-1.png
Figure_2_files/figure-html/unnamed-chunk-2-1.png
Figure_2_files/figure-html/unnamed-chunk-4-1.png
Figure_2_files/figure-html/unnamed-chunk-5-1.png
Figure_3.Rmd
Figure_3.html
Figure_3_files/figure-html/daf-28 temp curve-1.png
Figure_3_files/figure-html/daf-28 temp curve-2.png
Figure_3_files/figure-html/daf-28GFP rict-1 25v27-1.png
Figure_3_files/figure-html/daf-28GFP rict-1 25v27-2.png
Figure_3_files/figure-html/daf28 FISH analysis-1.png
Figure_3_files/figure-html/daf7 FISH analysis-1.png
Figure_3_files/figure-html/daf7 temp data-1.png
Figure_3_files/figure-html/daf7FISH plot-1.png
Figure_3_files/figure-html/plot daf28FISH-1.png
Figure_3_files/figure-html/unnamed-chunk-1-1.png
Figure_3_files/figure-html/unnamed-chunk-2-1.png
Figure_4.Rmd
Figure_4.html
Figure_4_files/figure-html/daf-28 increased by HB101-1.png
Figure_4_files/figure-html/pdf2 roam suppression plot-1.png
Figure_4_files/figure-html/pdfr-1 duaer plot-1.png
Figure_4_files/figure-html/pdfr-1 roam suppression plot-1.png
Figure_4_files/figure-html/plot starved roam quantified-1.png
Figure_4_files/figure-html/rict roam resuce plot-1.png
Figure_4_files/figure-html/rict-1 food plot-1.png
Figure_4_files/figure-html/roam beh plot-1.png
Figure_5.Rmd
Figure_5.html
Figure_5_files/figure-html/C327 corr plot-1.png
Figure_5_files/figure-html/pdfr-1 dauer phenotype-1.png
Figure_5_files/figure-html/pdfr-1 duaer plot-1.png
Figure_5_files/figure-html/pdfr-1 roam suppression plot-1.png
Figure_5_files/figure-html/pdfr-1 roam suppression plot-2.png
Figure_5_files/figure-html/pdfr-1 roam suppression plot-3.png
Figure_5_files/figure-html/plot starved roam quantified-1.png
Figure_5_files/figure-html/rict roam resuce plot-1.png
Figure_5_files/figure-html/rict-1 roam rescue plot-1.png
Figure_5_files/figure-html/rict-1 roam rescue plot-2.png
Figure_5_files/figure-html/rict-1 roam rescue plot-3.png
Figure_5_files/figure-html/roam beh plot-1.png
Figure_5_files/figure-html/roaming mutliple assays-1.png
Figure_5_files/figure-html/starved roam quantification-1.png
Figure_5_files/figure-html/wild isolate roaming-1.png
Figure_5_files/figure-html/wild screen dataload-1.png
Figure_6.Rmd
Figure_6.html
Figure_6_files/figure-html/C327 corr plot-1.png
Figure_6_files/figure-html/CSS glmm-1.png
Figure_6_files/figure-html/CSSII pheromone-1.png
Figure_6_files/figure-html/MONIL plot-1.png
Figure_6_files/figure-html/NKDG CRISPR-2.png
Figure_6_files/figure-html/glmm ewIR strains-1.png
Figure_6_files/figure-html/roam QTL-1.png
Figure_6_files/figure-html/wild isolate roaming-1.png
Figure_6_files/figure-html/wild isolate roaming-2.png
Figure_6_files/figure-html/wild isolate roaming-3.png
Figure_6_files/figure-html/wild screen dataload-1.png
Figure_7.Rmd
Figure_7.html
Figure_7_files/figure-html/CSS glmm-1.png
Figure_7_files/figure-html/CSSII pheromone-1.png
Figure_7_files/figure-html/MONIL plot-1.png
Figure_7_files/figure-html/NKDG CRISPR-1.png
Figure_7_files/figure-html/glmm ewIR strains-1.png
Figure_7_files/figure-html/roam QTL-1.png
Figure_7_files/figure-html/roam QTL-2.png
Figure_7_files/figure-html/roam QTL-3.png
NAMESPACE
R/MM_CI_trans_Tukey.R
R/MM_CI_trans_dunnett.R
R/MM_CIs.R
R/add.setts.attr.R
R/box_annot.R
R/dunnett_contrasts.R
R/flag_outliers.R
R/format_dauer.R
R/fun_length.R
R/getStan_CIs.R
R/get_alpha.R
R/ggplot_layers.R
R/par.replicate.R
R/plot_CIs.R
R/plot_CIs_dark.R
R/plot_cooksD.R
R/plot_dauer_SEs.R
R/plot_dauer_noCIs.R
R/plot_outlier.resids.R
R/plot_regression_se.R
R/plot_regression_seone.R
R/prange.R
R/run_dauer_stan.R
R/sim_dauer.R
R/sim_dauer_biased.R
R/sim_dauer_unbal.R
R/tukey_contrasts.R
README.html
README.md
_site.yml
about.Rmd
about.html
dauergut.Rproj
extdata/1A_hids.csv
extdata/1B_2D_rict-1_TORC2.csv
extdata/1C_ges-1_rescue_rict_sgk.csv
extdata/2A_3A_daf7GFP.csv
extdata/2B_daf7FISH_4frames.csv
extdata/2C_Daf28GFP_rescue.csv
extdata/3BEF_daf-28_GFP_rict-1.csv
extdata/3C_daf7_28_FISH.csv
extdata/4A_rict-1_food_allbinary.csv
extdata/4B_4E_gridentry.csv
extdata/4D_roam_dwell_all.csv
extdata/4F_pdf2_roam.csv
extdata/5A_wildHTdata_allbinary.csv
extdata/5B_6F_roam_wild_isolates.csv
extdata/6A_CSSdata_allbinary.csv
extdata/6C_chrII.markers.concise.csv
extdata/6C_ewIRdata_allbinary.csv
extdata/6E_MONIL_allbinary.csv
extdata/6E_MONIL_mapping.csv
extdata/N2_alldata.csv
extdata/S1C_rict1Pheromone.csv
extdata/S1D_daf7_daf28_suppression.csv
extdata/S1E_daf16_suppression.csv
extdata/S2B_starved_roam_dwell_all.csv
extdata/S2C_pdfr_dauer.csv
extdata/S3A_C3_sumstats.csv
extdata/S3_wildC3_data.csv
extdata/S4A_CSSII_ascr5.csv
extdata/S4C_NKDG_allbinary.csv
extdata/WS254.CHII.NIL59.variants.gff2
extdata/excluded_datasets/1C_hid_crispr.csv
extdata/excluded_datasets/RT_PCR_analysis.R
extdata/excluded_datasets/RT_rict-1.csv
extdata/excluded_datasets/RT_rict-1.xlsx
extdata/excluded_datasets/dia_chemotaxis.csv
extdata/excluded_datasets/fructose_dia_assay.csv
extdata/sim_data/I0_sP0.1_sD0.5_sG0.5_A0_B0_modelbalanced.alphas
extdata/sim_data/I0_sP0.1_sD0.5_sG0.5_A0_B0_modelbalanced.data
extdata/sim_data/I0_sP0.1_sD0.5_sG0.5_A0_B0_modelbiased.alphas
extdata/sim_data/I0_sP0.1_sD0.5_sG0.5_A0_B0_modelbiased.data
extdata/sim_data/biasmodel_sim_alphas
extdata/sim_data/biasmodel_simdata
extdata/sim_data/mean.0.b0.large_sG
extdata/sim_data/mean.0.b1.large_sG
extdata/sim_data/mean.neg2.2.b0.large_sG
extdata/sim_data/mean.neg2.2.b1.large_sG
extdata/sim_data/model_sim_alphas
extdata/sim_data/model_simdata
extdata/sim_data/sim_data_large_sD
extdata/sim_data/sim_data_large_sG
extdata/sim_data/table_S2_simulations.xlsx
figures/1A_TORC_model.png
figures/1B_mTORC2_dauer.pdf
figures/2A_daf7GFP.png
figures/2D_daf-28GFP.png
figures/4A_cartoon.png
figures/4C_roam_dwell_density.png
figures/6B_ewIR_map.png
figures/6D_QTL1.png
figures/7_model.png
figures/N2_SUM_daf28GFP_N2_27-08-1.tif
figures/N2_SUM_daf7GFP_L1_27deg-09.tif
figures/N2_SUM_daf7GFP_L1_27deg-09_inferno.tif
figures/N2_SUM_daf7GFP_L1_27deg-10.tif
figures/Rplot01.jpeg
figures/S1A_daf7FISH.png
figures/S2A_starve_roam_density.png
figures/S4B_rict-1_locus.png
figures/ft7_SUM_daf28GFP_ft7_27-03.tif
figures/ft7_SUM_daf7GFP_L1_27deg-07.tif
figures/ft7_SUM_daf7GFP_L1_27deg-07_inferno.tif
figures/ft7_SUM_daf7GFP_L1_27deg-08.tif
figures/mTOR_model.ai
figures/mTOR_model.png
index.Rmd
index.html
man/MM_CI_trans_Tukey.Rd
man/MM_CI_trans_dunnett.Rd
man/MM_CIs.Rd
man/add.setts.attr.Rd
man/box_annot.Rd
man/dunnett_contrasts.Rd
man/flag_outliers.Rd
man/format_dauer.Rd
man/fun_length.Rd
man/getStan_CIs.Rd
man/get_alpha.Rd
man/ggplot_layers.Rd
man/par.replicate.Rd
man/plot_CIs.Rd
man/plot_CIs_dark.Rd
man/plot_cooksD.Rd
man/plot_dauer_SEs.Rd
man/plot_dauer_noCIs.Rd
man/plot_outlier.resids.Rd
man/plot_regression_se.Rd
man/plot_regression_seone.Rd
man/prange.Rd
man/run_dauer_stan.Rd
man/sim_dauer.Rd
man/sim_dauer_biased.Rd
man/sim_dauer_unbal.Rd
man/tukey_contrasts.Rd
scripts/Count_CB4856_SNPs.R
scripts/N2_alldata_glmm.R
scripts/Speed_Curvature.R
scripts/Speed_curve_4xParallel.R
scripts/additional_data.Rmd
scripts/plot_CIs_ppt.R
scripts/plot_cmkGFP.R
scripts/select_variants.sh
scripts/sim_dauer.R
scripts/sim_dauer_data.R
scripts/sim_dauer_unbal.R
scripts/sim_dauer_unbal_biased.R
site_libs/bootstrap-3.3.5/css/bootstrap-theme.css
site_libs/bootstrap-3.3.5/css/bootstrap-theme.css.map
site_libs/bootstrap-3.3.5/css/bootstrap-theme.min.css
site_libs/bootstrap-3.3.5/css/bootstrap.css
site_libs/bootstrap-3.3.5/css/bootstrap.css.map
site_libs/bootstrap-3.3.5/css/bootstrap.min.css
site_libs/bootstrap-3.3.5/css/cerulean.min.css
site_libs/bootstrap-3.3.5/css/cosmo.min.css
site_libs/bootstrap-3.3.5/css/flatly.min.css
site_libs/bootstrap-3.3.5/css/fonts/Lato.ttf
site_libs/bootstrap-3.3.5/css/fonts/LatoBold.ttf
site_libs/bootstrap-3.3.5/css/fonts/LatoItalic.ttf
site_libs/bootstrap-3.3.5/css/fonts/NewsCycle.ttf
site_libs/bootstrap-3.3.5/css/fonts/NewsCycleBold.ttf
site_libs/bootstrap-3.3.5/css/fonts/OpenSans.ttf
site_libs/bootstrap-3.3.5/css/fonts/OpenSansBold.ttf
site_libs/bootstrap-3.3.5/css/fonts/OpenSansBoldItalic.ttf
site_libs/bootstrap-3.3.5/css/fonts/OpenSansItalic.ttf
site_libs/bootstrap-3.3.5/css/fonts/OpenSansLight.ttf
site_libs/bootstrap-3.3.5/css/fonts/OpenSansLightItalic.ttf
site_libs/bootstrap-3.3.5/css/fonts/Raleway.ttf
site_libs/bootstrap-3.3.5/css/fonts/RalewayBold.ttf
site_libs/bootstrap-3.3.5/css/fonts/Roboto.ttf
site_libs/bootstrap-3.3.5/css/fonts/RobotoBold.ttf
site_libs/bootstrap-3.3.5/css/fonts/RobotoLight.ttf
site_libs/bootstrap-3.3.5/css/fonts/RobotoMedium.ttf
site_libs/bootstrap-3.3.5/css/fonts/SourceSansPro.ttf
site_libs/bootstrap-3.3.5/css/fonts/SourceSansProBold.ttf
site_libs/bootstrap-3.3.5/css/fonts/SourceSansProItalic.ttf
site_libs/bootstrap-3.3.5/css/fonts/SourceSansProLight.ttf
site_libs/bootstrap-3.3.5/css/fonts/Ubuntu.ttf
site_libs/bootstrap-3.3.5/css/journal.min.css
site_libs/bootstrap-3.3.5/css/lumen.min.css
site_libs/bootstrap-3.3.5/css/paper.min.css
site_libs/bootstrap-3.3.5/css/readable.min.css
site_libs/bootstrap-3.3.5/css/sandstone.min.css
site_libs/bootstrap-3.3.5/css/simplex.min.css
site_libs/bootstrap-3.3.5/css/spacelab.min.css
site_libs/bootstrap-3.3.5/css/united.min.css
site_libs/bootstrap-3.3.5/css/yeti.min.css
site_libs/bootstrap-3.3.5/fonts/glyphicons-halflings-regular.eot
site_libs/bootstrap-3.3.5/fonts/glyphicons-halflings-regular.svg
site_libs/bootstrap-3.3.5/fonts/glyphicons-halflings-regular.ttf
site_libs/bootstrap-3.3.5/fonts/glyphicons-halflings-regular.woff
site_libs/bootstrap-3.3.5/fonts/glyphicons-halflings-regular.woff2
site_libs/bootstrap-3.3.5/js/bootstrap.js
site_libs/bootstrap-3.3.5/js/bootstrap.min.js
site_libs/bootstrap-3.3.5/js/npm.js
site_libs/bootstrap-3.3.5/shim/html5shiv.min.js
site_libs/bootstrap-3.3.5/shim/respond.min.js
site_libs/crosstalk-1.0.0/css/crosstalk.css
site_libs/crosstalk-1.0.0/js/crosstalk.js
site_libs/crosstalk-1.0.0/js/crosstalk.js.map
site_libs/crosstalk-1.0.0/js/crosstalk.min.js
site_libs/crosstalk-1.0.0/js/crosstalk.min.js.map
site_libs/highlightjs-1.1/default.css
site_libs/highlightjs-1.1/highlight.js
site_libs/highlightjs-1.1/textmate.css
site_libs/highlightjs-9.12.0/default.css
site_libs/highlightjs-9.12.0/highlight.js
site_libs/highlightjs-9.12.0/textmate.css
site_libs/htmlwidgets-0.9/htmlwidgets.js
site_libs/jquery-1.11.3/jquery.min.js
site_libs/navigation-1.1/codefolding.js
site_libs/navigation-1.1/sourceembed.js
site_libs/navigation-1.1/tabsets.js
site_libs/plotly-binding-4.7.1/plotly.js
site_libs/plotlyjs-1.29.2/LICENSE
site_libs/plotlyjs-1.29.2/plotly-htmlwidgets.css
site_libs/plotlyjs-1.29.2/plotly-latest.min.js
site_libs/typedarray-0.1/LICENSE
site_libs/typedarray-0.1/typedarray.min.js
tests/testthat.R
vectors/elt-2p_rict-1_SL2_mcherry.ape
vectors/ges-1p_akt-1b_SL2_mcherry.ape
vectors/ges-1p_rict-1_SL2_mcherry.ape
vectors/ges-1p_sgk-1b_SL2_mcherry.ape
vectors/gpa-42.6p_rict-1_SL2-mCherry
vectors/ifb-2p_rict-1_SL2_mcherry.ape
