Files in macmanes-lab/DoveParentsRNAseq
Dove Parents RNAseq
.Rbuildignore
.gitattributes
.gitignore
DESCRIPTION
DoveParentsRNAseq.Rproj
NAMESPACE
R/functions.R
R/genelists.R
R/themes.R
README.md
Rplots.pdf
Snakefile
_config.yml
analysis/00_wrangle.R
analysis/01_fig1.R
analysis/02_DESeq2.R
analysis/03_vsd.R
analysis/04_DEGs.R
analysis/05_figs23.R
analysis/06_figsup1.R
analysis/07_genesnhormones.R
analysis/08_randomforest.R
analysis/09_venndiagram.R
db-export/00-upload-to-do.R
db-export/01-test-db.R
figures/fig-geneshormones.pdf
figures/fig-geneshormones.png
figures/fig-randomforest-v2.pdf
figures/fig-randomforest-v2.png
figures/fig-randomforest.pdf
figures/fig-randomforest.png
figures/fig1-1.pdf
figures/fig1-1.png
figures/fig2-1.pdf
figures/fig2-1.png
figures/fig3-1.pdf
figures/fig3-1.png
figures/fig_S1.png
figures/fig_S2.png
figures/figsup1-1.pdf
figures/figsup1-1.png
figures/hormones/PCA-1.png
figures/hormones/PCA-2.png
figures/hormones/PCA-3.png
figures/hormones/PCA-4.png
figures/hormones/PCA-5.png
figures/hormones/PCA-6.png
figures/hormones/PRL-1.png
figures/hormones/PRL-2.png
figures/hormones/PRL-3.png
figures/hormones/PRL-4.png
figures/hormones/PRL-5.png
figures/hormones/PRL-6.png
figures/hormones/PRL-7.png
figures/hormones/PRL2-1.png
figures/hormones/PRL2-2.png
figures/hormones/PRL2-3.png
figures/hormones/PRL2-4.png
figures/hormones/PRL2-5.png
figures/hormones/PRLonly-1.png
figures/hormones/characterization-2.png
figures/hormones/characterizationplots-1.png
figures/hormones/characterizationplots-2.png
figures/hormones/characterizationplots-3.png
figures/hormones/characterizationplots-4.png
figures/hormones/characterizationplots-5.png
figures/hormones/correlations-1.png
figures/hormones/correlations-2.png
figures/hormones/correlations-3.png
figures/hormones/correlations-4.png
figures/hormones/correlations2-1.png
figures/hormones/correlations2-2.png
figures/hormones/correlations2-3.png
figures/hormones/correlations2-4.png
figures/hormones/correlations2-5.png
figures/hormones/correlations2-6.png
figures/hormones/cort-1.png
figures/hormones/cort-2.png
figures/hormones/cort-3.png
figures/hormones/cort-4.png
figures/hormones/cort-5.png
figures/hormones/cort-6.png
figures/hormones/estradiol-1.png
figures/hormones/figure2-1.png
figures/hormones/figure3-1.png
figures/hormones/manipulation-1.png
figures/hormones/manipulation-2.png
figures/hormones/manipulation-3.png
figures/hormones/manipulation-4.png
figures/hormones/manipulation-5.png
figures/hormones/manipulation-6.png
figures/hormones/progesterone-1.png
figures/hormones/removal-1.png
figures/hormones/sex-1.png
figures/hormones/sexsteroids-1.png
figures/hormones/sexsteroids-2.png
figures/hormones/sexsteroids-3.png
figures/hormones/sexsteroids-4.png
figures/hormones/sexsteroids-5.png
figures/hormones/sexsteroids-6.png
figures/hormones/sexsteroids2-1.png
figures/hormones/summary-1.png
figures/hormones/summary-2.png
figures/hormones/testosterone-1.png
figures/hormones/testosterone-2.png
figures/hormones/wrangle-prolactin-1.png
figures/images/Colorblind.png
figures/images/Parental_timeline.png
figures/images/draw-chick.png
figures/images/egg.png
figures/images/eggs.png
figures/images/fig_fig1a.png
figures/images/fig_samplesize.png
figures/images/fig_supfig1a.png
figures/images/hatch.png
figures/images/samplingtimepoints.png
figures/old/BRCA.pit.maip-2.png
figures/old/BRCA.pit.maip-4.png
figures/old/LDA-4.png
figures/old/LDAplots-1.png
figures/old/LDAplots-2.png
figures/old/LDAplots-3.png
figures/old/LDAplots-4.png
figures/old/LDAplots-5.png
figures/old/LDAplots-6.png
figures/old/LDAplots-7.png
figures/old/LDAplotsNew-1.png
figures/old/LDAplotsNew-2.png
figures/old/LDAplotsNew-3.png
figures/old/PCA-tSNE-1.png
figures/old/PCA-tSNE-2.png
figures/old/PRL-5.png
figures/old/WGCNAcandidates-1.png
figures/old/boxplots-1.png
figures/old/boxplots-2.png
figures/old/boxplots-3.png
figures/old/boxplots-4.png
figures/old/boxplots-5.png
figures/old/calisigenes-1.png
figures/old/fviz-2.png
figures/old/fviz-4.png
figures/old/hormone-1.png
figures/old/hormonesandgenes-1.png
figures/old/music-1.png
figures/old/respect-1.png
figures/old/sinnerman-1.png
figures/old/soulmusic-1.png
figures/old/totalDEGs-1.png
figures/old/volcanos-gonads-1.png
figures/old/volcanos-hypothalamus-1.png
figures/old/volcanos-pituitary-1.png
figures/sbnposter/DoveParentsRNAseq_approach-2.png
figures/sbnposter/DoveParentsRNAseq_approach-3.png
figures/sbnposter/DoveParentsRNAseq_correlations.png
figures/sbnposter/DoveParentsRNAseq_design.png
figures/sbnposter/DoveParentsRNAseq_logo.png
figures/sbnposter/DoveParentsRNAseq_summary.png
figures/sbnposter/DoveParentsRNAseq_totalDEGs.png
figures/sbnposter/SBN.png
install.R
manuscript/RJournal.log
manuscript/RJournal.sty
manuscript/RJreferences.bib
manuscript/RJwrapper.bbl
manuscript/RJwrapper.brf
manuscript/RJwrapper.pdf
manuscript/RJwrapper.tex
manuscript/Rlogo.png
manuscript/elife-v1.tex
manuscript/elife_v1.Rmd
manuscript/fig1-1.png
manuscript/fig2-1.png
manuscript/fig3-1.png
metadata/00_birds_sachecked.csv
metadata/00_colData.csv
metadata/00_geneinfo.csv
metadata/00_hugoasent.csv
metadata/00_hugopresent.csv
metadata/00_samples.csv
metadata/03_parentalcaregenes.csv
metadata/04_colData.csv
metadata/goterms/parentalbehavior.txt
metadata/kallistosamples.txt
metadata/nestpairs.csv
metadata/nestsummary.csv
metadata/parental1.tximport.txt
results/00_countData.csv
results/00_geneswithisoforms.csv
results/00_isoforms.csv
results/03_candidatevsd.csv
results/03_gonvsdAll.csv
results/03_gonvsdf.csv
results/03_gonvsdm.csv
results/03_hypvsdAll.csv
results/03_hypvsdf.csv
results/03_hypvsdm.csv
results/03_pitvsdAll.csv
results/03_pitvsdf.csv
results/03_pitvsdm.csv
results/03_shinyvsd.csv
results/04_allDEG.csv
results/04_candidateDEGs.csv
results/07_hormonecorrs.csv
results/07_topsigcorrsover50.csv
results/AllHorm_02042020_nomiss.csv
results/DEseq2/hypothesis/female_gonad_eggs_chicks_DEGs.csv
results/DEseq2/hypothesis/female_gonad_lo_hi_DEGs.csv
results/DEseq2/hypothesis/female_gonad_vsd.csv
results/DEseq2/hypothesis/female_gonads_eggs_chicks_DEGs.csv
results/DEseq2/hypothesis/female_gonads_lo_hi_DEGs.csv
results/DEseq2/hypothesis/female_gonads_nest_chicks_DEGs.csv
results/DEseq2/hypothesis/female_gonads_nest_eggs_DEGs.csv
results/DEseq2/hypothesis/female_gonads_vsd.csv
results/DEseq2/hypothesis/female_hypothalamus_eggs_chicks_DEGs.csv
results/DEseq2/hypothesis/female_hypothalamus_lo_hi_DEGs.csv
results/DEseq2/hypothesis/female_hypothalamus_nest_chicks_DEGs.csv
results/DEseq2/hypothesis/female_hypothalamus_nest_eggs_DEGs.csv
results/DEseq2/hypothesis/female_hypothalamus_vsd.csv
results/DEseq2/hypothesis/female_pituitary_eggs_chicks_DEGs.csv
results/DEseq2/hypothesis/female_pituitary_lo_hi_DEGs.csv
results/DEseq2/hypothesis/female_pituitary_nest_chicks_DEGs.csv
results/DEseq2/hypothesis/female_pituitary_nest_eggs_DEGs.csv
results/DEseq2/hypothesis/female_pituitary_vsd.csv
results/DEseq2/hypothesis/male_gonad_eggs_chicks_DEGs.csv
results/DEseq2/hypothesis/male_gonad_lo_hi_DEGs.csv
results/DEseq2/hypothesis/male_gonad_vsd.csv
results/DEseq2/hypothesis/male_gonads_eggs_chicks_DEGs.csv
results/DEseq2/hypothesis/male_gonads_lo_hi_DEGs.csv
results/DEseq2/hypothesis/male_gonads_nest_chicks_DEGs.csv
results/DEseq2/hypothesis/male_gonads_nest_eggs_DEGs.csv
results/DEseq2/hypothesis/male_gonads_vsd.csv
results/DEseq2/hypothesis/male_hypothalamus_eggs_chicks_DEGs.csv
results/DEseq2/hypothesis/male_hypothalamus_lo_hi_DEGs.csv
results/DEseq2/hypothesis/male_hypothalamus_nest_chicks_DEGs.csv
results/DEseq2/hypothesis/male_hypothalamus_nest_eggs_DEGs.csv
results/DEseq2/hypothesis/male_hypothalamus_vsd.csv
results/DEseq2/hypothesis/male_pituitary_eggs_chicks_DEGs.csv
results/DEseq2/hypothesis/male_pituitary_lo_hi_DEGs.csv
results/DEseq2/hypothesis/male_pituitary_nest_chicks_DEGs.csv
results/DEseq2/hypothesis/male_pituitary_nest_eggs_DEGs.csv
results/DEseq2/hypothesis/male_pituitary_vsd.csv
results/DEseq2/sex/gonads_DEGs.csv
results/DEseq2/sex/hypothalamus_DEGs.csv
results/DEseq2/sex/pituitary_DEGs.csv
results/DEseq2/tissue/hypothalamus_gonad_DEGs.csv
results/DEseq2/tissue/hypothalamus_pituitary_DEGs.csv
results/DEseq2/tissue/pituitary_gonad_DEGs.csv
results/DEseq2/treatment/female_gonads_bldg_control_DEGs.csv
results/DEseq2/treatment/female_gonads_bldg_hatch_DEGs.csv
results/DEseq2/treatment/female_gonads_bldg_inc.d17_DEGs.csv
results/DEseq2/treatment/female_gonads_bldg_inc.d3_DEGs.csv
results/DEseq2/treatment/female_gonads_bldg_inc.d9_DEGs.csv
results/DEseq2/treatment/female_gonads_bldg_lay_DEGs.csv
results/DEseq2/treatment/female_gonads_bldg_n5_DEGs.csv
results/DEseq2/treatment/female_gonads_bldg_n9_DEGs.csv
results/DEseq2/treatment/female_gonads_early_extend_DEGs.csv
results/DEseq2/treatment/female_gonads_hatch_early_DEGs.csv
results/DEseq2/treatment/female_gonads_hatch_extend_DEGs.csv
results/DEseq2/treatment/female_gonads_hatch_m.n2_DEGs.csv
results/DEseq2/treatment/female_gonads_hatch_n5_DEGs.csv
results/DEseq2/treatment/female_gonads_hatch_prolong_DEGs.csv
results/DEseq2/treatment/female_gonads_inc.d17_early_DEGs.csv
results/DEseq2/treatment/female_gonads_inc.d17_extend_DEGs.csv
results/DEseq2/treatment/female_gonads_inc.d17_hatch_DEGs.csv
results/DEseq2/treatment/female_gonads_inc.d17_m.inc.d17_DEGs.csv
results/DEseq2/treatment/female_gonads_inc.d17_prolong_DEGs.csv
results/DEseq2/treatment/female_gonads_inc.d3_inc.d9_DEGs.csv
results/DEseq2/treatment/female_gonads_inc.d3_m.inc.d3_DEGs.csv
results/DEseq2/treatment/female_gonads_inc.d9_early_DEGs.csv
results/DEseq2/treatment/female_gonads_inc.d9_extend_DEGs.csv
results/DEseq2/treatment/female_gonads_inc.d9_inc.d17_DEGs.csv
results/DEseq2/treatment/female_gonads_inc.d9_m.inc.d9_DEGs.csv
results/DEseq2/treatment/female_gonads_inc.d9_prolong_DEGs.csv
results/DEseq2/treatment/female_gonads_lay_inc.d3_DEGs.csv
results/DEseq2/treatment/female_gonads_n5_early_DEGs.csv
results/DEseq2/treatment/female_gonads_n5_extend_DEGs.csv
results/DEseq2/treatment/female_gonads_n5_n9_DEGs.csv
results/DEseq2/treatment/female_gonads_n5_prolong_DEGs.csv
results/DEseq2/treatment/female_gonads_prolong_early_DEGs.csv
results/DEseq2/treatment/female_gonads_prolong_extend_DEGs.csv
results/DEseq2/treatment/female_hypothalamus_bldg_control_DEGs.csv
results/DEseq2/treatment/female_hypothalamus_bldg_hatch_DEGs.csv
results/DEseq2/treatment/female_hypothalamus_bldg_inc.d17_DEGs.csv
results/DEseq2/treatment/female_hypothalamus_bldg_inc.d3_DEGs.csv
results/DEseq2/treatment/female_hypothalamus_bldg_inc.d9_DEGs.csv
results/DEseq2/treatment/female_hypothalamus_bldg_lay_DEGs.csv
results/DEseq2/treatment/female_hypothalamus_bldg_n5_DEGs.csv
results/DEseq2/treatment/female_hypothalamus_bldg_n9_DEGs.csv
results/DEseq2/treatment/female_hypothalamus_early_extend_DEGs.csv
results/DEseq2/treatment/female_hypothalamus_hatch_early_DEGs.csv
results/DEseq2/treatment/female_hypothalamus_hatch_extend_DEGs.csv
results/DEseq2/treatment/female_hypothalamus_hatch_m.n2_DEGs.csv
results/DEseq2/treatment/female_hypothalamus_hatch_n5_DEGs.csv
results/DEseq2/treatment/female_hypothalamus_hatch_prolong_DEGs.csv
results/DEseq2/treatment/female_hypothalamus_inc.d17_early_DEGs.csv
results/DEseq2/treatment/female_hypothalamus_inc.d17_extend_DEGs.csv
results/DEseq2/treatment/female_hypothalamus_inc.d17_hatch_DEGs.csv
results/DEseq2/treatment/female_hypothalamus_inc.d17_m.inc.d17_DEGs.csv
results/DEseq2/treatment/female_hypothalamus_inc.d17_prolong_DEGs.csv
results/DEseq2/treatment/female_hypothalamus_inc.d3_inc.d9_DEGs.csv
results/DEseq2/treatment/female_hypothalamus_inc.d3_m.inc.d3_DEGs.csv
results/DEseq2/treatment/female_hypothalamus_inc.d9_early_DEGs.csv
results/DEseq2/treatment/female_hypothalamus_inc.d9_extend_DEGs.csv
results/DEseq2/treatment/female_hypothalamus_inc.d9_inc.d17_DEGs.csv
results/DEseq2/treatment/female_hypothalamus_inc.d9_m.inc.d9_DEGs.csv
results/DEseq2/treatment/female_hypothalamus_inc.d9_prolong_DEGs.csv
results/DEseq2/treatment/female_hypothalamus_lay_inc.d3_DEGs.csv
results/DEseq2/treatment/female_hypothalamus_n5_early_DEGs.csv
results/DEseq2/treatment/female_hypothalamus_n5_extend_DEGs.csv
results/DEseq2/treatment/female_hypothalamus_n5_n9_DEGs.csv
results/DEseq2/treatment/female_hypothalamus_n5_prolong_DEGs.csv
results/DEseq2/treatment/female_hypothalamus_prolong_early_DEGs.csv
results/DEseq2/treatment/female_hypothalamus_prolong_extend_DEGs.csv
results/DEseq2/treatment/female_pituitary_bldg_control_DEGs.csv
results/DEseq2/treatment/female_pituitary_bldg_hatch_DEGs.csv
results/DEseq2/treatment/female_pituitary_bldg_inc.d17_DEGs.csv
results/DEseq2/treatment/female_pituitary_bldg_inc.d3_DEGs.csv
results/DEseq2/treatment/female_pituitary_bldg_inc.d9_DEGs.csv
results/DEseq2/treatment/female_pituitary_bldg_lay_DEGs.csv
results/DEseq2/treatment/female_pituitary_bldg_n5_DEGs.csv
results/DEseq2/treatment/female_pituitary_bldg_n9_DEGs.csv
results/DEseq2/treatment/female_pituitary_early_extend_DEGs.csv
results/DEseq2/treatment/female_pituitary_hatch_early_DEGs.csv
results/DEseq2/treatment/female_pituitary_hatch_extend_DEGs.csv
results/DEseq2/treatment/female_pituitary_hatch_m.n2_DEGs.csv
results/DEseq2/treatment/female_pituitary_hatch_n5_DEGs.csv
results/DEseq2/treatment/female_pituitary_hatch_prolong_DEGs.csv
results/DEseq2/treatment/female_pituitary_inc.d17_early_DEGs.csv
results/DEseq2/treatment/female_pituitary_inc.d17_extend_DEGs.csv
results/DEseq2/treatment/female_pituitary_inc.d17_hatch_DEGs.csv
results/DEseq2/treatment/female_pituitary_inc.d17_m.inc.d17_DEGs.csv
results/DEseq2/treatment/female_pituitary_inc.d17_prolong_DEGs.csv
results/DEseq2/treatment/female_pituitary_inc.d3_inc.d9_DEGs.csv
results/DEseq2/treatment/female_pituitary_inc.d3_m.inc.d3_DEGs.csv
results/DEseq2/treatment/female_pituitary_inc.d9_early_DEGs.csv
results/DEseq2/treatment/female_pituitary_inc.d9_extend_DEGs.csv
results/DEseq2/treatment/female_pituitary_inc.d9_inc.d17_DEGs.csv
results/DEseq2/treatment/female_pituitary_inc.d9_m.inc.d9_DEGs.csv
results/DEseq2/treatment/female_pituitary_inc.d9_prolong_DEGs.csv
results/DEseq2/treatment/female_pituitary_lay_inc.d3_DEGs.csv
results/DEseq2/treatment/female_pituitary_n5_early_DEGs.csv
results/DEseq2/treatment/female_pituitary_n5_extend_DEGs.csv
results/DEseq2/treatment/female_pituitary_n5_n9_DEGs.csv
results/DEseq2/treatment/female_pituitary_n5_prolong_DEGs.csv
results/DEseq2/treatment/female_pituitary_prolong_early_DEGs.csv
results/DEseq2/treatment/female_pituitary_prolong_extend_DEGs.csv
results/DEseq2/treatment/male_gonads_bldg_control_DEGs.csv
results/DEseq2/treatment/male_gonads_bldg_hatch_DEGs.csv
results/DEseq2/treatment/male_gonads_bldg_inc.d17_DEGs.csv
results/DEseq2/treatment/male_gonads_bldg_inc.d3_DEGs.csv
results/DEseq2/treatment/male_gonads_bldg_inc.d9_DEGs.csv
results/DEseq2/treatment/male_gonads_bldg_lay_DEGs.csv
results/DEseq2/treatment/male_gonads_bldg_n5_DEGs.csv
results/DEseq2/treatment/male_gonads_bldg_n9_DEGs.csv
results/DEseq2/treatment/male_gonads_early_extend_DEGs.csv
results/DEseq2/treatment/male_gonads_hatch_early_DEGs.csv
results/DEseq2/treatment/male_gonads_hatch_extend_DEGs.csv
results/DEseq2/treatment/male_gonads_hatch_m.n2_DEGs.csv
results/DEseq2/treatment/male_gonads_hatch_n5_DEGs.csv
results/DEseq2/treatment/male_gonads_hatch_prolong_DEGs.csv
results/DEseq2/treatment/male_gonads_inc.d17_early_DEGs.csv
results/DEseq2/treatment/male_gonads_inc.d17_extend_DEGs.csv
results/DEseq2/treatment/male_gonads_inc.d17_hatch_DEGs.csv
results/DEseq2/treatment/male_gonads_inc.d17_m.inc.d17_DEGs.csv
results/DEseq2/treatment/male_gonads_inc.d17_prolong_DEGs.csv
results/DEseq2/treatment/male_gonads_inc.d3_inc.d9_DEGs.csv
results/DEseq2/treatment/male_gonads_inc.d3_m.inc.d3_DEGs.csv
results/DEseq2/treatment/male_gonads_inc.d9_early_DEGs.csv
results/DEseq2/treatment/male_gonads_inc.d9_extend_DEGs.csv
results/DEseq2/treatment/male_gonads_inc.d9_inc.d17_DEGs.csv
results/DEseq2/treatment/male_gonads_inc.d9_m.inc.d9_DEGs.csv
results/DEseq2/treatment/male_gonads_inc.d9_prolong_DEGs.csv
results/DEseq2/treatment/male_gonads_lay_inc.d3_DEGs.csv
results/DEseq2/treatment/male_gonads_n5_early_DEGs.csv
results/DEseq2/treatment/male_gonads_n5_extend_DEGs.csv
results/DEseq2/treatment/male_gonads_n5_n9_DEGs.csv
results/DEseq2/treatment/male_gonads_n5_prolong_DEGs.csv
results/DEseq2/treatment/male_gonads_prolong_early_DEGs.csv
results/DEseq2/treatment/male_gonads_prolong_extend_DEGs.csv
results/DEseq2/treatment/male_hypothalamus_bldg_control_DEGs.csv
results/DEseq2/treatment/male_hypothalamus_bldg_hatch_DEGs.csv
results/DEseq2/treatment/male_hypothalamus_bldg_inc.d17_DEGs.csv
results/DEseq2/treatment/male_hypothalamus_bldg_inc.d3_DEGs.csv
results/DEseq2/treatment/male_hypothalamus_bldg_inc.d9_DEGs.csv
results/DEseq2/treatment/male_hypothalamus_bldg_lay_DEGs.csv
results/DEseq2/treatment/male_hypothalamus_bldg_n5_DEGs.csv
results/DEseq2/treatment/male_hypothalamus_bldg_n9_DEGs.csv
results/DEseq2/treatment/male_hypothalamus_early_extend_DEGs.csv
results/DEseq2/treatment/male_hypothalamus_hatch_early_DEGs.csv
results/DEseq2/treatment/male_hypothalamus_hatch_extend_DEGs.csv
results/DEseq2/treatment/male_hypothalamus_hatch_m.n2_DEGs.csv
results/DEseq2/treatment/male_hypothalamus_hatch_n5_DEGs.csv
results/DEseq2/treatment/male_hypothalamus_hatch_prolong_DEGs.csv
results/DEseq2/treatment/male_hypothalamus_inc.d17_early_DEGs.csv
results/DEseq2/treatment/male_hypothalamus_inc.d17_extend_DEGs.csv
results/DEseq2/treatment/male_hypothalamus_inc.d17_hatch_DEGs.csv
results/DEseq2/treatment/male_hypothalamus_inc.d17_m.inc.d17_DEGs.csv
results/DEseq2/treatment/male_hypothalamus_inc.d17_prolong_DEGs.csv
results/DEseq2/treatment/male_hypothalamus_inc.d3_inc.d9_DEGs.csv
results/DEseq2/treatment/male_hypothalamus_inc.d3_m.inc.d3_DEGs.csv
results/DEseq2/treatment/male_hypothalamus_inc.d9_early_DEGs.csv
results/DEseq2/treatment/male_hypothalamus_inc.d9_extend_DEGs.csv
results/DEseq2/treatment/male_hypothalamus_inc.d9_inc.d17_DEGs.csv
results/DEseq2/treatment/male_hypothalamus_inc.d9_m.inc.d9_DEGs.csv
results/DEseq2/treatment/male_hypothalamus_inc.d9_prolong_DEGs.csv
results/DEseq2/treatment/male_hypothalamus_lay_inc.d3_DEGs.csv
results/DEseq2/treatment/male_hypothalamus_n5_early_DEGs.csv
results/DEseq2/treatment/male_hypothalamus_n5_extend_DEGs.csv
results/DEseq2/treatment/male_hypothalamus_n5_n9_DEGs.csv
results/DEseq2/treatment/male_hypothalamus_n5_prolong_DEGs.csv
results/DEseq2/treatment/male_hypothalamus_prolong_early_DEGs.csv
results/DEseq2/treatment/male_hypothalamus_prolong_extend_DEGs.csv
results/DEseq2/treatment/male_pituitary_bldg_control_DEGs.csv
results/DEseq2/treatment/male_pituitary_bldg_hatch_DEGs.csv
results/DEseq2/treatment/male_pituitary_bldg_inc.d17_DEGs.csv
results/DEseq2/treatment/male_pituitary_bldg_inc.d3_DEGs.csv
results/DEseq2/treatment/male_pituitary_bldg_inc.d9_DEGs.csv
results/DEseq2/treatment/male_pituitary_bldg_lay_DEGs.csv
results/DEseq2/treatment/male_pituitary_bldg_n5_DEGs.csv
results/DEseq2/treatment/male_pituitary_bldg_n9_DEGs.csv
results/DEseq2/treatment/male_pituitary_early_extend_DEGs.csv
results/DEseq2/treatment/male_pituitary_hatch_early_DEGs.csv
results/DEseq2/treatment/male_pituitary_hatch_extend_DEGs.csv
results/DEseq2/treatment/male_pituitary_hatch_m.n2_DEGs.csv
results/DEseq2/treatment/male_pituitary_hatch_n5_DEGs.csv
results/DEseq2/treatment/male_pituitary_hatch_prolong_DEGs.csv
results/DEseq2/treatment/male_pituitary_inc.d17_early_DEGs.csv
results/DEseq2/treatment/male_pituitary_inc.d17_extend_DEGs.csv
results/DEseq2/treatment/male_pituitary_inc.d17_hatch_DEGs.csv
results/DEseq2/treatment/male_pituitary_inc.d17_m.inc.d17_DEGs.csv
results/DEseq2/treatment/male_pituitary_inc.d17_prolong_DEGs.csv
results/DEseq2/treatment/male_pituitary_inc.d3_inc.d9_DEGs.csv
results/DEseq2/treatment/male_pituitary_inc.d3_m.inc.d3_DEGs.csv
results/DEseq2/treatment/male_pituitary_inc.d9_early_DEGs.csv
results/DEseq2/treatment/male_pituitary_inc.d9_extend_DEGs.csv
results/DEseq2/treatment/male_pituitary_inc.d9_inc.d17_DEGs.csv
results/DEseq2/treatment/male_pituitary_inc.d9_m.inc.d9_DEGs.csv
results/DEseq2/treatment/male_pituitary_inc.d9_prolong_DEGs.csv
results/DEseq2/treatment/male_pituitary_lay_inc.d3_DEGs.csv
results/DEseq2/treatment/male_pituitary_n5_early_DEGs.csv
results/DEseq2/treatment/male_pituitary_n5_extend_DEGs.csv
results/DEseq2/treatment/male_pituitary_n5_n9_DEGs.csv
results/DEseq2/treatment/male_pituitary_n5_prolong_DEGs.csv
results/DEseq2/treatment/male_pituitary_prolong_early_DEGs.csv
results/DEseq2/treatment/male_pituitary_prolong_extend_DEGs.csv
results/kallistocounts.txt
results/sharedsexdifs.csv
results/table1.csv
results/table2.csv
results/tableS1.csv
results/tableS2.csv
results/tableS3.csv
results/tableS4.csv
runtime.txt
