Files in macmanes-lab/DoveParentsRNAseq
Dove Parents RNAseq

.Rbuildignore
.gitignore
DESCRIPTION
DoveParentsRNAseq.Rproj
NAMESPACE
R/functions.R R/themes.R README.md analysis/00_datawrangling.Rmd analysis/00_datawrangling.md analysis/01_limma_all.Rmd analysis/01_limma_all.md analysis/02_pca_all.Rmd analysis/02_pca_all.md analysis/03_DESeq2_characterization.Rmd analysis/03_DESeq2_characterization.md analysis/04_DESeq2_sexes.Rmd analysis/04_DESeq2_sexes.md analysis/04_DESeq2_sexes_manipulate.Rmd analysis/04_DESeq2_sexes_manipulate.md analysis/05_DESeq2_manipulate.Rmd analysis/05_DESeq2_manipulate.md analysis/06_musicalgenes.Rmd analysis/06_musicalgenes.md analysis/07_hormones.Rmd analysis/07_hormones.md analysis/08_WGCNA_1.R analysis/08_WGCNA_2.R analysis/08_WGCNA_3.R analysis/08_wgcna.Rmd analysis/08_wgcna.md analysis/09_egdeR.Rmd analysis/10_specificgenes.Rmd analysis/10_specificgenes.md analysis/11_pcalda.Rmd analysis/11_pcalda.md docs/SICB2020.Rmd docs/SICB2020.pdf docs/grant.Rmd docs/grant.md
figures/characterization/DoveParentsRNAseq_model2.png
figures/characterization/barplots-1.png
figures/characterization/barplots.pdf
figures/characterization/candidates-1.png
figures/characterization/candidates-2.png
figures/characterization/candidates-3.png
figures/characterization/candidates-4.png
figures/characterization/candidates-5.png
figures/characterization/candidates-6.png
figures/characterization/correlationheatmaps-1.png
figures/characterization/correlationheatmaps-2.png
figures/characterization/correlationheatmaps-3.png
figures/characterization/correlationheatmaps-4.png
figures/characterization/correlationheatmaps-5.png
figures/characterization/correlationheatmaps-6.png
figures/characterization/linegraphs-1.png
figures/characterization/linegraphs.pdf
figures/characterization/musicalgenes-05.png
figures/characterization/musicalgenes-06.png
figures/characterization/musicalgenes-1.pdf
figures/characterization/musicalgenes-1.png
figures/characterization/musicalgenes-10.png
figures/characterization/musicalgenes-2.png
figures/characterization/musicalgenes-3.png
figures/characterization/musicalgenes-4.png
figures/characterization/musicalgenes-5.pdf
figures/characterization/musicalgenes-5.png
figures/characterization/musicalgenes-6.pdf
figures/characterization/musicalgenes-6.png
figures/characterization/musicalgenes-7-02.png
figures/characterization/musicalgenes-7-03.png
figures/characterization/musicalgenes-7.png
figures/characterization/musicalgenes-8.png
figures/characterization/musicalgenes-9.png
figures/characterization/musicalgenes-ab.pdf figures/characterization/musicalgenes-cd.pdf figures/characterization/musicalgenes-ef.pdf
figures/characterization/note-black-04.png
figures/characterization/note-blue-04.png
figures/characterization/note-darkgrey-04.png
figures/characterization/note-lightgrey-04.png
figures/characterization/note-orange-04.png
figures/characterization/note-purple-04.png
figures/characterization/note-teal-04.png
figures/characterization/pca-1.png
figures/characterization/pca-2.png
figures/characterization/pca-3.png
figures/characterization/pca-4.png
figures/characterization/pca-5.png
figures/characterization/pca-6.png
figures/characterization/pheatmap-1.png
figures/characterization/pheatmap-2.png
figures/characterization/pheatmap-3.png
figures/characterization/pheatmap-4.png
figures/characterization/pheatmap-5.png
figures/characterization/pheatmap-6.png
figures/characterization/prolactin-1.png
figures/characterization/totalDEGs-1.png
figures/characterization/totalDEGs-2.png
figures/characterization/totalDEGs-3.png
figures/characterization/totalDEGs-4.png
figures/characterization/totalDEGs-5.png
figures/characterization/totalDEGs-6.png
figures/characterization/totalDEGs-7.png
figures/characterization/totalDEGs2-1.png
figures/hormones/characterization-1.png
figures/hormones/manipulation-1.png
figures/hormones/manipulation-2.png
figures/hormones/removal-1.png
figures/images/Parental_timeline.png
figures/images/PigeonHPGaxis.png
figures/images/samplingtimepoints.png
figures/images/timeline_timeline.png
figures/limma/01-contrasts-1.png
figures/limma/01-contrasts-2.png
figures/limma/01-contrasts-3.png
figures/limma/01-contrasts-4.png
figures/limma/01-contrasts-5.png
figures/limma/01-contrasts-6.png
figures/limma/plotMDS-1.png
figures/limma/plotMDS-colored-1.png
figures/limma/plotMDS-colored-2.png
figures/limma/plotMDS-colored-3.png
figures/limma/plotMDS-colorshape-1.png
figures/limma/volcanoplots-1.png
figures/manipulation/LDA-1.png
figures/manipulation/LDA-2.png
figures/manipulation/LDA-3.png
figures/manipulation/LDA-4.png
figures/manipulation/candidates-1.png
figures/manipulation/candidates-2.png
figures/manipulation/candidates-3.png
figures/manipulation/candidates-4.png
figures/manipulation/candidates-5.png
figures/manipulation/candidates-6.png
figures/manipulation/manipVchar-1.pdf
figures/manipulation/manipVchar-1.png
figures/manipulation/manipVchar-2.png
figures/manipulation/manipulationVcontrol-1.pdf
figures/manipulation/manipulationVcontrol-1.png
figures/manipulation/offspringremoval-1.pdf
figures/manipulation/offspringremoval-1.png
figures/manipulation/pca-1.png
figures/manipulation/pca-2.png
figures/manipulation/pca-3.png
figures/manipulation/pca-4.png
figures/manipulation/pca-5.png
figures/manipulation/pca-6.png
figures/manipulation/pheatmap-1.png
figures/manipulation/pheatmap-2.png
figures/manipulation/pheatmap-3.png
figures/manipulation/pheatmap-4.png
figures/manipulation/pheatmap-5.png
figures/manipulation/pheatmap-6.png
figures/manipulation/prolongextend-1.pdf
figures/manipulation/prolongextend-1.png
figures/manipulation/sharedmodule-1.png
figures/manipulation/sharedmodule-2.png
figures/manipulation/totalDEGs-1.png
figures/manipulation/wgcna-1.png
figures/manipulation/wgcna-2.png
figures/manipulation/wgcna-3.png
figures/manipulation/wgcna-4.png
figures/manipulation/wgcna-5.png
figures/manipulation/wgcna-6.png
figures/manipulation/wgcna-7.png
figures/pca/MDS-1.png
figures/pca/normalized-1.png
figures/pca/normalized-2.png
figures/pca/pca-1.png
figures/pca/pca-2.png
figures/pca/pca-3.png
figures/pca/pca.tSNE-1.png
figures/pca/pca.tSNE-2.png
figures/pca/pca.tSNE-3.png
figures/pca/raw-1.png
figures/pca/sidebyside-1.png
figures/pca/tSNE-1.png
figures/pca/tSNE-2.png
figures/pca/timepointsex-1.png
figures/pca/timepointsex-2.png
figures/pca/tissuesex-1.png
figures/pca/tissuesex-2.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
figures/sexes/DoveParentsRNAseq_model2.png
figures/sexes/LDA-1.png
figures/sexes/LDA-2.png
figures/sexes/LDA-3.png
figures/sexes/LDA-4.png
figures/sexes/LDA-5.png
figures/sexes/LDA-6.png
figures/sexes/LDA-7.png
figures/sexes/LDA-8.png
figures/sexes/pca-1.png
figures/sexes/pca-2.png
figures/sexes/pca-3.png
figures/sexes/topPCAloadings-1.png
figures/sexes/topPCAloadings-2.png
figures/sexes/topPCAloadings-3.png
figures/sexes/totalDEGs-1.png
figures/sexes/wgcna-1.png
figures/sexes/wgcna-10.png
figures/sexes/wgcna-11.png
figures/sexes/wgcna-12.png
figures/sexes/wgcna-13.png
figures/sexes/wgcna-14.png
figures/sexes/wgcna-15.png
figures/sexes/wgcna-2.png
figures/sexes/wgcna-3.png
figures/sexes/wgcna-4.png
figures/sexes/wgcna-5.png
figures/sexes/wgcna-6.png
figures/sexes/wgcna-7.png
figures/sexes/wgcna-8.png
figures/sexes/wgcna-9.png
figures/sexes/wgcna2-1.png
figures/sexes/wgcna2-2.png
figures/sexes/wgcna2-3.png
figures/sexes/wgcna2-4.png
figures/sexes/wgcna2-5.png
figures/sexes/wgcna2-6.png
figures/sexes/wgcna2-7.png
figures/sexes/wgcna2-8.png
figures/specificgenes/PRL-1.png
figures/specificgenes/PRL-2.png
figures/specificgenes/PRL-3.png
install.R
metadata/00_birds.csv
metadata/00_colData_characterization.csv
metadata/00_colData_manipluation.csv
metadata/00_geneinfo.csv
metadata/00_samples.csv
metadata/kallistosamples.txt
metadata/parental1.tximport.txt
results/00_countData_characterization.csv
results/00_countData_manipluation.csv
results/00_counts.csv
results/04_colData_gon.csv
results/04_colData_hyp.csv
results/04_colData_pit.csv
results/04_vsd_gon.csv
results/04_vsd_hyp.csv
results/04_vsd_pit.csv
results/08_AR_associated.csv
results/08_POMC_associated.csv
results/08_PRLR_associated.csv
results/08_PRLR_manipulated.csv
results/08_PRL_associated.csv
results/08_PRL_manipulated.csv
results/08_VIPR1_associated.csv
results/08_datExpr.csv
results/08_datTraits.csv
results/10_hypcandidatecounts.csv
results/Pigeon prolactin concentrations juil 2018.xlsx
results/hormones.csv
results/kallistocounts.txt
results/parental_care_hormone_RIA_data_master.xlsx
runtime.txt
macmanes-lab/DoveParentsRNAseq documentation built on Oct. 20, 2019, 6:03 a.m.