├── .DS_Store ├── Orthoclust_Results_GmxAth_Pval0.001-Cor0.99_20170809.RData_kappa3.RData ├── Orthoclust_Results_GmxAth_Pval0.001-Cor0.99_20170809.RData_kappa3.csv ├── README.md ├── docs ├── .DS_Store └── figures │ ├── .DS_Store │ ├── Clone_Download_GitRep.png │ ├── Figure2.png │ ├── Inital_FolderStructure.png │ └── Materials_FolderStructure.png ├── processed_data ├── .DS_Store ├── ARATH2GLYMA.BLAST_ARATH2GLYMA.subset.txt ├── ARATH2GLYMA.BLAST_GLYMA2ARATH.subset.txt ├── ARATH2GLYMA.RBH.subset.txt └── fpkm │ ├── .DS_Store │ ├── ATH │ └── PRJNA301162.csv │ └── GMA │ └── PRJNA197379.csv ├── raw_data ├── PRJNA197379.txt ├── PRJNA301162.txt └── PRJNAtest.txt ├── results ├── 1_FPKM-PCC-orthoPairsATH_mergedOnly_ATH-Emb_normMeanFPKM_Pval0.001-Cor0.99_20170808.RData ├── 1_FPKM-PCC-orthoPairsGMX_mergedOnly_GMX-Emb_normMeanFPKM_Pval0.001-Cor0.99_20170808.RData ├── 1_FPKM-PCC_ATH_mergedOnly_ATH-Emb_normMeanFPKM_Pval0.001-Cor0.99_20170809.RData ├── 1_FPKM-PCC_GMX_mergedOnly_GMX-Emb_normMeanFPKM_Pval0.001-Cor0.99_20170809.RData ├── ATH_FPKM.csv ├── ATH_mergedOnly_ATH-Emb_normMeanFPKM_Pval0.001-Cor0.99.csv ├── GMX_FPKM.csv └── GMX_mergedOnly_GMX-Emb_normMeanFPKM_Pval0.001-Cor0.99.csv ├── scripts ├── .DS_Store ├── OrthologousGenes_OneWayTopNBestHit.py ├── ReciprocalBlastHit.py ├── Section2.1_setup_directory.sh ├── Section2.2_download_software.sh ├── Section2.3_install_r_packages.R ├── Section2.3_install_r_packages.sh ├── Section2.4_download_data.sh ├── Section2.5_download_fastq.sh ├── Section3.2.1_BLAST.sh ├── Section3.2.2_RBH.sh ├── Section3.3.Step1.MakeIndex.sh ├── Section3.3.Step2.Mapping.ATH.sh ├── Section3.3.Step2.Mapping.GMA.sh ├── Section3.3.Step3.ReadCount.ATH.sh ├── Section3.3.Step3.ReadCount.GMA.sh ├── Section3.3.Step4.FPKM.R ├── Section3.3.Step5_FPKM2NETWORK.R ├── Section3.4.Step1_OrthoClust.R ├── Section3.4.Step2_CytoscapeInput.R └── Section4.4_k-BestHits.sh └── software └── OrthoClust_1.0.tar.gz /.DS_Store: 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