├── .DS_Store ├── .gitattributes ├── .gitignore ├── 01_Vmap1.1R ├── .DS_Store ├── 01_Xp-clr_Smooth_V1.r ├── 01_Xp-clr_Smooth_V2.r ├── 02_Xp-clr_SelectGene_V1.sh ├── 02_Xp-clr_SelectGene_V2.sh ├── 03_Xp-clr_BayenvOver.sh ├── 03_Xp-clr_Haplotype.sh ├── 03_Xp-clr_NegativeContral.r ├── 03_Xp-clr_to_jiao.r ├── 04_9VIP_Gene_Seq_anno.r ├── 04_9VIP_Xp-clr_Haplotype.sh ├── 04_GeneStructureMa.r ├── 04_GeneStructureMap.r ├── 04_Qmatrix_Visual.r ├── 04_VIP_Gene_XpCLR_signal.r ├── 05_Sample_Cluster.r ├── 06_Pheatmap.r ├── 06_Qmatrix_PieMap.r ├── 07_VCF_Haplotype_Visual.r ├── 08_Fst_density.r ├── 08_Fst_density.sh ├── 08_VIP_Gene_Heatmap.r ├── 09_RDA.r ├── 09_RDA_02(invalid).R ├── 10_Density.r ├── 11_Drift_pi.r ├── 12_FST.r ├── 13_IBS(invalid).r ├── 13_IBS2.r ├── 13_Xp-clr.sh ├── 14_PI.r ├── 15_PCA.r ├── 15_PCA_climate.r ├── 15_VRN.r ├── 16_Barcode.r ├── 17_CreateHmp.r ├── 18_Daf.r ├── 19_Enrich.r ├── 20_ExtractMap.r ├── 21_LDjump.r ├── 22_Maf.r ├── 23_Merge_DoneFile.r ├── 24_MergeTest.r ├── 25_MergeVCF.r ├── 26_Migration.r ├── 27_Permut.r ├── 28_Pluk.r ├── 29_Statistic.r ├── 30_Wenn.r ├── 31_WheatMap.r ├── 32_NeSize.r ├── 33_vf_pipe.sh ├── 34_Vmap3.sh ├── 35_ChrBin.R ├── 35_Storage.sh ├── 36_LDJump.R ├── 37_permut.R ├── 38_Venn.R ├── 39_42-21chr.sh ├── 40_MDS.r ├── 41_Method1.sh ├── 42_MCMC.sh ├── 43_est.sh ├── 44_Bayenv.r ├── 45_Admixture.sh ├── 46_VMap3流程.sh ├── 47_TestGF.r ├── 49_Variants_Age.sh ├── 50_LFMM.r ├── 51_105XD.r ├── 52_37gene_snpEff.r ├── 53_37gene_haplotype.r ├── 55_VMap3_siteQC.r ├── 56_VMap3_taxaQC.r ├── 57_Gene_HaploType.r ├── 57_Gene_HaploType_Map.r ├── 58_PPD.r ├── 59_Depth.R ├── 60_response.R ├── LICENSE ├── Scripts.Rproj ├── assets │ └── 16442473466436.jpg └── 可能有用的smcpp.R ├── 02_Vmap3R ├── .DS_Store ├── 01_Tree_Anno.r ├── 02_Enrich.r ├── 03_Filt_vcf.r ├── 04_IBS.r ├── 05_Map.r ├── 06_Map2.r ├── 07_Nucdiff.sh ├── 08_PCA.r ├── 09_PCA2.r ├── 10_Maf-Dis.r ├── 11_Statistic.sh ├── 12_VcfQc.r ├── 13_VcfStatistic.r └── 14_Snp_Density.sh ├── 03_Analysis ├── .DS_Store ├── 01_ChangeFileFormat_1.r ├── 02_ChangeFileFormat_2.r ├── 03_Basic_Statistic.sh ├── 04_Basic_Statistic_2.r ├── 05_FST_Calculate.r ├── 06_SeperationSite_Calculate.r ├── 07_TajimasD_Calculate.sh ├── 08_PI_Calculate.sh ├── 09_IBS.r ├── 09_IBS_Calculate.sh ├── 10_IceData.r ├── 11_ReadDepth.sh └── 12_BWA.sh ├── 04_GWAS ├── .DS_Store ├── 01_WEGA_gwas.sh ├── 02_Manhattan.r ├── 03_Gene_Domain.r ├── 04_Gene_trait.r ├── 05_Plot_Gene_Trait.r ├── 06_Plot_Rht.r ├── 08_Correlation.r └── 09_envGWAS.r ├── 05_Plot ├── Plot_Density.r ├── Plot_Drift_Pi.r ├── Plot_Finder.r ├── Plot_Fst.r ├── Plot_Haplotype.r ├── Plot_IBS.r ├── Plot_MapPie.r ├── Plot_Pi.r ├── Plot_Pi_02.r └── Plot_Tajima'D.r ├── 06_MarkDown ├── ASMC.md ├── GATK.md ├── MCMC.md ├── Wheat migration routes.md └── bayenv_method.md ├── 07_VMap3 ├── .DS_Store ├── 01_Map.r ├── 02_ASMC.r ├── 03_FastSMC.r ├── 04_BasicStatistics.r ├── 05_TasselGWAS.sh ├── 06_Selscan.r ├── 07_scam.r ├── 08_Raxml-ng.r ├── 09_WheatGo.r ├── 10_SDS.r ├── 11_PiRatio.r ├── 12_Selection.R ├── 13_Baypass.r ├── 14_snpEff.R ├── 15_Rareallele.R ├── 16_Network.R ├── 17_N-content.R ├── 18_Haplotype.R ├── 19_lm.R ├── 20_fst-piR.R ├── 20_smcpp.R ├── 21_sweed.R ├── 22_recombinationRate.R ├── 23_clustersample.R ├── 24_h12.R ├── 25_ehh.R ├── 26_ppi.R ├── 27_xpclr.R ├── 28_envgwas.R ├── 29_correlation.R ├── 30_polygraph.R ├── 31_gradientForest.R ├── 32_coFu.Rmd ├── 33_环境变量降维.r ├── 34_adapgene.R ├── 35_表型处理.R ├── 36_checksample.R ├── 37_traitgwas.R ├── 38_bayesR.R ├── 39_coXiao.R ├── 40_环境适应性位点.R ├── 41_表型环境关联.R ├── 42_群体结构分析.R ├── 43_RDA.R ├── 44_polygenic_adaptation.R ├── 45_partialRda.R ├── 46_fastcall2测试.R ├── 47-物种分布模型.R ├── 48_lassip.R ├── 49_RAiSD.R ├── 50_riskscore.R ├── 51_LinkNe.R ├── 52_JM44.R ├── 53_coTian.R ├── 54_density.R ├── Lulab_germplasm_Info.xlsx ├── Lulab_germplasm_Storage.xlsx ├── VMap3.info ├── VMap3.info2 ├── VMap3_382landrace_82clim_PC10.txt ├── VMap3_523landrace_climPC.txt ├── VMap3_523landrace_withBioclimate.txt └── vmap3.Rmd ├── 08_SingleCell ├── 01_ED_develop.R ├── 02_combineCluster_ED.R ├── 03_extractEDcell.R ├── 04_embro.R ├── 04_scGLUE.py ├── 05_GRN_step3.GRN_scheme1.py ├── 1.scRNAseq.R ├── 10_encoDevelop_motif.R ├── 10_endoDevelop.R ├── 11_soybean_spatial.R ├── 12_stereopy.py ├── 13_spagrn.py ├── 14_ATAC_RNA_anchor.R ├── 2.scATAC_ArchR_整合.R ├── 2.seATAC_ArchR.R ├── 2.愈伤芽分化.sh ├── 3.愈伤芽分化.R ├── 4.scATAC_Seurat.R ├── 4_pseudotime.R ├── 5.ArchR_statistic.R ├── 6.BayPass.R ├── 7.scPagwas.R ├── 8.spatio.sh ├── 9.ath_seed_ATAC.sh ├── bash.sh └── original.R ├── BSAseq ├── BSA-seq混合分组鉴定功能基因.md ├── BSAseq.R ├── QTLseq_BSA.R ├── gatk_step1_Index.sh ├── gatk_step2_callvar.sh ├── gatk_step3_gvcfmerg.sh └── gatk_step4_filter_SNP.sh ├── Basic_Path.sh ├── Basic_R.r ├── Basic_Shell.sh ├── Code ├── .DS_Store ├── 01_Density.r ├── 02_IBS.r ├── 03_PI.r ├── 04_FST.r ├── 05_Drift_pi.r ├── 06_MDS.r ├── 07_PCA.r ├── 08_ExtractMap.r ├── 09_Admixture.sh ├── 10_Xp-clr.sh ├── 11_Xp-clr_Smooth.r ├── 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