Index of /shares/gillislab/temp/septation/chicken

[ICO]NameLast modifiedSizeDescription
[PARENTDIR]Parent Directory   -  
[DIR]MetaNeighbor_ref/ 2024-12-21 23:07 -  
[DIR]QC/ 2024-12-21 23:06 -  
[DIR]annotations/ 2024-12-21 23:07 -  
[DIR]data/ 2024-12-21 23:07 -  
[DIR]expressolog/ 2024-12-21 23:07 -  
[TXT]chicken_ssSTACAS_cel..>2024-12-21 23:07 1.4K 
[ ]convert_to_seuratObj..>2024-12-21 23:07 1.5K 
[TXT]chicken_scib_metrics..>2024-12-21 23:07 2.0K 
[ ]stage23_monocle_clus..>2024-12-21 23:06 3.3K 
[TXT]chicken_manual_anno1..>2024-12-21 23:06 6.6K 
[ ]label_transfer_Seura..>2024-12-21 23:07 7.9K 
[ ]annotate_Farah.ipynb 2024-12-21 23:06 7.9K 
[ ]annotate_Cui.ipynb 2024-12-21 23:06 7.9K 
[ ]chicken_cross_stage_..>2024-12-21 23:07 7.9K 
[ ]annotate_Feng.ipynb 2024-12-21 23:07 7.9K 
[ ]annotate_Xu.ipynb 2024-12-21 23:06 8.0K 
[ ]get_pseudobulk.ipynb 2024-12-21 23:07 9.0K 
[ ]convert_to_anndata_s..>2024-12-21 23:07 9.0K 
[ ]annotate_Asp.ipynb 2024-12-21 23:07 9.4K 
[ ]build_pseudobulk_coe..>2024-12-21 23:07 9.8K 
[ ]stage28_monocle_clus..>2024-12-21 23:06 10K 
[ ]convert_to_anndata.i..>2024-12-21 23:07 11K 
[ ]annotate_Hill.ipynb 2024-12-21 23:07 11K 
[ ]stage32_monocle_clus..>2024-12-21 23:06 12K 
[ ]get_cluster_anno1.ipynb2024-12-21 23:06 12K 
[ ]label_transfer_Symph..>2024-12-21 23:06 12K 
[ ]label_transfer_Seura..>2024-12-21 23:06 12K 
[ ]annotate_hierarchica..>2024-12-21 23:06 12K 
[ ]merge_metacells1.ipynb 2024-12-21 23:07 13K 
[ ]annotate_hierarchica..>2024-12-21 23:07 13K 
[ ]get_pseudobulk2.ipynb 2024-12-21 23:07 14K 
[ ]turtle_cross_stage_M..>2024-12-21 23:07 14K 
[ ]annotate_hierarchica..>2024-12-21 23:07 14K 
[ ]get_connected_graph1..>2024-12-21 23:06 15K 
[ ]build_coexp_network1..>2024-12-21 23:06 16K 
[ ]annotate_CM_devCellP..>2024-12-21 23:07 17K 
[ ]stage23_CCA_MN_score..>2024-12-21 23:07 17K 
[ ]get_connected_graph2..>2024-12-21 23:06 18K 
[ ]get_consensus_cellty..>2024-12-21 23:07 19K 
[ ]stage32_CCA_MN_score..>2024-12-21 23:07 23K 
[ ]stage28_CCA_MN_score..>2024-12-21 23:07 24K 
[ ]get_DEG.ipynb 2024-12-21 23:07 42K 
[ ]get_metacells1.ipynb 2024-12-21 23:07 58K 
[ ]stage32_sample5_clus..>2024-12-21 23:07 58K 
[ ]get_metacells2.ipynb 2024-12-21 23:07 59K 
[ ]stage23_sample3_clus..>2024-12-21 23:07 65K 
[ ]stage32_sample10_clu..>2024-12-21 23:07 65K 
[ ]Untitled.ipynb 2024-12-21 23:07 65K 
[ ]calc_expressolog.ipynb 2024-12-21 23:07 79K 
[ ]stage28_sample10_clu..>2024-12-21 23:07 85K 
[ ]calc_coexp_cons_pseu..>2024-12-21 23:07 86K 
[ ]pairwise_MN.ipynb 2024-12-21 23:06 89K 
[ ]stage28_sample5_clus..>2024-12-21 23:07 93K 
[ ]stage23_sample10_clu..>2024-12-21 23:07 98K 
[ ]visualize_celltype_p..>2024-12-21 23:07 99K 
[ ]stage32_sample12_clu..>2024-12-21 23:07 101K 
[ ]stage28_sample11_clu..>2024-12-21 23:07 105K 
[ ]plot_celltype_dist.i..>2024-12-21 23:07 109K 
[ ]stage32_6_7_metacell..>2024-12-21 23:06 120K 
[ ]stage32_6_8_metacell..>2024-12-21 23:06 149K 
[ ]stage32_7_8_metacell..>2024-12-21 23:06 155K 
[ ]pairwise_MN_cluster...>2024-12-21 23:06 158K 
[ ]get_markers_celltype..>2024-12-21 23:07 191K 
[ ]manual_anno1.ipynb 2024-12-21 23:06 201K 
[ ]pairwise_MN_metacell..>2024-12-21 23:07 233K 
[ ]get_clusters_monocle..>2024-12-21 23:06 245K 
[ ]annotate_Mantri.ipynb 2024-12-21 23:06 246K 
[ ]annotate_clusters1.i..>2024-12-21 23:06 250K 
[ ]stage23_metacell_MN...>2024-12-21 23:06 256K 
[ ]run_MN2.ipynb 2024-12-21 23:07 263K 
[ ]batch_metrics_scib.i..>2024-12-21 23:07 266K 
[ ]run_MN_cross_sample...>2024-12-21 23:06 282K 
[ ]stage28_4_5_metacell..>2024-12-21 23:06 325K 
[ ]stage32_metacell_MN...>2024-12-21 23:06 335K 
[ ]run_MN_cross_stage_K..>2024-12-21 23:06 342K 
[ ]stage28_3_4_metacell..>2024-12-21 23:06 345K 
[ ]batch_correction_scG..>2024-12-21 23:07 345K 
[TXT]stages33_cluster_san..>2024-12-21 23:07 354K 
[ ]stage28_3_5_metacell..>2024-12-21 23:06 361K 
[TXT]stages3_cluster_sank..>2024-12-21 23:06 366K 
[ ]plot_sankey_cross_st..>2024-12-21 23:07 367K 
[ ]plot_celltype_dist_b..>2024-12-21 23:07 368K 
[ ]get_stage_specific_g..>2024-12-21 23:07 403K 
[ ]DA_speckle_KS.ipynb 2024-12-21 23:06 407K 
[ ]batch_corrected_data..>2024-12-21 23:07 416K 
[ ]compare_clusters1.ipynb2024-12-21 23:07 423K 
[ ]slingshot.ipynb 2024-12-21 23:07 433K 
[ ]batch_correction_fas..>2024-12-21 23:07 437K 
[ ]run_MN_cross_stage.i..>2024-12-21 23:07 454K 
[ ]cross_sample_mapping..>2024-12-21 23:06 487K 
[ ]run_GBA.ipynb 2024-12-21 23:06 554K 
[ ]DA_milo.ipynb 2024-12-21 23:06 563K 
[ ]batch_correction_ssS..>2024-12-21 23:06 580K 
[ ]get_clusters_scSHC.i..>2024-12-21 23:07 658K 
[ ]batch_effects_seurat..>2024-12-21 23:07 667K 
[ ]Untitled3.ipynb 2024-12-21 23:06 679K 
[ ]batch_correction_rpc..>2024-12-21 23:07 703K 
[ ]batch_correction_cca..>2024-12-21 23:07 732K 
[ ]annotate_SCimilarity..>2024-12-21 23:06 732K 
[ ]plot_sankey.ipynb 2024-12-21 23:07 741K 
[TXT]chicken_GRCg7b_chr_t..>2024-12-21 23:06 742K 
[ ]stage28_metacell_MN...>2024-12-21 23:06 792K 
[ ]stage23_metacell_MN_..>2024-12-21 23:07 846K 
[ ]batch_correction_sca..>2024-12-21 23:06 904K 
[ ]manual_anno2.ipynb 2024-12-21 23:07 960K 
[TXT]human_chicken_orthol..>2024-12-21 23:06 1.1M 
[ ]stage23_integrated_p..>2024-12-21 23:06 1.1M 
[ ]stage23_pseudobulk_e..>2024-12-21 23:07 1.2M 
[TXT]mouse_chicken_orthol..>2024-12-21 23:06 1.2M 
[ ]stage28_pseudobulk_e..>2024-12-21 23:07 1.2M 
[ ]cross_sample_mapping..>2024-12-21 23:06 1.3M 
[ ]harmonize_labels1.ipynb2024-12-21 23:06 1.3M 
[ ]stage32_integrated_p..>2024-12-21 23:06 1.3M 
[ ]stage28_integrated_p..>2024-12-21 23:06 1.3M 
[ ]stage32_pseudobulk_e..>2024-12-21 23:07 1.5M 
[ ]batch_correction_sca..>2024-12-21 23:07 1.5M 
[ ]get_clusters_monocle..>2024-12-21 23:06 1.5M 
[TXT]chicken_scVI_cluster..>2024-12-21 23:07 1.8M 
[TXT]chicken_scANVI_clust..>2024-12-21 23:07 1.8M 
[TXT]chicken_scanorama_cl..>2024-12-21 23:07 1.9M 
[ ]batch_correction_scV..>2024-12-21 23:06 2.1M 
[TXT]chicken_scanorama_um..>2024-12-21 23:07 2.4M 
[ ]stage32_metacell_MN_..>2024-12-21 23:07 2.7M 
[ ]chicken_full_integra..>2024-12-21 23:07 3.6M 
[ ]chicken_integrated_p..>2024-12-21 23:07 3.8M 
[ ]stage28_metacell_MN_..>2024-12-21 23:07 6.0M 
[ ]stage32_sample10_hvg..>2024-12-21 23:06 6.1M 
[ ]stage32_sample10_hvg..>2024-12-21 23:06 6.3M 
[ ]stage32_sample5_hvg...>2024-12-21 23:06 7.2M 
[ ]stage32_sample5_hvg...>2024-12-21 23:07 7.3M 
[TXT]chicken_celltype_ann..>2024-12-21 23:07 8.2M 
[ ]stage32_sample12_hvg..>2024-12-21 23:06 9.3M 
[ ]stage28_sample11_hvg..>2024-12-21 23:07 9.3M 
[ ]stage32_sample12_hvg..>2024-12-21 23:06 9.4M 
[ ]stage23_sample3_hvg...>2024-12-21 23:07 9.4M 
[ ]stage28_sample11_hvg..>2024-12-21 23:07 9.4M 
[ ]stage23_sample3_hvg...>2024-12-21 23:07 9.5M 
[ ]stage28_sample10_hvg..>2024-12-21 23:07 11M 
[ ]stage28_sample10_hvg..>2024-12-21 23:07 11M 
[ ]stage28_sample5_hvg...>2024-12-21 23:07 11M 
[ ]stage28_sample5_hvg...>2024-12-21 23:07 11M 
[ ]stage23_sample10_hvg..>2024-12-21 23:07 12M 
[ ]stage23_sample10_hvg..>2024-12-21 23:07 12M 
[TXT]chicken_RPCA_embeddi..>2024-12-21 23:07 26M 
[TXT]chicken_SCT_embeddin..>2024-12-21 23:07 26M 
[TXT]chicken_raw_embeddin..>2024-12-21 23:07 26M 
[TXT]chicken_ssSTACAS_emb..>2024-12-21 23:07 26M 
[ ]chicken_scVI.h5ad 2024-12-21 23:07 27M 
[TXT]chicken_scVI_embeddi..>2024-12-21 23:07 37M 
[ ]stage32_sample10_raw..>2024-12-21 23:07 40M 
[ ]stage32_sample5_raw_..>2024-12-21 23:07 42M 
[ ]stage32_sample12_raw..>2024-12-21 23:07 53M 
[ ]stage23_sample3_raw_..>2024-12-21 23:07 65M 
[ ]stage28_sample10_raw..>2024-12-21 23:07 79M 
[ ]stage28_sample11_raw..>2024-12-21 23:07 85M 
[ ]stage28_sample5_raw_..>2024-12-21 23:07 87M 
[ ]stage23_sample10_raw..>2024-12-21 23:07 97M 
[TXT]chicken_scanorama_pc..>2024-12-21 23:07 123M 
[ ]stage32_fastMNN.Rdata 2024-12-21 23:07 143M 
[ ]stage23_sample4_raw_..>2024-12-21 23:07 155M 
[ ]stage23_fastMNN.Rdata 2024-12-21 23:07 161M 
[ ]stage28_fastMNN.Rdata 2024-12-21 23:07 244M 
[ ]stage28_2_top6000.Rdata2024-12-21 23:06 248M 
[ ]stage28_3_top6000.Rdata2024-12-21 23:06 251M 
[ ]stage28_1_top6000.Rdata2024-12-21 23:06 251M 
[ ]stage28_sample_aggre..>2024-12-21 23:06 258M 
[ ]stage23_2_top6000.Rdata2024-12-21 23:06 258M 
[ ]stage23_1_top6000.Rdata2024-12-21 23:06 258M 
[ ]stage32_2_top6000.Rdata2024-12-21 23:06 258M 
[ ]stage32_1_top6000.Rdata2024-12-21 23:06 258M 
[ ]stage32_3_top6000.Rdata2024-12-21 23:06 259M 
[ ]stage32_sample_aggre..>2024-12-21 23:06 259M 
[ ]stage23_sample_aggre..>2024-12-21 23:06 259M 
[ ]chicken_scVI2.h5Seurat 2024-12-21 23:07 347M 
[ ]chicken_scVI2.h5ad 2024-12-21 23:07 349M 
[ ]chicken_integrated_d..>2024-12-21 23:07 403M 
[ ]stage32_sample10_dat..>2024-12-21 23:06 531M 
[ ]stage32_sample5_data..>2024-12-21 23:06 585M 
[ ]chicken_stage28_coex..>2024-12-21 23:07 622M 
[ ]chicken_stage23_coex..>2024-12-21 23:07 630M 
[ ]stage28_sample11_dat..>2024-12-21 23:06 744M 
[ ]stage32_sample12_dat..>2024-12-21 23:06 747M 
[ ]stage23_sample3_data..>2024-12-21 23:06 753M 
[ ]chicken_stage32_coex..>2024-12-21 23:07 785M 
[ ]stage28_sample10_dat..>2024-12-21 23:06 816M 
[ ]stage28_sample5_data..>2024-12-21 23:06 859M 
[ ]stage23_sample10_dat..>2024-12-21 23:06 1.0G 
[ ]chicken_scANVI_new2...>2024-12-21 23:07 1.1G 
[ ]chicken_scVI_new2.h5ad 2024-12-21 23:07 1.1G 
[ ]chicken_scanorama.h5ad 2024-12-21 23:07 1.2G 
[ ]stage23_integrated_r..>2024-12-21 23:07 1.5G 
[ ]stage23_integrated_c..>2024-12-21 23:06 1.5G 
[ ]stage32_integrated_c..>2024-12-21 23:07 1.6G 
[ ]stage32_integrated_r..>2024-12-21 23:07 1.6G 
[ ]chicken_integrated_s..>2024-12-21 23:06 1.6G 
[ ]stage23_sample4_data..>2024-12-21 23:06 2.2G 
[ ]chicken_integrated_s..>2024-12-21 23:07 2.2G 
[ ]stage28_integrated_r..>2024-12-21 23:07 2.4G 
[ ]stage28_integrated_c..>2024-12-21 23:07 2.4G