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