Batch-effect-removal-benchmarking
A benchmark of batch-effect correction methods for single-cell RNA sequencing data
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Download Latest Version (.zip)- dataset1_sm_uc3.txt.gz
- sample_sm_uc3.txt.gz
- b1_celltype.txt.gz
- b1_exprs.txt.gz
- b2_celltype.txt.gz
- b2_exprs.txt.gz
- filtered_total_batch1_seqwell_batch2_10x.txt.gz
- filtered_total_sample_ext_organ_celltype_batch.txt.gz
- cellinfo.txt
- counts.txt
- counts_HVG.txt
- geneinfo.txt
- parameters.txt
- cellinfo.txt
- counts.txt
- counts_HVG.txt
- geneinfo.txt
- parameters.txt
- cellinfo.txt
- counts.txt
- counts_HVG.txt
- geneinfo.txt
- parameters.txt
- cellinfo.txt
- counts.txt
- counts_HVG.txt
- geneinfo.txt
- parameters.txt
- cellinfo.txt
- counts.txt
- counts_HVG.txt
- geneinfo.txt
- parameters.txt
- cellinfo.txt
- counts.txt
- counts_HVG.txt
- geneinfo.txt
- parameters.txt
- myData_pancreatic_5batches.txt.gz
- mySample_pancreatic_5batches.txt.gz
- b1_celltype.txt.gz
- b1_exprs.txt.gz
- b2_celltype.txt.gz
- b2_exprs.txt.gz
- b1_celltype.txt.gz
- b1_exprs.txt.gz
- b2_celltype.txt.gz
- b2_exprs.txt.gz
- b3_celltype.txt.gz
- b3_exprs.txt.gz
- b1_celltype.txt.gz
- b1_exprs.txt.gz
- b2_celltype.txt.gz
- b2_exprs.txt.gz
- downsample.rds
- downsample_meta.rds
- dropviz_and_nuclei_combined_filtered_cell_info.txt.gz
- dropviz_and_nuclei_combined_filtered_UMI.RDS
- downsample.rds
- downsample_meta.rds
- HCA_genes_cells_filtered_filtered_cell_info.txt.gz
- HCA_genes_cells_filtered_filtered_UMI.RDS
- run_bbknn_dataset1.ipynb
- run_bbknn_dataset10.ipynb
- run_bbknn_dataset2.ipynb
- run_bbknn_dataset4.ipynb
- run_bbknn_dataset5.ipynb
- run_bbknn_dataset6.ipynb
- run_bbknn_dataset7.ipynb
- run_bbknn_dataset8.py
- run_bbknn_dataset9.ipynb
- combat_atlas_dataset2.R
- combat_cellline_dataset6.R
- combat_dataset3.R
- combat_dataset8_withlog.R
- combat_dataset9_withlog.R
- combat_DC_dataset1.R
- combat_functions.R
- combat_HSC_dataset10.R
- combat_pancreas_dataset4.R
- combat_pbmc_dataset5.R
- combat_retina_dataset7.R
- ari_calcul_sampled.R
- ari_calcul_sampled_dat6.R
- ari_calcul_sampled_dat9.R
- ARI_files_consolidate.R
- conclude_ARISampled.R
- conclude_ARISampled_dat6.R
- conclude_ARISampled_dat9.R
- run_ARISampled.R
- run_ARISampled_dat6.R
- run_ARISampled_dat9.R
- run_ARISampled_dataset1.R
- run_ARISampled_dataset10.R
- run_ARISampled_dataset2.R
- run_ARISampled_dataset4.R
- run_ARISampled_dataset5.R
- run_ARISampled_dataset6.R
- run_ARISampled_dataset7.R
- run_ARISampled_dataset8.R
- run_ARISampled_dataset9.R
- asw_dataset1.ipynb
- asw_dataset10.ipynb
- asw_dataset2.ipynb
- asw_dataset4.ipynb
- asw_dataset5.ipynb
- asw_dataset6.ipynb
- asw_dataset7.ipynb
- asw_dataset8.ipynb
- asw_dataset9.ipynb
- asw_Hoa.py
- kbet_utils.R
- run_kBET_d1.R
- run_kBET_d10.R
- run_kBET_d2.R
- run_kBET_d4.R
- run_kBET_d5.R
- run_kBET_d6.R
- run_kBET_d7.R
- run_kBET_d8.R
- run_kBET_d9.R
- run_kBET_d9_downsample.R
- lisi_utils.R
- run_LISI_dataset1.R
- run_LISI_dataset10.R
- run_LISI_dataset2.R
- run_LISI_dataset4.R
- run_lisi_dataset5.R
- run_LISI_dataset6.R
- run_LISI_dataset7.R
- run_LISI_dataset8.R
- run_LISI_dataset9.R
- functions.R
- tsne_visualization_dataset10_cjm.R
- tsne_visualization_dataset1_cjm.R
- tsne_visualization_dataset2_cjm.R
- tsne_visualization_dataset4_cjm.R
- tsne_visualization_dataset6_cjm.R
- tsne_visualization_dataset7_cjm.R
- tsne_visualization_dataset8_cjm.R
- tsne_visualization_dataset9_cjm.R
- umap_visualization_dataset10_cjm.R
- umap_visualization_dataset1_cjm.R
- umap_visualization_dataset2_cjm.R
- umap_visualization_dataset4_cjm.R
- umap_visualization_dataset5_cjm.R
- umap_visualization_dataset6_cjm.R
- umap_visualization_dataset7_cjm.R
- umap_visualization_dataset8_cjm.R
- umap_visualization_dataset9_cjm.R
- evaluation_utils.R
- statistical_test_updated.R
- call_fastMNN.R
- call_fastMNN_04.R
- call_fastMNN_06.R
- run_fastMNN_01.R
- run_fastMNN_02.R
- run_fastMNN_04.R
- run_fastMNN_05.R
- run_fastMNN_06.R
- run_fastMNN_07.R
- run_fastMNN_08.R
- run_fastMNN_08_downsample.R
- run_fastMNN_09.R
- run_fastMNN_09_downsample.R
- run_fastMNN_10.R
- call_harmony.R
- run_harmony_01.R
- run_harmony_02.R
- run_harmony_04.R
- run_harmony_05.R
- run_harmony_06.R
- run_harmony_07.R
- run_harmony_08.R
- run_harmony_08_downsample.R
- run_harmony_09.R
- run_harmony_09_downsample.R
- run_harmony_10.R
- call_liger.R
- run_liger_01.R
- run_liger_02.R
- run_liger_04.R
- run_liger_05.R
- run_liger_06.R
- run_liger_07.R
- run_liger_08.R
- run_liger_09.R
- run_liger_10.R
- limma_dataset1.R
- limma_dataset10.R
- limma_dataset2.R
- limma_dataset4.R
- limma_dataset5.R
- limma_dataset6.R
- limma_dataset7.R
- limma_dataset8.R
- limma_dataset9.R
- limma_functions.R
- limma_utils.R
- resnet_dataset1.ipynb
- resnet_dataset10.ipynb
- resnet_dataset2.ipynb
- resnet_dataset4.ipynb
- resnet_dataset5.ipynb
- resnet_dataset6.ipynb
- resnet_dataset7.ipynb
- resnet_dataset8.ipynb
- resnet_dataset9.ipynb
- call_MNNCorrect.R
- call_MNNCorrect_03.R
- call_MNNCorrect_04.R
- call_MNNCorrect_06.R
- run_mnn_correct_01.R
- run_mnn_correct_02.R
- run_mnn_correct_04.R
- run_mnn_correct_05.R
- run_mnn_correct_06.R
- run_mnn_correct_07.R
- run_mnn_correct_08.R
- run_mnn_correct_08_downsample.R
- run_mnn_correct_09.R
- run_mnn_correct_09_downsample.R
- run_mnn_correct_10.R
- scanorama_dataset1.ipynb
- scanorama_dataset10.ipynb
- scanorama_dataset2.ipynb
- scanorama_dataset4.ipynb
- scanorama_dataset5.ipynb
- scanorama_dataset6.ipynb
- scanorama_dataset7.ipynb
- scanorama_dataset8.ipynb
- scanorama_dataset9.ipynb
- dataset10_scGene.ipynb
- dataset1_without_celltype_scGene.ipynb
- dataset4_scGene.ipynb
- dataset5_scGene.ipynb
- dataset7_scGene.ipynb
- dataset8_scGene.ipynb
- dataset9_scGene.ipynb
- dataset2_scgen.ipynb
- dataset6_scgen.ipynb
- call_scMerge.R
- run_scMerge_01.R
- run_scMerge_02.R
- run_scMerge_03.R
- run_scMerge_04.R
- run_scMerge_05.R
- run_scMerge_06.R
- run_scMerge_07.R
- run_scMerge_08.R
- run_scMerge_09.R
- run_scMerge_10.R
- call_seurat_2.R
- run_seurat2_01.R
- run_seurat2_02.R
- run_seurat2_04.R
- run_seurat2_05.R
- run_seurat2_06.R
- run_seurat2_07.R
- run_seurat2_08.R
- run_seurat2_08_downsample.R
- run_seurat2_09.R
- run_seurat2_10.R
- call_seurat_3.R
- run_seurat3_01.R
- run_seurat3_02.R
- run_seurat3_04.R
- run_seurat3_05.R
- run_seurat3_06.R
- run_seurat3_07.R
- run_seurat3_08.R
- run_seurat3_08_downsample.R
- run_seurat3_09.R
- run_seurat3_09_downsample.R
- run_seurat3_10.R
- design_simulation_splatter.R
- highly_variable_genes_from_Seurat.R
- run_combat.R
- run_limma.R
- run_MNN.R
- run_scanorama.ipynb
- run_scGen.ipynb
- run_scmerge.R
- run_seurat3.R
- run_zinbwave.R
- confusion_matrix_Fscore.R
- run_DEGs_from_Seurat.R
- Seurat_DEG_analysis.R
- zinbwave_dataset10.R
- preprocess.R
- zinbwave_dataset1.R
- zinbwave_dataset2.R
- zinbwave_dataset4.R
- zinbwave_dataset5.R
- zinbwave_dataset6.R
- zinbwave_dataset7.R
- zinbwave_dataset8.R
- zinbwave_dataset9.R
- ZINB_WaVE_analysis.R
- .gitattributes
- README.md
// repository documentation
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