├── Instruction_for_old_versions ├── Install_by_miniconda.md ├── Instruction_of_example_projects.md ├── README.md ├── TSNE_by_APEC.jpg ├── cell_quality.jpg ├── louvain_cluster_by_APEC.jpg ├── mergeAll.RefSeqTSS.jpg └── motif_FOS_on_TSNE_by_APEC.jpg ├── License.txt ├── README.md ├── Updates.md ├── code_v1.0.5 ├── APEC_prepare_steps.sh ├── Bias_corrected_deviation.py ├── Bias_corrected_deviation.pyc ├── cluster_byAccesson.py ├── cluster_byMotif.py ├── cluster_comparison.py ├── generate_UCSCtrack.py ├── generate_differential_Accesson.py ├── generate_differential_markers.py ├── generate_markers_on_plots.py ├── generate_superEnhancer.py ├── generate_trajectory.py ├── prepare_countMatrix.py ├── prepare_geneScore.py ├── prepare_mapping.py ├── prepare_peakCalling.py ├── prepare_premappedMatrix.py ├── prepare_qualityControl.py ├── prepare_trimming.py ├── run_monocle.R ├── subroutines.py └── subroutines.pyc ├── code_v1.0.6 ├── APEC_prepare_steps.sh ├── Bias_corrected_deviation.py ├── cluster_byAccesson.py ├── cluster_byMotif.py ├── cluster_comparison.py ├── generate_UCSCtrack.py ├── generate_differential_Accesson.py ├── generate_differential_markers.py ├── generate_gene_score_by_accesson.py ├── generate_markers_on_plots.py ├── generate_superEnhancer.py ├── generate_trajectory.py ├── generate_umap.py ├── prepare_countMatrix.py ├── prepare_geneScore.py ├── prepare_mapping.py ├── prepare_peakCalling.py ├── prepare_premappedMatrix.py ├── prepare_qualityControl.py ├── prepare_trimming.py └── subroutines.py ├── code_v1.1.0 ├── APEC_prepare_steps.sh ├── generate_UCSCtrack.py ├── prepare_countMatrix.py ├── prepare_mapping.py ├── prepare_peakCalling.py ├── prepare_qualityControl.py ├── prepare_trimming.py ├── subroutines.py └── subroutines.pyc ├── code_v1.2 ├── APEC_prepare_steps.sh ├── generate_UCSCtrack.py ├── prepare_countMatrix.py ├── prepare_mapping.py ├── prepare_peakCalling.py ├── prepare_qualityControl.py ├── prepare_trimming.py ├── subroutines.py └── subroutines.pyc ├── examples ├── .gitattributes ├── README.md ├── project01.tar.gz ├── project02.tar.gz ├── project03.tar.gz ├── script_for_project01.py ├── script_for_project02.py ├── script_for_project03.py ├── script_python_for_Figure_2c_2d.py └── script_python_for_Figure_2f_2g.py ├── images ├── TSNE_by_APEC_with_cluster_label.jpg ├── TSNE_by_APEC_with_notes_label.jpg ├── motif_GATA1_on_trajectory_by_APEC.jpg ├── pseudotime_trajectory_with_notes_label.jpg └── workflow.jpg └── reference └── README.md /Instruction_for_old_versions/Install_by_miniconda.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QuKunLab/APEC/HEAD/Instruction_for_old_versions/Install_by_miniconda.md -------------------------------------------------------------------------------- /Instruction_for_old_versions/Instruction_of_example_projects.md: -------------------------------------------------------------------------------- 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