.gitbook.yaml
.gitignore
LICENSE.txt
README.md
SUMMARY.md
setup.cfg
setup.py
.gitbook/assets/alt_3 (1).png
.gitbook/assets/alt_3.png
.gitbook/assets/alt_5 (1).png
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code-documentation/swangraph.md
code-documentation/utils.md
faqs/Data structure.ipynb
faqs/data_structure.md
faqs/file_formats.md
faqs/understanding_swan_vis.md
faqs/utilities.ipynb
faqs/utilities.md
figures/swan_logo.png
figures/teaching_2.png
figures/teaching_4.png
figures/teaching_5.png
figures/teaching_6.png
figures/teaching_7.png
swan_vis/__init__.py
swan_vis/graph.py
swan_vis/networkx_patch.py
swan_vis/nx_pylab.py
swan_vis/plottedgraph.py
swan_vis/report.py
swan_vis/swangraph.py
swan_vis/talon_utils.py
swan_vis/utils.py
swan_vis.egg-info/PKG-INFO
swan_vis.egg-info/SOURCES.txt
swan_vis.egg-info/dependency_links.txt
swan_vis.egg-info/requires.txt
swan_vis.egg-info/top_level.txt
testing/test_abundance.py
testing/test_add_data.py
testing/test_analysis.py
testing/test_graph.py
testing/test_plotting.py
testing/test_utils.py
testing/files/Canx.gtf
testing/files/Canx_transcript.tsv
testing/files/chr11_and_Tcf3.gtf
testing/files/chr11_and_Tcf3_PB65_B017_B018_dpi.tsv
testing/files/chr11_and_Tcf3_cluster_dpi.tsv
testing/files/chr11_and_Tcf3_metadata.tsv
testing/files/chr11_and_Tcf3_metadata_2.tsv
testing/files/chr11_and_Tcf3_metadata_dupecols.tsv
testing/files/chr11_and_Tcf3_no_gname.db
testing/files/chr11_and_Tcf3_swan_abundance.tsv
testing/files/chr11_and_Tcf3_talon_abundance.tsv
testing/files/chr11_and_Tcf3_talon_abundance_D12.tsv
testing/files/chr11_and_Tcf3_talon_abundance_PB65.tsv
testing/files/chr11_and_Tcf3_talon_abundance_clusters_pi.tsv
testing/files/chr11_and_Tcf3_talon_abundance_clusters_pi_scrach.xlsx
testing/files/chr11_and_Tcf3_talon_abundance_clusters_tpm.tsv
testing/files/chr11_and_Tcf3_talon_abundance_pi.tsv
testing/files/chr11_and_Tcf3_talon_abundance_tpm.tsv
testing/files/plot_minus_gene_summary_edge_df.tsv
testing/files/plot_minus_gene_summary_loc_df.tsv
testing/files/test_ab_1.tsv
testing/files/test_ab_dataset1.tsv
testing/files/test_ab_dataset2.tsv
testing/files/test_ab_talon_1.tsv
testing/files/test_add_edge_coords_result.tsv
testing/files/test_edge_df.tsv
testing/files/test_full.db
testing/files/test_full.gtf
testing/files/test_full_annotation.gtf
testing/files/test_full_for_talon.gtf
testing/files/test_full_pass_list.csv
testing/files/test_known.gtf
testing/files/test_known_talon.gtf
testing/files/test_loc_df.tsv
testing/files/test_novel.gtf
testing/files/test_novel_1.gtf
testing/files/test_novel_talon.gtf
testing/files/test_pi_1.tsv
testing/files/test_pi_1_reference.tsv
testing/files/test_preexisting_edge_df.tsv
testing/files/test_preexisting_loc_df.tsv
testing/files/test_preexisting_result_edge_df.tsv
testing/files/test_preexisting_result_loc_df.tsv
testing/files/test_preexisting_result_t_df.tsv
testing/files/test_preexisting_t_df.tsv
testing/files/test_t_df.tsv
tutorials/Analysis tools.ipynb
tutorials/Getting started.ipynb
tutorials/README.md
tutorials/Visualization.ipynb
tutorials/analysis_tools.md
tutorials/data_processing.md
tutorials/full_tutorial.py
tutorials/getting_started.md
tutorials/scanpy_compatibility.ipynb
tutorials/scanpy_compatibility.md
tutorials/test_dev.ipynb
tutorials/visualization.md
tutorials/data/Canx.db
tutorials/data/Canx_pass_list.csv
tutorials/data/all_talon_abundance_filtered.tsv
tutorials/data/all_talon_abundance_filtered_counts.tsv
tutorials/data/all_talon_abundance_filtered_counts_hffc6_hepg2.tsv
tutorials/data/all_talon_abundance_filtered_counts_k562.tsv
tutorials/data/chr11_and_Tcf3.gtf
tutorials/data/chr11_and_Tcf3_PB65_B017_B018_dpi.tsv
tutorials/data/chr11_and_Tcf3_cluster_dpi.tsv
tutorials/data/chr11_and_Tcf3_metadata.tsv
tutorials/data/chr11_and_Tcf3_metadata_2.tsv
tutorials/data/chr11_and_Tcf3_metadata_dupecols.tsv
tutorials/data/chr11_and_Tcf3_no_gname.db
tutorials/data/chr11_and_Tcf3_swan_abundance.tsv
tutorials/data/chr11_and_Tcf3_talon_abundance.tsv
tutorials/data/chr11_and_Tcf3_talon_abundance_D12.tsv
tutorials/data/chr11_and_Tcf3_talon_abundance_PB65.tsv
tutorials/data/chr11_and_Tcf3_talon_abundance_clusters_pi.tsv
tutorials/data/chr11_and_Tcf3_talon_abundance_clusters_tpm.tsv
tutorials/data/chr11_and_Tcf3_talon_abundance_pi.tsv
tutorials/data/chr11_and_Tcf3_talon_abundance_tpm.tsv
tutorials/data/gencode.v29.annotation.gtf
tutorials/data/hepg2_1_talon.gtf
tutorials/data/hepg2_2_talon.gtf
tutorials/data/hepg2_whitelist.csv
tutorials/data/hepg2_whitelist.csv.1
tutorials/data/hffc6_1_talon.gtf
tutorials/data/hffc6_2_talon.gtf
tutorials/data/hffc6_3_talon.gtf
tutorials/data/hffc6_whitelist.csv
tutorials/data/swan_chr20.p
tutorials/data/talon.db
tutorials/data/test_edge_df.tsv
tutorials/data/test_loc_df.tsv
tutorials/data/test_pi.tsv
tutorials/data/test_pi_1.tsv
tutorials/data/test_pi_1_reference.tsv
tutorials/data/test_preexisting_edge_df.tsv
tutorials/data/test_preexisting_loc_df.tsv
tutorials/data/test_preexisting_result.xlsx
tutorials/data/test_preexisting_result_edge_df.tsv
tutorials/data/test_preexisting_result_loc_df.tsv
tutorials/data/test_preexisting_result_t_df.tsv
tutorials/data/test_preexisting_sg.xlsx
tutorials/data/test_preexisting_t_df.tsv
tutorials/data/test_sg_dfs.xlsx
tutorials/data/test_t_df.tsv
tutorials/figures/adrm1_browser_ENSG00000130706.12_report.png
tutorials/figures/adrm1_browser_color_cell_line_ENSG00000130706.12_report.png
tutorials/figures/adrm1_browser_color_replicate_cell_line_ENSG00000130706.12_report.png
tutorials/figures/adrm1_novel_ENSG00000130706.12_report.png
tutorials/figures/adrm1_novel_ENSG00000130706.12_summary.png
tutorials/figures/adrm1_paper_novel_ENSG00000130706.12_report.png
tutorials/figures/adrm1_paper_novel_qval_ENSG00000130706.12_report.png
tutorials/figures/multi_gene_ENSG00000130706.12_report.png
tutorials/figures/multi_gene_ENSG00000197746.13_report.png
tutorials/figures/my_gene_summary.png
tutorials/figures/nipal3_ENSG00000001461.16_report.png
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tutorials/figures/nipal3_novel_ENSG00000001461.16_report.png
tutorials/figures/nipal3_novel_cell_line_ENSG00000001461.16_report.png
tutorials/figures/srf_ENSMUSG00000015605.6_report.png