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CellNEST_PDAC_chiSquare_hypergeometric_test.py
CellNEST_PDAC_chiSquare_hypergeometric_test.py
 
 
CellNEST_figures_input_LUAD.7z
CellNEST_figures_input_LUAD.7z
 
 
Cytosignal_human_lymph.csv
Cytosignal_human_lymph.csv
 
 
Human_lymph_TCellZone_relay_plot.py
Human_lymph_TCellZone_relay_plot.py
 
 
Human_lymph_relay_plot.py
Human_lymph_relay_plot.py
 
 
LUAD_relay_plot.py
LUAD_relay_plot.py
 
 
MERFISH_relay_plot.py
MERFISH_relay_plot.py
 
 
NEST_figures_input_MERFISH_plot.7z
NEST_figures_input_MERFISH_plot.7z
 
 
NEST_figures_input_PDAC.7z
NEST_figures_input_PDAC.7z
 
 
NEST_figures_input_human_lymph.7z
NEST_figures_input_human_lymph.7z
 
 
NEST_figures_input_pdo.7z
NEST_figures_input_pdo.7z
 
 
NEST_figures_input_synthetic.7z
NEST_figures_input_synthetic.7z
 
 
PDAC_140694_morphology_plot.py
PDAC_140694_morphology_plot.py
 
 
PDAC_140694_niches.py
PDAC_140694_niches.py
 
 
PDAC_140694_relay_plot.py
PDAC_140694_relay_plot.py
 
 
PDAC_140694_subtype_plot.py
PDAC_140694_subtype_plot.py
 
 
PDAC_64630_morphology_plot.py
PDAC_64630_morphology_plot.py
 
 
PDAC_64630_niches.R
PDAC_64630_niches.R
 
 
PDAC_64630_relay_plot.py
PDAC_64630_relay_plot.py
 
 
PDAC_64630_subtype_plot.py
PDAC_64630_subtype_plot.py
 
 
PDAC_COMMOT.py
PDAC_COMMOT.py
 
 
README.md
README.md
 
 
benchmark_cell_type_prep.py
benchmark_cell_type_prep.py
 
 
cellnest_logo.svg
cellnest_logo.svg
 
 
fig3d_sfig10c_cell_type.py
fig3d_sfig10c_cell_type.py
 
 
fig3d_sfig10c_sfig2i_deconvolution.sh
fig3d_sfig10c_sfig2i_deconvolution.sh
 
 
fig3ij_sfig2g_sfig3cd_cellchat.R
fig3ij_sfig2g_sfig3cd_cellchat.R
 
 
fig3ij_sfig2h_sfig3cd_giotto.R
fig3ij_sfig2h_sfig3cd_giotto.R
 
 
fig3ij_sfig2i_sfig3cd_twcom.R
fig3ij_sfig2i_sfig3cd_twcom.R
 
 
fig3ij_sfig3cd_synthetic_benchmark.py
fig3ij_sfig3cd_synthetic_benchmark.py
 
 
figure_2_f_human_lymph_Niches.R
figure_2_f_human_lymph_Niches.R
 
 
figure_2_g_human_lymph_COMMOT.py
figure_2_g_human_lymph_COMMOT.py
 
 
figure_2_human_lymph_b_c_d.py
figure_2_human_lymph_b_c_d.py
 
 
figure_2_human_lymph_e.py
figure_2_human_lymph_e.py
 
 
figure_3_synthetic_benchmark.py
figure_3_synthetic_benchmark.py
 
 
figure_4_merfish_a_d.py
figure_4_merfish_a_d.py
 
 
figure_4_merfish_b_e.py
figure_4_merfish_b_e.py
 
 
figure_4_merfish_c_f.py
figure_4_merfish_c_f.py
 
 
figure_4_merfish_g_h.py
figure_4_merfish_g_h.py
 
 
figure_5_LUAD.py
figure_5_LUAD.py
 
 
figure_5_LUAD_heatmaps.py
figure_5_LUAD_heatmaps.py
 
 
figure_6_pdac_d_e_i.py
figure_6_pdac_d_e_i.py
 
 
figure_6_pdac_f.py
figure_6_pdac_f.py
 
 
figure_6_pdac_j_k.py
figure_6_pdac_j_k.py
 
 
figure_7_01_rds_to_csv.R
figure_7_01_rds_to_csv.R
 
 
figure_7_02_deseq2_preprocess.py
figure_7_02_deseq2_preprocess.py
 
 
figure_7_03_deseq2.R
figure_7_03_deseq2.R
 
 
figure_7_04_box_plot.py
figure_7_04_box_plot.py
 
 
figure_7_05_fisher_test.R
figure_7_05_fisher_test.R
 
 
figure_7_06_heatmap.py
figure_7_06_heatmap.py
 
 
figure_7_run.sh
figure_7_run.sh
 
 
intradb_download.sh
intradb_download.sh
 
 
intradb_nichenet_process.R
intradb_nichenet_process.R
 
 
intradb_process.py
intradb_process.py
 
 
nest_logo.svg
nest_logo.svg
 
 
p_value_generation_NEST.py
p_value_generation_NEST.py
 
 
sfig10c_pdac_atlas.R
sfig10c_pdac_atlas.R
 
 
sfig2f_lymph_cluster.py
sfig2f_lymph_cluster.py
 
 
sfig2hi_lymph_benchmark.py
sfig2hi_lymph_benchmark.py
 
 
sfig2jk_efficiency.py
sfig2jk_efficiency.py
 
 
sfig3b_relay_conf.py
sfig3b_relay_conf.py
 
 
sfig3b_relay_conf_compare.py
sfig3b_relay_conf_compare.py
 
 
utilities.py
utilities.py
 
 

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alt text CellNEST

This repository can be used to generate all the figures and plots from the corresponding paper.

Please download and extract all the *.7z files. The scripts will read input from those directories for the figure generation.

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