motifs_v0.1.0.zip
labowitz-motifs-342c2f1
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57.9 MB
.Rhistory
18.3 kB
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pcs
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sources
prop
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INDEX
27.7 kB
unsaved-notebooks
243C9073
1
chunks.json
28 Bytes
DA82AF1A
1
chunks.json
28 Bytes
shared
notebooks
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paths
2.1 kB
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3.2 kB
.gitignore
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4.5 kB
codemeta.json
2.4 kB
html_imports.R
905 Bytes
html_module.R
65.7 kB
html_script.R
11.2 kB
installed_packages.txt
3.6 kB
module
.ipynb_checkpoints
module-checkpoint.R
53.8 kB
module.R
73.9 kB
motifs.Rproj
205 Bytes
paper
bioRxiv_submission
Supplementary Files
Figure 2–source data 1.csv
33.5 kB
Figure 3–figure supplement 1.csv
33.0 kB
Figure 3–figure supplement 2.csv
108.5 kB
Figure 5–source data 1.csv
54.6 kB
scripts
analysis
.ipynb_checkpoints
Figure_5_figure_supplement_1A_computations_NivUpdate-checkpoint.R
27.2 kB
Figure_5_figure_supplement_1A_computations_NivUpdate.R
27.2 kB
Supp_pdfs.R
14.6 kB
aws_pathways_silh_score.R
11.6 kB
bmpr_analysis.R
1.9 kB
eph-ephrin_analysis.R
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eph-ephrin_analysis_max.R
15.7 kB
eph-ephrin_analysis_percentile.R
15.7 kB
eph-ephrin_computation.R
4.8 kB
eph_ab_analysis.R
7.3 kB
imports.R
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imports_max.R
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imports_new.R
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imports_percentile.R
1.5 kB
imports_trial.R
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interpathway_analysis.R
4.8 kB
merged_dendrogram.R
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notch_analysis.R
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notch_analysis_max.R
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notch_analysis_percentile.R
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outputs
bmpr_profiles.csv
41.1 kB
eph-ephrin_analysis
eph-ephrin_profile_cell_ontology_class.csv
33.0 kB
max
eph-ephrin_profile_cell_ontology_class.csv
33.0 kB
percentile
eph-ephrin_profile_cell_ontology_class.csv
33.0 kB
eph-ephrin_profiles.csv
26.9 kB
eph-ephrin_scaled_gene_exp.csv
18.6 kB
eph_ab.csv
13.2 kB
notch_analysis
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32.6 kB
notch_profile_cell_ontology_class.csv
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percentile
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notch_profiles.csv
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rna_splicing_sr.csv
66.3 kB
tgfb_analysis
max
tgfb_profile_cell_ontology_class.csv
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percentile
tgfb_profile_cell_ontology_class.csv
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tgfb_profile_cell_ontology_class.csv
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tgfb_profiles.csv
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ubi_prot.csv
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wnt_analysis
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wnt_profile_cell_ontology_class.csv
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percentile
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wnt_profile_cell_ontology_class.csv
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wnt_analysis.zip
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wnt_profiles.csv
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server_trial_1.R
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server_trial_2.R
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tgfb_analysis.R
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tgfb_analysis_max.R
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tgfb_new.R
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wnt_analysis.R
16.2 kB
wnt_analysis_max.R
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wnt_analysis_percentile.R
15.8 kB
figures
.ipynb_checkpoints
fig_1c_forelimb_umap-checkpoint.ipynb
14.7 MB
BMP_Motifs.R
6.8 kB
Rachael
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notch_profiles.ai
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Rachael_Notch_Motifs.R
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notch _profile_19.csv
713 Bytes
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notch_devel_cell_types.csv
3.4 kB
notch_tissue.csv
1.0 kB
peak_analysis
silhouette_res
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5.2 kB
silh_optk_figure5.csv
5.6 kB
silh_rds
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29.8 kB
tgfb_tissue.csv
783 Bytes
tissue_distribution_ordered_fig5.R
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wnt_tissue.csv
833 Bytes
helper.R
51.2 kB
max_module.R
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module.R
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module_new.R
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module_percentile.R
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cell_submission
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139.1 kB
Revisions
Supplementary File 1.csv
33.0 kB
Supplementary File 3.csv
475.2 kB
Supplementary File 5.csv
105.0 kB
Supplementary File 1.csv
33.0 kB
Supplementary File 3.csv
54.6 kB
Supplementary File 5.csv
105.0 kB
figures
Knobs for final panel_04.ai
1.3 MB
Notch_notes.docx
16.6 kB
Pathway Expression Motif Figures_v25.ai
20.6 MB
renv
.gitignore
39 Bytes
activate.R
18.3 kB
settings.dcf
192 Bytes
renv.lock
351 Bytes
scripts
analysis
.ipynb_checkpoints
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4.5 kB
FACS_TMS-checkpoint.ipynb
158.7 kB
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Figure_6A-checkpoint.ipynb
10.9 MB
Figure_6AB_Interactive_Revise-checkpoint.ipynb
7.9 MB
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93.3 kB
Figure_6C-checkpoint.ipynb
5.7 MB
Figure_6D-checkpoint.ipynb
96.1 kB
Figure_7A-checkpoint.ipynb
10.9 MB
Figure_7B-checkpoint.ipynb
77.4 kB
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5.7 MB
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80.0 kB
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12.3 MB
Old_Figure_2C-checkpoint.R
1.8 kB
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14.8 MB
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1.8 MB
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Distance_Density_Tgf_beta.Rmd
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Distance_Density_Tgf_beta.nb.html
807.5 kB
Figure_2A.R
1.5 kB
Figure_2B_Revise.R
963 Bytes
Figure_2B_main.R
315 Bytes
Figure_2C_3_4BCDE_S2ABC_S3D.R
6.2 kB
Figure_4F.R
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Figure_4F_Unordered.R
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Figure_5_Computations.R
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Figure_5_Functions.R
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Figure_5_S4A.R
4.6 kB
Figure_5_S4A_Niv_Computations.R
2.5 kB
Figure_6C.R
4.7 kB
Figure_6C_motifs.R
0 Bytes
Figure_7A.ipynb
10.9 MB
Figure_7B.ipynb
77.4 kB
Figure_7C.ipynb
5.7 MB
Figure_7D.ipynb
80.0 kB
Figure_S1A.ipynb
12.3 MB
Figure_S1B.R
1.1 kB
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Figure_S3A.R
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Figure_S3C.R
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Notch_ECDF.R
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Pathway_vs_Global_Distance_Density.R
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Pathway_vs_Global_Distance_Scatter.R
3.2 kB
Supplementary_File_4.R
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Zara_Adelynyl_PDE.R
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__pycache__
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module.cpython-38.pyc
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python_imports.cpython-38.pyc
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imports.R
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knn_profiles.py
4.1 kB
module.py
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python_imports.py
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scatter_motifs_may2023.r
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.ipynb_checkpoints
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359.8 kB
fig_1c_forelimb_umap-checkpoint.ipynb
14.7 MB
Figure_2A.pdf
6.7 kB
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Figure_3B.pdf
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Figure_3B_BreaksSpec.jpeg
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Figure_3B_trial.jpeg
51.0 kB
Figure_3C.html
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Figure_3C.pdf
329.4 kB
Figure_3C_Inset.pdf
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Figure_3C_files
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d3.min.js
214.2 kB
htmlwidgets-1.5.4
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sankey-1
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sankeyNetwork-binding-0.4
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Pathway_Global_Distance
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1.4 MB
euclidean_global_Ephrins.png
1.4 MB
euclidean_global_Ephrins_18m 10x.pdf
15.5 kB
euclidean_global_Ephrins_18m 10x.png
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euclidean_global_Ephrins_21m 10x.png
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euclidean_global_Ephrins_30m 10x.png
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euclidean_global_Ephrins_3m 10x.pdf
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euclidean_global_Ephrins_3m 10x.png
223.8 kB
euclidean_global_Ephrins_E5.5_Nowotschin.pdf
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euclidean_global_Ephrins_E5.5_Nowotschin.png
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euclidean_global_Ephrins_E6.5_8.5_Chan.pdf
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euclidean_global_Ephrins_E6.5_8.5_Chan.png
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euclidean_global_Ephrins_E6.5_8.5_Marioni.pdf
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euclidean_global_Ephrins_E6.5_8.5_Marioni.png
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euclidean_global_Ephrins_E9.5_11.5_Tang.pdf
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euclidean_global_Ephrins_E9.5_11.5_Tang.png
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euclidean_global_Ephrins_FACS 18m.pdf
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euclidean_global_Ephrins_FACS 18m.png
176.4 kB
euclidean_global_Ephrins_FACS 24m.pdf
5.2 kB
euclidean_global_Ephrins_FACS 24m.png
166.7 kB
euclidean_global_Ephrins_FACS 3m.pdf
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euclidean_global_Ephrins_FACS 3m.png
206.6 kB
euclidean_global_Ephrins_Forelimb_E10.5_15.0.pdf
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euclidean_global_Ephrins_Forelimb_E10.5_15.0.png
820.1 kB
euclidean_global_LPS and Citrate Signaling and Inflammation.pdf
37.8 MB
euclidean_global_LPS and Citrate Signaling and Inflammation.png
1.5 MB
euclidean_global_LPS and Citrate Signaling and Inflammation_18m 10x.pdf
316.8 kB
euclidean_global_LPS and Citrate Signaling and Inflammation_18m 10x.png
1.4 MB
euclidean_global_LPS and Citrate Signaling and Inflammation_1m 10x.pdf
138.1 kB
euclidean_global_LPS and Citrate Signaling and Inflammation_1m 10x.png
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euclidean_global_LPS and Citrate Signaling and Inflammation_21m 10x.pdf
259.4 kB
euclidean_global_LPS and Citrate Signaling and Inflammation_21m 10x.png
1.2 MB
euclidean_global_LPS and Citrate Signaling and Inflammation_24m 10x.pdf
95.1 kB
euclidean_global_LPS and Citrate Signaling and Inflammation_24m 10x.png
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euclidean_global_LPS and Citrate Signaling and Inflammation_30m 10x.pdf
270.2 kB
euclidean_global_LPS and Citrate Signaling and Inflammation_30m 10x.png
1.3 MB
euclidean_global_LPS and Citrate Signaling and Inflammation_3m 10x.pdf
254.6 kB
euclidean_global_LPS and Citrate Signaling and Inflammation_3m 10x.png
1.3 MB
euclidean_global_LPS and Citrate Signaling and Inflammation_E5.5_Nowotschin.pdf
16.6 kB
euclidean_global_LPS and Citrate Signaling and Inflammation_E5.5_Nowotschin.png
280.4 kB
euclidean_global_LPS and Citrate Signaling and Inflammation_E6.5_8.5_Chan.pdf
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euclidean_global_LPS and Citrate Signaling and Inflammation_E6.5_8.5_Chan.png
1.3 MB
euclidean_global_LPS and Citrate Signaling and Inflammation_E6.5_8.5_Marioni.pdf
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euclidean_global_LPS and Citrate Signaling and Inflammation_E6.5_8.5_Marioni.png
1.1 MB
euclidean_global_LPS and Citrate Signaling and Inflammation_E9.5_11.5_Tang.pdf
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euclidean_global_LPS and Citrate Signaling and Inflammation_E9.5_11.5_Tang.png
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euclidean_global_LPS and Citrate Signaling and Inflammation_FACS 18m.pdf
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euclidean_global_LPS and Citrate Signaling and Inflammation_FACS 18m.png
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euclidean_global_LPS and Citrate Signaling and Inflammation_FACS 24m.pdf
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euclidean_global_LPS and Citrate Signaling and Inflammation_FACS 24m.png
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euclidean_global_LPS and Citrate Signaling and Inflammation_FACS 3m.pdf
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euclidean_global_LPS and Citrate Signaling and Inflammation_FACS 3m.png
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euclidean_global_LPS and Citrate Signaling and Inflammation_Forelimb_E10.5_15.0.pdf
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euclidean_global_LPS and Citrate Signaling and Inflammation_Forelimb_E10.5_15.0.png
1.2 MB
euclidean_global_NF-kB Signaling Pathway.pdf
30.1 MB
euclidean_global_NF-kB Signaling Pathway.png
1.5 MB
euclidean_global_NF-kB Signaling Pathway_18m 10x.pdf
329.3 kB
euclidean_global_NF-kB Signaling Pathway_18m 10x.png
1.5 MB
euclidean_global_NF-kB Signaling Pathway_1m 10x.pdf
142.3 kB
euclidean_global_NF-kB Signaling Pathway_1m 10x.png
1.0 MB
euclidean_global_NF-kB Signaling Pathway_21m 10x.pdf
265.0 kB
euclidean_global_NF-kB Signaling Pathway_21m 10x.png
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euclidean_global_NF-kB Signaling Pathway_24m 10x.pdf
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euclidean_global_NF-kB Signaling Pathway_24m 10x.png
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euclidean_global_NF-kB Signaling Pathway_30m 10x.pdf
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euclidean_global_NF-kB Signaling Pathway_30m 10x.png
1.3 MB
euclidean_global_NF-kB Signaling Pathway_3m 10x.pdf
260.0 kB
euclidean_global_NF-kB Signaling Pathway_3m 10x.png
1.4 MB
euclidean_global_NF-kB Signaling Pathway_E5.5_Nowotschin.pdf
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euclidean_global_NF-kB Signaling Pathway_E5.5_Nowotschin.png
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euclidean_global_NF-kB Signaling Pathway_E6.5_8.5_Chan.pdf
450.7 kB
euclidean_global_NF-kB Signaling Pathway_E6.5_8.5_Chan.png
1.2 MB
euclidean_global_NF-kB Signaling Pathway_E6.5_8.5_Marioni.pdf
78.8 kB
euclidean_global_NF-kB Signaling Pathway_E6.5_8.5_Marioni.png
637.6 kB
euclidean_global_NF-kB Signaling Pathway_E9.5_11.5_Tang.pdf
27.7 kB
euclidean_global_NF-kB Signaling Pathway_E9.5_11.5_Tang.png
410.2 kB
euclidean_global_NF-kB Signaling Pathway_FACS 18m.pdf
123.5 kB
euclidean_global_NF-kB Signaling Pathway_FACS 18m.png
961.5 kB
euclidean_global_NF-kB Signaling Pathway_FACS 24m.pdf
83.2 kB
euclidean_global_NF-kB Signaling Pathway_FACS 24m.png
767.6 kB
euclidean_global_NF-kB Signaling Pathway_FACS 3m.pdf
180.8 kB
euclidean_global_NF-kB Signaling Pathway_FACS 3m.png
1.1 MB
euclidean_global_NF-kB Signaling Pathway_Forelimb_E10.5_15.0.pdf
236.5 kB
euclidean_global_NF-kB Signaling Pathway_Forelimb_E10.5_15.0.png
1.1 MB
euclidean_global_Notch receptors, Dll ligands, and Fringe proteins.pdf
5.9 MB
euclidean_global_Notch receptors, Dll ligands, and Fringe proteins.png
2.0 MB
euclidean_global_Notch receptors, Dll ligands, and Fringe proteins_18m 10x.pdf
115.8 kB
euclidean_global_Notch receptors, Dll ligands, and Fringe proteins_18m 10x.png
619.0 kB
euclidean_global_Notch receptors, Dll ligands, and Fringe proteins_1m 10x.pdf
60.7 kB
euclidean_global_Notch receptors, Dll ligands, and Fringe proteins_1m 10x.png
472.6 kB
euclidean_global_Notch receptors, Dll ligands, and Fringe proteins_21m 10x.pdf
102.0 kB
euclidean_global_Notch receptors, Dll ligands, and Fringe proteins_21m 10x.png
597.1 kB
euclidean_global_Notch receptors, Dll ligands, and Fringe proteins_24m 10x.pdf
27.4 kB
euclidean_global_Notch receptors, Dll ligands, and Fringe proteins_24m 10x.png
326.1 kB
euclidean_global_Notch receptors, Dll ligands, and Fringe proteins_30m 10x.pdf
76.9 kB
euclidean_global_Notch receptors, Dll ligands, and Fringe proteins_30m 10x.png
522.0 kB
euclidean_global_Notch receptors, Dll ligands, and Fringe proteins_3m 10x.pdf
79.9 kB
euclidean_global_Notch receptors, Dll ligands, and Fringe proteins_3m 10x.png
536.1 kB
euclidean_global_Notch receptors, Dll ligands, and Fringe proteins_E6.5_8.5_Chan.pdf
29.3 kB
euclidean_global_Notch receptors, Dll ligands, and Fringe proteins_E6.5_8.5_Chan.png
360.5 kB
euclidean_global_Notch receptors, Dll ligands, and Fringe proteins_E6.5_8.5_Marioni.pdf
6.5 kB
euclidean_global_Notch receptors, Dll ligands, and Fringe proteins_E6.5_8.5_Marioni.png
179.4 kB
euclidean_global_Notch receptors, Dll ligands, and Fringe proteins_E9.5_11.5_Tang.pdf
5.4 kB
euclidean_global_Notch receptors, Dll ligands, and Fringe proteins_E9.5_11.5_Tang.png
172.5 kB
euclidean_global_Notch receptors, Dll ligands, and Fringe proteins_FACS 18m.pdf
25.9 kB
euclidean_global_Notch receptors, Dll ligands, and Fringe proteins_FACS 18m.png
322.1 kB
euclidean_global_Notch receptors, Dll ligands, and Fringe proteins_FACS 24m.pdf
11.2 kB
euclidean_global_Notch receptors, Dll ligands, and Fringe proteins_FACS 24m.png
221.7 kB
euclidean_global_Notch receptors, Dll ligands, and Fringe proteins_FACS 3m.pdf
30.7 kB
euclidean_global_Notch receptors, Dll ligands, and Fringe proteins_FACS 3m.png
343.1 kB
euclidean_global_Notch receptors, Dll ligands, and Fringe proteins_Forelimb_E10.5_15.0.pdf
58.1 kB
euclidean_global_Notch receptors, Dll ligands, and Fringe proteins_Forelimb_E10.5_15.0.png
466.7 kB
euclidean_global_Ras Signaling Pathway .pdf
40.0 MB
euclidean_global_Ras Signaling Pathway .png
1.4 MB
euclidean_global_Ras Signaling Pathway _18m 10x.pdf
329.4 kB
euclidean_global_Ras Signaling Pathway _18m 10x.png
1.5 MB
euclidean_global_Ras Signaling Pathway _1m 10x.pdf
142.3 kB
euclidean_global_Ras Signaling Pathway _1m 10x.png
1.0 MB
euclidean_global_Ras Signaling Pathway _21m 10x.pdf
259.8 kB
euclidean_global_Ras Signaling Pathway _21m 10x.png
1.3 MB
euclidean_global_Ras Signaling Pathway _24m 10x.pdf
95.0 kB
euclidean_global_Ras Signaling Pathway _24m 10x.png
756.6 kB
euclidean_global_Ras Signaling Pathway _30m 10x.pdf
281.5 kB
euclidean_global_Ras Signaling Pathway _30m 10x.png
1.3 MB
euclidean_global_Ras Signaling Pathway _3m 10x.pdf
260.2 kB
euclidean_global_Ras Signaling Pathway _3m 10x.png
1.4 MB
euclidean_global_Ras Signaling Pathway _E5.5_Nowotschin.pdf
16.6 kB
euclidean_global_Ras Signaling Pathway _E5.5_Nowotschin.png
274.8 kB
euclidean_global_Ras Signaling Pathway _E6.5_8.5_Chan.pdf
947.6 kB
euclidean_global_Ras Signaling Pathway _E6.5_8.5_Chan.png
1.5 MB
euclidean_global_Ras Signaling Pathway _E6.5_8.5_Marioni.pdf
520.8 kB
euclidean_global_Ras Signaling Pathway _E6.5_8.5_Marioni.png
1.3 MB
euclidean_global_Ras Signaling Pathway _E9.5_11.5_Tang.pdf
27.6 kB
euclidean_global_Ras Signaling Pathway _E9.5_11.5_Tang.png
404.2 kB
euclidean_global_Ras Signaling Pathway _FACS 18m.pdf
142.5 kB
euclidean_global_Ras Signaling Pathway _FACS 18m.png
964.7 kB
euclidean_global_Ras Signaling Pathway _FACS 24m.pdf
102.2 kB
euclidean_global_Ras Signaling Pathway _FACS 24m.png
809.9 kB
euclidean_global_Ras Signaling Pathway _FACS 3m.pdf
194.5 kB
euclidean_global_Ras Signaling Pathway _FACS 3m.png
1.1 MB
euclidean_global_Ras Signaling Pathway _Forelimb_E10.5_15.0.pdf
237.7 kB
euclidean_global_Ras Signaling Pathway _Forelimb_E10.5_15.0.png
1.1 MB
euclidean_global_SRSF Splicing Protein Family.pdf
36.7 MB
euclidean_global_SRSF Splicing Protein Family.png
1.4 MB
euclidean_global_SRSF Splicing Protein Family_18m 10x.pdf
315.6 kB
euclidean_global_SRSF Splicing Protein Family_18m 10x.png
1.2 MB
euclidean_global_SRSF Splicing Protein Family_1m 10x.pdf
137.9 kB
euclidean_global_SRSF Splicing Protein Family_1m 10x.png
815.8 kB
euclidean_global_SRSF Splicing Protein Family_21m 10x.pdf
253.0 kB
euclidean_global_SRSF Splicing Protein Family_21m 10x.png
1.1 MB
euclidean_global_SRSF Splicing Protein Family_24m 10x.pdf
88.6 kB
euclidean_global_SRSF Splicing Protein Family_24m 10x.png
633.4 kB
euclidean_global_SRSF Splicing Protein Family_30m 10x.pdf
269.1 kB
euclidean_global_SRSF Splicing Protein Family_30m 10x.png
1.1 MB
euclidean_global_SRSF Splicing Protein Family_3m 10x.pdf
253.5 kB
euclidean_global_SRSF Splicing Protein Family_3m 10x.png
1.1 MB
euclidean_global_SRSF Splicing Protein Family_E5.5_Nowotschin.pdf
16.6 kB
euclidean_global_SRSF Splicing Protein Family_E5.5_Nowotschin.png
253.7 kB
euclidean_global_SRSF Splicing Protein Family_E6.5_8.5_Chan.pdf
938.1 kB
euclidean_global_SRSF Splicing Protein Family_E6.5_8.5_Chan.png
1.4 MB
euclidean_global_SRSF Splicing Protein Family_E6.5_8.5_Marioni.pdf
518.2 kB
euclidean_global_SRSF Splicing Protein Family_E6.5_8.5_Marioni.png
1.2 MB
euclidean_global_SRSF Splicing Protein Family_E9.5_11.5_Tang.pdf
27.6 kB
euclidean_global_SRSF Splicing Protein Family_E9.5_11.5_Tang.png
349.2 kB
euclidean_global_SRSF Splicing Protein Family_FACS 18m.pdf
105.4 kB
euclidean_global_SRSF Splicing Protein Family_FACS 18m.png
714.4 kB
euclidean_global_SRSF Splicing Protein Family_FACS 24m.pdf
74.1 kB
euclidean_global_SRSF Splicing Protein Family_FACS 24m.png
574.8 kB
euclidean_global_SRSF Splicing Protein Family_FACS 3m.pdf
119.2 kB
euclidean_global_SRSF Splicing Protein Family_FACS 3m.png
721.8 kB
euclidean_global_SRSF Splicing Protein Family_Forelimb_E10.5_15.0.pdf
237.6 kB
euclidean_global_SRSF Splicing Protein Family_Forelimb_E10.5_15.0.png
1.1 MB
euclidean_global_Scrambled Tgf-beta family receptors.pdf
4.9 MB
euclidean_global_Scrambled Tgf-beta family receptors.png
1.8 MB
euclidean_global_Scrambled Tgf-beta family receptors_18m 10x.pdf
51.2 kB
euclidean_global_Scrambled Tgf-beta family receptors_18m 10x.png
579.7 kB
euclidean_global_Scrambled Tgf-beta family receptors_1m 10x.pdf
20.5 kB
euclidean_global_Scrambled Tgf-beta family receptors_1m 10x.png
339.0 kB
euclidean_global_Scrambled Tgf-beta family receptors_21m 10x.pdf
30.9 kB
euclidean_global_Scrambled Tgf-beta family receptors_21m 10x.png
432.3 kB
euclidean_global_Scrambled Tgf-beta family receptors_24m 10x.pdf
8.5 kB
euclidean_global_Scrambled Tgf-beta family receptors_24m 10x.png
212.5 kB
euclidean_global_Scrambled Tgf-beta family receptors_30m 10x.pdf
26.3 kB
euclidean_global_Scrambled Tgf-beta family receptors_30m 10x.png
395.6 kB
euclidean_global_Scrambled Tgf-beta family receptors_3m 10x.pdf
38.5 kB
euclidean_global_Scrambled Tgf-beta family receptors_3m 10x.png
496.5 kB
euclidean_global_Scrambled Tgf-beta family receptors_E5.5_Nowotschin.pdf
16.7 kB
euclidean_global_Scrambled Tgf-beta family receptors_E5.5_Nowotschin.png
298.7 kB
euclidean_global_Scrambled Tgf-beta family receptors_E6.5_8.5_Chan.pdf
283.2 kB
euclidean_global_Scrambled Tgf-beta family receptors_E6.5_8.5_Chan.png
1.4 MB
euclidean_global_Scrambled Tgf-beta family receptors_E6.5_8.5_Marioni.pdf
8.5 kB
euclidean_global_Scrambled Tgf-beta family receptors_E6.5_8.5_Marioni.png
213.6 kB
euclidean_global_Scrambled Tgf-beta family receptors_E9.5_11.5_Tang.pdf
7.9 kB
euclidean_global_Scrambled Tgf-beta family receptors_E9.5_11.5_Tang.png
205.6 kB
euclidean_global_Scrambled Tgf-beta family receptors_FACS 18m.pdf
6.4 kB
euclidean_global_Scrambled Tgf-beta family receptors_FACS 18m.png
187.0 kB
euclidean_global_Scrambled Tgf-beta family receptors_FACS 24m.pdf
5.4 kB
euclidean_global_Scrambled Tgf-beta family receptors_FACS 24m.png
172.0 kB
euclidean_global_Scrambled Tgf-beta family receptors_FACS 3m.pdf
9.9 kB
euclidean_global_Scrambled Tgf-beta family receptors_FACS 3m.png
228.5 kB
euclidean_global_Scrambled Tgf-beta family receptors_Forelimb_E10.5_15.0.pdf
214.3 kB
euclidean_global_Scrambled Tgf-beta family receptors_Forelimb_E10.5_15.0.png
1.4 MB
euclidean_global_Tgf-beta family receptors.pdf
4.9 MB
euclidean_global_Tgf-beta family receptors.png
1.7 MB
euclidean_global_Tgf-beta family receptors_18m 10x.pdf
51.3 kB
euclidean_global_Tgf-beta family receptors_18m 10x.png
577.8 kB
euclidean_global_Tgf-beta family receptors_1m 10x.pdf
20.4 kB
euclidean_global_Tgf-beta family receptors_1m 10x.png
336.1 kB
euclidean_global_Tgf-beta family receptors_21m 10x.pdf
31.0 kB
euclidean_global_Tgf-beta family receptors_21m 10x.png
431.5 kB
euclidean_global_Tgf-beta family receptors_24m 10x.pdf
8.5 kB
euclidean_global_Tgf-beta family receptors_24m 10x.png
211.2 kB
euclidean_global_Tgf-beta family receptors_30m 10x.pdf
26.2 kB
euclidean_global_Tgf-beta family receptors_30m 10x.png
392.3 kB
euclidean_global_Tgf-beta family receptors_3m 10x.pdf
38.4 kB
euclidean_global_Tgf-beta family receptors_3m 10x.png
494.7 kB
euclidean_global_Tgf-beta family receptors_E5.5_Nowotschin.pdf
16.6 kB
euclidean_global_Tgf-beta family receptors_E5.5_Nowotschin.png
282.1 kB
euclidean_global_Tgf-beta family receptors_E6.5_8.5_Chan.pdf
280.6 kB
euclidean_global_Tgf-beta family receptors_E6.5_8.5_Chan.png
1.1 MB
euclidean_global_Tgf-beta family receptors_E6.5_8.5_Marioni.pdf
8.4 kB
euclidean_global_Tgf-beta family receptors_E6.5_8.5_Marioni.png
209.0 kB
euclidean_global_Tgf-beta family receptors_E9.5_11.5_Tang.pdf
7.9 kB
euclidean_global_Tgf-beta family receptors_E9.5_11.5_Tang.png
202.5 kB
euclidean_global_Tgf-beta family receptors_FACS 18m.pdf
6.4 kB
euclidean_global_Tgf-beta family receptors_FACS 18m.png
185.8 kB
euclidean_global_Tgf-beta family receptors_FACS 24m.pdf
5.4 kB
euclidean_global_Tgf-beta family receptors_FACS 24m.png
170.1 kB
euclidean_global_Tgf-beta family receptors_FACS 3m.pdf
9.9 kB
euclidean_global_Tgf-beta family receptors_FACS 3m.png
227.7 kB
euclidean_global_Tgf-beta family receptors_Forelimb_E10.5_15.0.pdf
213.4 kB
euclidean_global_Tgf-beta family receptors_Forelimb_E10.5_15.0.png
1.3 MB
violin_cutoff_hist_Tgf-beta family receptors.pdf
8.1 kB
violin_cutoff_hist_Tgf-beta family receptors.png
195.7 kB
violin_plot_Tgf-beta family receptors.pdf
35.4 kB
violin_plot_Tgf-beta family receptors.png
230.3 kB
Supplementary File 5.csv
105.0 kB
Tdgf1_Tgfb_heatmap
56.7 kB
density_dist
Captura de pantalla 2023-05-21 a las 11.14.10 a. m..png
1.0 MB
peak_analysis
silhouette_res
dispersion_states_figure5.csv
5.2 kB
silh_optk_figure5.csv
5.6 kB
silh_rds
.Rhistory
29.8 kB
Activation of cAMP-dependent protein kinase, PKA.RDS_silhPeak.pdf
8.5 kB
Amino Sugar Metabolism.RDS_silhPeak.pdf
8.4 kB
Ammonia Recycling.RDS_silhPeak.pdf
8.3 kB
Androstenedione Metabolism.RDS_silhPeak.pdf
8.4 kB
Apoptotic DNA Fragmentation and Tissue Homeostasis.RDS_silhPeak.pdf
8.5 kB
Arachidonic Acid Metabolism.RDS_silhPeak.pdf
8.4 kB
Arginine and Proline Metabolism.RDS_silhPeak.pdf
8.4 kB
Aspartate Metabolism.RDS_silhPeak.pdf
8.4 kB
BCR Signaling Pathway.RDS_silhPeak.pdf
8.5 kB
BCR Signaling Pathway_profiles.csv
30.8 kB
BTG Family Proteins and Cell Cycle Regulation.RDS_silhPeak.pdf
8.4 kB
Beta Oxidation of Very Long Chain Fatty Acids.RDS_silhPeak.pdf
8.4 kB
Bile Acid Biosynthesis.RDS_silhPeak.pdf
8.4 kB
Bmp_down.RDS_silhPeak.pdf
8.4 kB
Bmp_down_profiles.csv
15.9 kB
Bmp_fun.RDS_silhPeak.pdf
8.5 kB
Bmp_profiles.csv
7.4 kB
CD40L Signalling Pathway.RDS_silhPeak.pdf
8.4 kB
CD40L Signalling Pathway_profiles.csv
17.9 kB
CXCR4 Signaling Pathway.RDS_silhPeak.pdf
8.4 kB
Cadmium Induces DNA Synthesis and Proliferation in Macrophages .RDS_silhPeak.pdf
8.5 kB
Cardiolipin Biosynthesis.RDS_silhPeak.pdf
8.4 kB
Citric Acid Cycle.RDS_silhPeak.pdf
8.4 kB
Cysteine Metabolism.RDS_silhPeak.pdf
8.4 kB
D4-GDI Signaling Pathway.RDS_silhPeak.pdf
8.4 kB
D4-GDI Signaling Pathway_profiles.csv
24.4 kB
Eph A-B receptors_profiles.csv
5.7 kB
Eph receptors and ligands_profiles.csv
11.7 kB
Eph_l_profiles.csv
5.9 kB
FGF cell signaling proteins_profiles.csv
13.7 kB
Frizzled and Lrp5 6 receptors for Wnt B Catenin Signaling_profiles.csv
10.0 kB
Intracellular Signalling Through Adenosine Receptor A2a and Adenosine_profiles.csv
31.2 kB
Ion Channels and Their Functional Role in Vascular Endothelium_profiles.csv
5.9 kB
LPS and Citrate Signaling and Inflammation_profiles.csv
29.7 kB
Leucine Stimulation on Insulin Signaling_profiles.csv
24.3 kB
Lysophosphatidic Acid LPA2 Signalling_profiles.csv
17.0 kB
Mitochondrial Electron Transport Chain_profiles.csv
28.3 kB
NF-kB Signaling Pathway_profiles.csv
25.9 kB
Nitric Oxide Signaling Pathway_profiles.csv
7.5 kB
Notch receptors, Dll ligands, and Fringe proteins_profiles.csv
5.6 kB
RNA-splicing by SR protein family_profiles.csv
28.9 kB
Ras Signaling Pathway _profiles.csv
30.3 kB
Tgf-beta family receptors_profiles.csv
11.0 kB
Ubiquitin-Proteasome Pathway_profiles.csv
30.3 kB
alejo_res
BCR Signaling Pathway_profiles.csv
30.8 kB
Bmp_down_profiles.csv
15.9 kB
Bmp_profiles.csv
7.4 kB
CD40L Signalling Pathway_profiles.csv
17.9 kB
D4-GDI Signaling Pathway_profiles.csv
24.4 kB
Eph A-B receptors_profiles.csv
5.7 kB
Eph receptors and ligands_profiles.csv
11.7 kB
Eph_l_profiles.csv
5.9 kB
FGF cell signaling proteins_profiles.csv
13.7 kB
Frizzled and Lrp5 6 receptors for Wnt B Catenin Signaling_profiles.csv
10.0 kB
Intracellular Signalling Through Adenosine Receptor A2a and Adenosine_profiles.csv
31.2 kB
Ion Channels and Their Functional Role in Vascular Endothelium_profiles.csv
5.9 kB
LPS and Citrate Signaling and Inflammation_profiles.csv
29.7 kB
Leucine Stimulation on Insulin Signaling_profiles.csv
24.3 kB
Lysophosphatidic Acid LPA2 Signalling_profiles.csv
17.0 kB
Mitochondrial Electron Transport Chain_profiles.csv
28.3 kB
NF-kB Signaling Pathway_profiles.csv
25.9 kB
Nitric Oxide Signaling Pathway_profiles.csv
7.5 kB
Notch receptors, Dll ligands, and Fringe proteins_profiles.csv
5.6 kB
RNA-splicing by SR protein family_profiles.csv
28.9 kB
Ras Signaling Pathway _profiles.csv
30.3 kB
Tgf-beta family receptors_profiles.csv
11.0 kB
Ubiquitin-Proteasome Pathway_profiles.csv
30.3 kB
preprocessing
.ipynb_checkpoints
Figure_6A-checkpoint.ipynb
10.9 MB
Figure_6AB_Interactive-checkpoint.ipynb
7.9 MB
Figure_6B-checkpoint.ipynb
93.9 kB
Figure_6C-checkpoint.ipynb
5.7 MB
Figure_6D-checkpoint.ipynb
96.1 kB
Integration_Dong-checkpoint.ipynb
1.6 MB
Integration_Forelimb-checkpoint.ipynb
128.5 kB
Integration_Grosswendt-checkpoint.R
2.7 kB
Integration_Marioni_6.5-checkpoint.ipynb
764.5 kB
Integration_Marioni_6.75-checkpoint.ipynb
803.2 kB
Integration_Marioni_7.0-checkpoint.ipynb
3.0 MB
Integration_Marioni_7.25-checkpoint.ipynb
3.9 MB
Integration_Marioni_7.75-checkpoint.ipynb
1.1 MB
Integration_Marioni_8.0-checkpoint.ipynb
1.1 MB
Integration_Marioni_8.25-checkpoint.ipynb
998.7 kB
Integration_Marioni_8.5-checkpoint.ipynb
1.1 MB
Integration_Nowotschin-checkpoint.R
6.5 kB
Integration_PijuanSala_8.5-checkpoint.ipynb
1.1 MB
Integration_TMS_10X-checkpoint.ipynb
10.8 kB
Processing_Marioni_All-checkpoint.ipynb
94.3 kB
Processing_TMS_FACS-checkpoint.Rmd
17.6 kB
dataset-checkpoint.py
4.1 kB
knn_profiles-checkpoint.py
4.1 kB
processCountMatrix-checkpoint.R
17.6 kB
python_imports-checkpoint.py
1.7 kB
Integration_Chan.R
2.8 kB
Integration_Dong.ipynb
1.6 MB
Integration_He.ipynb
123.0 kB
Integration_Nowotschin.R
6.5 kB
Integration_PijuanSala_6.5.ipynb
764.5 kB
Integration_PijuanSala_6.75.ipynb
803.2 kB
Integration_PijuanSala_7.0.ipynb
3.0 MB
Integration_PijuanSala_7.25.ipynb
3.9 MB
Integration_PijuanSala_7.75.ipynb
1.1 MB
Integration_PijuanSala_8.0.ipynb
1.1 MB
Integration_PijuanSala_8.25.ipynb
998.7 kB
Integration_PijuanSala_8.5.ipynb
1.1 MB
Integration_TMS_10X.ipynb
11.0 kB
Processing_Pathbank.R
1.6 kB
Processing_PijuanSala_All.ipynb
94.3 kB
Processing_TMS_FACS.R
2.8 kB
Processing_TMS_FACS_Ale.Rmd
17.6 kB
__pycache__
module.cpython-38.pyc
34.2 kB
module.py
41.4 kB
processCountMatrix.R
17.6 kB