| Deposited data |
|
| STRING |
(Szklarczyk et al., 2019) |
https://stringdb-static.org/download/protein.links.full.v11.5/9606.protein.links.full.v11.5.txt.gz |
| HI-union |
(Luck et al., 2020) |
http://www.interactome-atlas.org/data/HI-union.tsv |
| BioPlex 3.0 |
(Huttlin et al., 2015) |
http://wren.hms.harvard.edu/bioplex/data/BioPlex_293T_Network_10K_Dec_2019.tsv |
| CoFrac |
(Wan et al., 2015) |
https://static-content.springer.com/esm/art%3A10.1038%2Fnature14877/MediaObjects/41586_2015_BFnature14877_MOESM13_ESM.zip |
| QUBIC |
(Hein et al., 2015) |
https://ars.els-cdn.com/content/image/1-s2.0-S0092867415012702-mmc3.xlsx |
| HPIDB 3.0 |
(Ammari et al., 2016; Kumar and Nanduri, 2010) |
https://hpidb.igbb.msstate.edu/ |
| Herpes simplex virus type I (HSV-1) RNA-Seq |
N/A |
Gene Expression Omnibus (GEO): GSE124118
|
| Human papillomavirus (HPV) RNA-Seq |
(Qin et al., 2018, 2020; Zhang et al., 2016) |
Gene Expression Omnibus (GEO): GSE74927
|
|
| Software and algorithms |
|
| glob2 (0.7) |
N/A |
pip install glob2 |
| GSEApy (0.10.8) |
(Mootha et al., 2003; Subramanian et al., 2005) |
pip install gseapy |
| Matplotlib (3.5.1) |
(Hunter, 2007) |
pip install matplotlib |
| NetworkX (2.6.3) |
(Hagberg et al., 2008) |
pip install networkx |
| NumPy (1.22.1) |
(Harris et al., 2020) |
pip install numpy |
| pandas (1.3.5) |
(McKinney, 2010) |
pip install pandas |
| Plotly (5.5.0) |
(Inc., 2022) |
pip install plotly |
| kaleido (0.2.1) |
N/A |
pip install kaleido |
| UpSetplot (0.6.0) |
(Lex et al., 2014) |
pip install UpSetPlot |
| poppler (0.3.0) |
|
pip install python-poppler |
| Cytoscape (3.9.1) |
(Shannon et al., 2003) |
https://cytoscape.org/download.html |
| Wk-shell-decomposition |
N/A |
https://apps.cytoscape.org/apps/wkshelldecomposition |
