first update

.idea/.gitignore

+# Default ignored files
+/shelf/
+/workspace.xml
+# Editor-based HTTP Client requests
+/httpRequests/
+# Datasource local storage ignored files
+/dataSources/
+/dataSources.local.xml

.idea/inspectionProfiles/profiles_settings.xml

+<component name="InspectionProjectProfileManager">
+  <settings>
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.idea/misc.xml

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+</project>
\ No newline at end of file

.idea/modules.xml

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+    <modules>
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+    </modules>
+  </component>
+</project>
\ No newline at end of file

.idea/network-medicine-and-single-cell-for-alzheimer.iml

+<?xml version="1.0" encoding="UTF-8"?>
+<module type="PYTHON_MODULE" version="4">
+  <component name="NewModuleRootManager">
+    <content url="file://$MODULE_DIR$" />
+    <orderEntry type="inheritedJdk" />
+    <orderEntry type="sourceFolder" forTests="false" />
+  </component>
+</module>
\ No newline at end of file

.idea/vcs.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="VcsDirectoryMappings">
+    <mapping directory="$PROJECT_DIR$" vcs="Git" />
+  </component>
+</project>
\ No newline at end of file

data/complete/degs_T cell_mapped.csv

+gene_id,gene_symbol,protein_id,names,logfoldchanges,pvals,pvals_adj,scores
+,,,ENSG00000198846,1.7838787,1.5007386566395886e-06,0.0423433411970859,4.811137

data/filtered/degs_endothelial cell of vascular tree_mapped_filt.csv

+protein_id,gene_id,gene_symbol,names,logfoldchanges,pvals,pvals_adj,scores
+Q8TEW0,56288.0,PARD3,ENSG00000148498,0.5368612,1.5761695881190673e-06,0.0003532824952216,4.8013277
+P05362,3383.0,ICAM1,ENSG00000090339,-1.3582723,1.7388582545100387e-06,0.0003803246949689,-4.781623
+P46934,4734.0,NEDD4,ENSG00000069869,0.6356499,8.374938899556305e-07,0.0002054773052617,4.926421
+P01130,3949.0,LDLR,ENSG00000130164,0.67354864,0.0003863433928951,0.0311328830467343,3.549241
+P07900,3320.0,HSP90AA1,ENSG00000080824,1.269916,2.9426643130860597e-42,2.7675757864574393e-38,13.622513
+P10321,3107.0,HLA-C,ENSG00000204525,-0.41342628,3.163860622378613e-05,0.004132792937982,-4.1613398
+O60493,8724.0,SNX3,ENSG00000112335,0.8747631,7.703805971530028e-09,3.196513021863525e-06,5.774814
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+P46531,4851.0,NOTCH1,ENSG00000148400,0.7782756,3.2816812325586995e-06,0.0006430044165044,4.6523533
+P00441,6647.0,SOD1,ENSG00000142168,0.7630747,3.447448892863547e-05,0.0044213532050974,4.1416974
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+P34932,3308.0,HSPA4,ENSG00000170606,0.8810992,0.0004808639722918,0.0370698824541381,3.4911957
+Q01650,8140.0,SLC7A5,ENSG00000103257,0.43621567,2.152752228741109e-05,0.003067671925956,4.248429
+P04792,3315.0,HSPB1,ENSG00000106211,2.3521888,9.755175041694644e-62,1.3762113190070718e-57,16.579802
+Q13480,2549.0,GAB1,ENSG00000109458,0.89539665,6.313816856577873e-10,3.125339344006047e-07,6.18239
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+P00338,3939.0,LDHA,ENSG00000134333,0.5848978,3.962902240384812e-05,0.0049916645853775,4.109632
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+P43490,10135.0,NAMPT,ENSG00000105835,-0.43115568,2.7067072869136e-08,9.918148844190546e-06,-5.559421
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+Q9NWB1,54715.0,RBFOX1,ENSG00000078328,-0.68668795,1.5597803964219047e-05,0.0024048745292373,-4.320072
+Q9BXM7,65018.0,PINK1,ENSG00000158828,0.81410664,0.0001102392602958,0.0109728589314465,3.8668742
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+P51825,4299.0,AFF1,ENSG00000172493,0.37787962,0.0004067848093838,0.0324221282394475,3.5356424
+Q99576,1831.0,TSC22D3,ENSG00000157514,0.8531887,9.479360531537753e-08,3.0051703078352547e-05,5.3364315
+P0CG48,7316.0,UBC,ENSG00000150991,0.3710061,0.0004952246036005,0.0378665642021373,3.4833262
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+P00533,1956.0,EGFR,ENSG00000146648,0.4316732,0.0004066555853747,0.0324221282394475,3.5357263
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+O95817,9531.0,BAG3,ENSG00000151929,1.0001198,5.294114941536285e-05,0.006187393095115,4.0422482
+P31948,10963.0,STIP1,ENSG00000168439,1.4755228,8.899504081812222e-09,3.639123299541041e-06,5.750471
+O95714,8924.0,HERC2,ENSG00000128731,0.68953896,6.492361526719836e-14,7.045460787553851e-11,7.497748
+O95433,10598.0,AHSA1,ENSG00000100591,1.3292919,2.7090769339768005e-05,0.0036225879474955,4.196637
+Q02790,2288.0,FKBP4,ENSG00000004478,1.8447479,2.71308035627686e-11,1.7011013833855907e-08,6.6613584
+P42336,5290.0,PIK3CA,ENSG00000121879,0.5751339,0.0001715913492335,0.0163011781771866,3.757541
+P0DP23,801.0,CALM1,ENSG00000198668,0.56518525,6.829908165889458e-08,2.294117367863941e-05,5.3955894
+P10809,3329.0,HSPD1,ENSG00000144381,1.0832922,1.1819477592842113e-07,3.624853916109132e-05,5.2962656
+Q9UNQ0,9429.0,ABCG2,ENSG00000118777,0.5178807,2.482786307609128e-06,0.0005076218526753,4.7095385
+Q9HB71,27101.0,CACYBP,ENSG00000116161,2.0156648,3.298392564509553e-12,2.658975605932487e-09,6.964386
+P32320,978.0,CDA,ENSG00000158825,1.4935253,1.7721334146178481e-09,8.474702422617387e-07,6.017425
+Q08117,166.0,TLE5,ENSG00000104964,0.51631445,0.0006748575810173,0.0482053332871016,3.3995948
+P01023,2.0,A2M,ENSG00000175899,0.37962964,0.0004483922848503,0.0349238907959132,3.5098305
+P04439,3105.0,HLA-A,ENSG00000206503,-0.38561535,9.379683837862748e-06,0.0015847172424269,-4.4310007
+Q13627,1859.0,DYRK1A,ENSG00000157540,0.50807405,4.812537425784263e-06,0.0008648773469331,4.5727983
+Q9NX09,54541.0,DDIT4,ENSG00000168209,1.310385,7.300146644259293e-12,5.2813753222506654e-09,6.851653
+P22694,5567.0,PRKACB,ENSG00000142875,0.54072803,4.519030700316048e-05,0.0054489081713426,4.079203
+Q13464,6093.0,ROCK1,ENSG00000067900,0.44965607,0.0002866263622903,0.0245810419818301,3.6270964

data/filtered/degs_pericyte_mapped_filt.csv

+protein_id,gene_id,gene_symbol,names,logfoldchanges,pvals,pvals_adj,scores
+P07900,3320.0,HSP90AA1,ENSG00000080824,1.1101086,2.7611934434650644e-13,1.1129581858195254e-09,7.3055577
+O94875,8470.0,SORBS2,ENSG00000154556,0.82707316,1.6243543107902054e-06,0.0015803847199636,4.7952952
+P60484,5728.0,PTEN,ENSG00000171862,-0.7821016,9.017273639072147e-12,2.8269152858491187e-08,-6.821376
+Q15303,2066.0,ERBB4,ENSG00000178568,1.1079869,0.0001496004136413,0.0429268010255183,3.7917318
+P04792,3315.0,HSPB1,ENSG00000106211,1.8847187,1.905079425515209e-24,5.375181599091162e-20,10.203879
+P08238,3326.0,HSP90AB1,ENSG00000096384,0.86155623,2.5669080707434486e-06,0.0023363003618073,4.702742
+P54253,6310.0,ATXN1,ENSG00000124788,0.712304,3.498666958075107e-05,0.0141021268888698,4.1383142
+P09619,5159.0,PDGFRB,ENSG00000113721,-0.37845042,0.0001948203671026,0.0491749611715363,-3.7256398
+Q92598,10808.0,HSPH1,ENSG00000120694,1.6761034,1.3386021284377312e-05,0.0070970556189187,4.353698
+O43524,2309.0,FOXO3,ENSG00000118689,0.8544231,1.617127040075925e-05,0.007893088224653,4.312098
+P61586,387.0,RHOA,ENSG00000067560,0.7855196,0.0001640082051415,0.0440713476958808,3.7688396
+P0DMV8,3304.0,HSPA1B,ENSG00000204388,1.9751459,1.293792057365848e-07,0.0001738302042789,5.279723
+P17676,1051.0,CEBPB,ENSG00000172216,1.105564,9.147367736274876e-06,0.0054913400144467,4.436405
+P02511,1410.0,CRYAB,ENSG00000109846,1.5257127,8.710331282157682e-10,1.7554428366148503e-06,6.1314106
+P13693,7178.0,TPT1,ENSG00000133112,0.80236536,0.0001618386637882,0.0439065182575621,3.7721627
+Q15185,10728.0,PTGES3,ENSG00000110958,0.8664793,3.1435963398396926e-05,0.0128545754679096,4.1628065
+P08670,7431.0,VIM,ENSG00000026025,1.1177812,8.111714376110418e-09,1.4304501320122216e-05,5.7661204
+Q7Z6G8,56899.0,ANKS1B,ENSG00000185046,0.9782406,2.711834689109385e-05,0.0115930932959426,4.1964064
+Q09666,79026.0,AHNAK,ENSG00000124942,0.9890392,0.0001952009800181,0.0491749611715363,3.7251475
+P49716,1052.0,CEBPD,ENSG00000221869,0.70893383,0.00011939636024,0.0374307589352667,3.8473623

data/filtered/graphs/gephi/degs_pericyte_mapped_gephi.csv

+Id,gene_id,gene_symbol,names,logfoldchanges,pvals,pvals_adj,scores,-log10(pvals_adj),flag
+P07900,3320.0,HSP90AA1,ENSG00000080824,1.1101086,2.7611934434650644e-13,1.1129581858195254e-09,7.3055577,8.953521151935709,False
+O94875,8470.0,SORBS2,ENSG00000154556,0.82707316,1.6243543107902054e-06,0.0015803847199636,4.7952952,2.8012371779703256,False
+P60484,5728.0,PTEN,ENSG00000171862,-0.7821016,9.017273639072147e-12,2.8269152858491187e-08,-6.821376,7.548687205815226,False
+Q15303,2066.0,ERBB4,ENSG00000178568,1.1079869,0.0001496004136413,0.0429268010255183,3.7917318,1.3672714746402954,False
+P04792,3315.0,HSPB1,ENSG00000106211,1.8847187,1.905079425515209e-24,5.375181599091162e-20,10.203879,19.26960685864009,True
+P08238,3326.0,HSP90AB1,ENSG00000096384,0.86155623,2.5669080707434486e-06,0.0023363003618073,4.702742,2.631471323764307,False
+P54253,6310.0,ATXN1,ENSG00000124788,0.712304,3.498666958075107e-05,0.0141021268888698,4.1383142,1.8507153819233328,False
+P09619,5159.0,PDGFRB,ENSG00000113721,-0.37845042,0.0001948203671026,0.0491749611715363,-3.7256398,1.3082559743266569,False
+Q92598,10808.0,HSPH1,ENSG00000120694,1.6761034,1.3386021284377312e-05,0.0070970556189187,4.353698,2.1489217912351357,True
+O43524,2309.0,FOXO3,ENSG00000118689,0.8544231,1.617127040075925e-05,0.007893088224653,4.312098,2.1027530428596757,False
+P61586,387.0,RHOA,ENSG00000067560,0.7855196,0.0001640082051415,0.0440713476958808,3.7688396,1.3558436686202133,False
+P0DMV8,3304.0,HSPA1B,ENSG00000204388,1.9751459,1.293792057365848e-07,0.0001738302042789,5.279723,3.759874759464139,True
+P17676,1051.0,CEBPB,ENSG00000172216,1.105564,9.147367736274876e-06,0.0054913400144467,4.436405,2.260321664681399,False
+P02511,1410.0,CRYAB,ENSG00000109846,1.5257127,8.710331282157681e-10,1.7554428366148503e-06,6.1314106,5.755613308122264,True
+P13693,7178.0,TPT1,ENSG00000133112,0.80236536,0.0001618386637882,0.0439065182575621,3.7721627,1.3574710006428374,False
+Q15185,10728.0,PTGES3,ENSG00000110958,0.8664793,3.1435963398396926e-05,0.0128545754679096,4.1628065,1.8909422616884664,False
+P08670,7431.0,VIM,ENSG00000026025,1.1177812,8.111714376110418e-09,1.4304501320122216e-05,5.7661204,4.844527277858312,True
+Q7Z6G8,56899.0,ANKS1B,ENSG00000185046,0.9782406,2.711834689109385e-05,0.0115930932959426,4.1964064,1.93580066911681,False
+Q09666,79026.0,AHNAK,ENSG00000124942,0.9890392,0.0001952009800181,0.0491749611715363,3.7251475,1.3082559743266569,False
+P49716,1052.0,CEBPD,ENSG00000221869,0.70893383,0.00011939636024,0.0374307589352667,3.8473623,1.4267713671667168,False

data/results/cell_type_summary_stats.tsv

+Cell Type	Total DEGs	DEGs mapped to protein	Cell Type proteins in main LCC	Cell Type LCC size	LCC mean	LCC std	z_score	p_value	adj_p_value
+astrocyte	3176	2878	532	183	53.963	13.744803781793324	9.38805690125059	6.111731180474914e-21	8.556423652664879e-21
+microglial cell	1585	1501	334	62	7.218	3.662031676542408	14.959455525989249	1.3512704020147547e-50	4.729446407051641e-50
+oligodendrocyte	3383	3052	554	191	57.553	14.372584701437663	9.284829609433544	1.6196611631703173e-20	1.8896046903653702e-20
+glutamatergic neuron	4436	3963	733	277	120.873	12.425573266453345	12.564973595344116	3.2898485031548154e-36	7.676313174027903e-36
+inhibitory interneuron	4130	3769	673	251	93.186	14.119752264115686	11.176824992962	5.295061666016266e-29	9.266357915528465e-29
+endothelial cell of vascular tree	379	367	73	4	1.115	0.3282910294235893	8.787934306537279	1.523350010447622e-18	1.523350010447622e-18
+oligodendrocyte precursor cell	1963	1832	320	49	4.996	2.286915827047423	19.241635166263386	1.6589169671898575e-82	1.1612418770329002e-81
+pericyte	111	107	20	1	1.0	0.0