diff --git a/data/testdata_counts_prot.csv b/data/testdata_counts_prot.csv new file mode 100644 index 0000000..50b0439 --- /dev/null +++ b/data/testdata_counts_prot.csv @@ -0,0 +1,270 @@ +gene_ID,site_ID,Con_1,Exp_1,Con_2,Exp_2,Con_3,Exp_3,Con_4,Exp_4,Con_5,Exp_5 +(E3-independent) E2 ubiquitin-conjugating enzyme,S839,126500,156300,69740,117300,78700,138400,49010,186100,91240,166600 +(E3-independent) E2 ubiquitin-conjugating enzyme,S836; S839,18174,24911,18737,26171,13548,22593,11531,28280,12539,26714 +(E3-independent) E2 ubiquitin-conjugating enzyme,T488,1240,1508,2576,1653,1697,1312,991.6,1142,1170,1748 +[F-actin]-monooxygenase MICAL1,T822,12240,39580,16010,27810,12550,44710,8252,26270,13760,38550 +[F-actin]-monooxygenase MICAL1,S818,7280,18690,5858,24640,5342,32240,3660,16130,5807,20820 +[F-actin]-monooxygenase MICAL1,S887,10988,7790,9890.8,5002.4,10823.8,6554,10925,6415,12043,8891 +[F-actin]-monooxygenase MICAL3,S1794; S1797,17190,20190,10950,16670,9439,15650,8282,20320,11860,15500 +[F-actin]-monooxygenase MICAL3,S1337,3652,13210,4851,15450,5643,14890,2655,15990,5086,13940 +[F-actin]-monooxygenase MICAL3,S1310,9026,11490,6506,7371,4693,7463,5396,11760,4144,9380 +[F-actin]-monooxygenase MICAL3,T1454; S1457; S1458,8480,9853,7054,6866,5631,7045,7450,10010,5294,6433 +[F-actin]-monooxygenase MICAL3,S1512,4393,8270,5256,5593,1340,4664,2257,12000,2173,4425 +[F-actin]-monooxygenase MICAL3,S1516,3703,1789,2330,1138,4484,2715,4374,2068,2656,1344 +1-phosphatidylinositol 3-phosphate 5-kinase,T477,7327,7085,5144,6846,5270,6963,5899,8309,6867,6811 +"1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-2",S964,358367,265550,194913,170694,320940,262690,325030,291630,263690,242540 +"1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3",S1105,292400,1054000,237600,809300,447100,933100,420400,965200,710000,1077000 +"1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-2",Y753,3258,19750,2259,19590,2463,19250,1851,14660,1545,17890 +14-3-3 protein epsilon,S210,4440,3165,2435,1124,1215,658.8,6167,4348,2872,2973 +14-3-3 protein sigma; 14-3-3 protein beta/alpha; 14-3-3 protein eta; 14-3-3 protein gamma; 14-3-3 protein theta,S64,110500,71820,144500,92710,120000,83280,116200,78790,103300,85040 +14-3-3 protein sigma; 14-3-3 protein beta/alpha; 14-3-3 protein eta; 14-3-3 protein gamma; 14-3-3 protein theta,S64,110500,71820,144500,92710,120000,83280,116200,78790,103300,85040 +14-3-3 protein zeta/delta,S64,83880,58610,98940,64950,93920,67330,102700,76020,86750,57920 +14-3-3 protein zeta/delta,S207,35135,29723,17387,15581,14034,9236,48690,16637,22579,26731 +14-3-3 protein zeta/delta,T232,5640,5325,7331,6376,5637,4454,4741,5150,4606,5370 +"2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial; Uncharacterized protein",S347,15460,20790,14380,15740,19810,13050,18270,11290,18780,25860 +2'-deoxynucleoside 5'-phosphate N-hydrolase 1,S169,1339,1579,1235,902.3,927,1134,1403,1736,1718,2094 +26S proteasome non-ATPase regulatory subunit 2,S363,65070,48790,52250,43500,59450,45740,60270,51160,69640,65080 +28 kDa heat- and acid-stable phosphoprotein,S60; S63,170300,116600,177900,111000,163600,99180,164800,123500,153400,115300 +28 kDa heat- and acid-stable phosphoprotein,S60,92940,73910,81740,59362,114060,89140,114440,79760,90530,66870 +28 kDa heat- and acid-stable phosphoprotein,S60; S63,90985,62671,98635,57428,80054,47227,83630,57584,84860,53414 +28 kDa heat- and acid-stable phosphoprotein,S63,44130,34579,43290,25993,52960,40780,55830,33327,46650,37720 +28 kDa heat- and acid-stable phosphoprotein,S60; S63,16890,15230,66150,51740,62080,36740,8308,14310,37210,36280 +28 kDa heat- and acid-stable phosphoprotein,S63,2617,2591,3084,3000,3759,2181,4812,2330,3179,2842 +"28S ribosomal protein S17, mitochondrial; HCG1984214, isoform CRA_a",S128,5882,3807,7222,5133,7839,6483,5335,6186,4542,1450 +3-phosphoinositide-dependent protein kinase 1; Putative 3-phosphoinositide-dependent protein kinase 2,T245,90190,55850,101500,63560,92480,62770,85190,60320,94110,67620 +5'-AMP-activated protein kinase subunit beta-1,S108,280265,350598,184077,302039,238561,271154,507500,341558,339790,406670 +5'-AMP-activated protein kinase subunit beta-2,S108,58483,78364,39261,61634,45613,56474,92980,78320,80182,98757 +5'-AMP-activated protein kinase subunit beta-2,S184,61580,46336,64810,41201,56340,37136,57540,43588,70960,55130 +55 kDa erythrocyte membrane protein,S110,74560,165012,80910,141471,125095,145882,127604,138562,103644,139164 +55 kDa erythrocyte membrane protein,S260; S261,50534,37514.6,35104,22630,74177,33580.6,102461,51874,50457,27282 +55 kDa erythrocyte membrane protein,S57,24840,34980,32440,27280,30230,31040,25010,25320,23420,25290 +"60 kDa heat shock protein, mitochondrial",S70,56750,38870,57400,32630,58690,36880,65920,47470,55500,39050 +60S acidic ribosomal protein P1; 60S acidic ribosomal protein P2,S104,57480,45390,62740,26560,41820,25300,116800,42680,60730,43990 +60S acidic ribosomal protein P1; 60S acidic ribosomal protein P2,S101; S104,20341,71237,51574,44651,30940,22120,28327,12635.6,18220.4,37598 +"A-kinase anchor protein 10, mitochondrial",S187,160500,244100,112800,208400,101100,223200,70830,284200,117200,194800 +"A-kinase anchor protein 10, mitochondrial",S96,18700,22170,17100,18680,16830,23170,22970,24750,23210,24850 +A-kinase anchor protein 13,S2498,119480,137710,156710,177920,145460,176230,100930,130040,130450,146220 +A-kinase anchor protein 13,S2709; S2711,28000,34840,19370,33300,21940,39970,26480,36720,27770,31380 +A-kinase anchor protein 13,S1645,19985,11984,15274,8781,14780,9337,22797,10401,13113,6824 +A-kinase anchor protein 13,S1876,8840,10570,7079,7083,4987,9526,6177,8191,6897,6596 +A-kinase anchor protein 13,S1876,2447,1640,2370,792.5,1258,1583,1859,1930,1965,1421 +A-kinase anchor protein 13,S1942,974.5,656.5,916.5,736,50,827.1,776.9,644.2,994.3,1176 +A-kinase anchor protein 13,S1647,645.8,50,1204,926.5,2218,50,767.9,813.5,908.1,50 +A-kinase anchor protein 2,S720,23718,49950,11259,20791,9433,33019,18323,62290,22053,42394 +A-kinase anchor protein 2,S393,26241,22038,18961,17146,24699,21857,27043,29104,23769,16083 +A-kinase anchor protein 2,S155,8720,8450,4754,6043,6084,9026,6068,10480,6985,8180 +Abl interactor 1,S183,3640820,2281240,3545600,2065710,3627590,2276750,3881410,2651610,3612500,2630540 +Abl interactor 1,S222; S225; S231,2014,24980,1610,28410,1220,34450,50,13350,7318,27790 +Abl interactor 2,S183,179900,104500,165500,103400,166000,115300,212100,149000,196300,128100 +Abl interactor 2,S368,30037,26280,37680,25061,40630,23352,33400,30640,42380,32868 +Abl interactor 2,S224,10120,6835,9340,5832,10250,9581,8959,13170,10930,9344 +Abscission/NoCut checkpoint regulator,S354,178170,103459,225160,162163,205400,145661,127216,153200,251690,175930 +Acetyl-CoA carboxylase 1,S23; S25,44557,36280,47994.9,29280,48534.3,32570,65717.3,53360,55495,36410 +Acetyl-CoA carboxylase 1,S23; S25; S29,2657,3735,3381,4176,3664,3616,5866,6182,3034,3230 +Actin filament-associated protein 1,S668,575350,385530,652360,399260,70501,46189,41721,35368,975090,700270 +Actin filament-associated protein 1,S548,54720,89150,51130,120020,11530,16753,5824.5,13780,124280,227480 +Actin filament-associated protein 1,S665; S668,16990,11810,19150,16150,3370,2237,3069,2046,22840,20380 +Actin-binding LIM protein 1,S706,59490,37610,175300,95930,276700,130900,121800,81920,189600,149500 +Actin-binding LIM protein 1,T433,51489,35236,106009,88823,161800,132110,50443,57992,134870,119093 +Actin-binding LIM protein 1,S458,28264,33230,83150,68730,113810,88340,45280,45750,84500,88740 +Actin-binding LIM protein 3,S373,357948,256200,450598,315858,465244,311943,501795,362206,328401,261283 +Actin-binding LIM protein 3,S576,88800,67220,61520,53720,68980,68590,89240,81150,67130,56170 +Actin-binding LIM protein 3,S372; S379,38771,78749,23773,58617,29766.2,78426,34989,65366.9,20890,47246 +Actin-binding LIM protein 3,S286,59646,30437,61878,29058,64798,25301,64010,38990,46121,32718 +Actin-binding LIM protein 3,S493,42320,12230,41870,14410,41970,16930,63890,19810,29890,13680 +Actin-binding LIM protein 3,S282,40900,20280,41190,18780,35280,15510,38820,23580,33050,17260 +Actin-binding LIM protein 3,S503; S504,32874,30351,26391,24701,20915,18596,51710,28922,23903,23399 +Actin-binding LIM protein 3,S277; T279; S290,15130,21810,15600,17060,11060,18730,18380,20360,9340,18350 +Actin-binding LIM protein 3,S599; S607,8538,6944,13240,7341,18200,11350,9813,10780,8326,7682 +Actin-related protein 2/3 complex subunit 5,S77,46040,148700,44500,147100,45990,128700,37310,143300,81080,181100 +"Actin, aortic smooth muscle; Beta-actin-like protein 2; Putative beta-actin-like protein 3; Actin, cytoplasmic 1; Actin, alpha cardiac muscle 1; Actin, cytoplasmic 2; Actin, gamma-enteric smooth muscle; Actin, alpha skeletal muscle; POTE ankyrin domain family member E; POTE ankyrin domain family member F",S241,37150,42210,35160,39170,38080,25070,30190,18800,26800,38440 +"Actin, cytoplasmic 1; Actin, cytoplasmic 2",Y294,51600,37440,33650,22150,37080,38870,46250,41580,40870,40740 +"Actin, cytoplasmic 1; Actin, cytoplasmic 2",Y294,5141,2384,3969,2652,4493,5783,5031,3048,3476,2984 +"Actin, cytoplasmic 1; Actin, cytoplasmic 2; POTE ankyrin domain family member E",T229,7329,4661,9983,8050,10190,9264,6066,6116,6837,9129 +Activated CDC42 kinase 1,Y284,9570,5732,9516,6362,6960,4097,10550,5965,8228,7018 +Adenine phosphoribosyltransferase,S66,16650,13290,35190,35280,31770,20850,18080,9201,25730,31260 +Adenylate cyclase type 3,S580,4296,2671,4626,1921,2263,1792,4561,2705,3496,2867 +Adenylate cyclase type 6,S54,84496,69186,72750,58846,77698,63979,56296,62180,73118,58749 +Adenylate cyclase type 6,S576,53450,42910,41440,32690,36400,38100,48640,39240,49630,46030 +Adenylate cyclase type 6,T614,808.8,970.5,895.5,50,1771,1185,1332,621.3,2021,1514 +Adenylyl cyclase-associated protein 1,S34,379250,427300,478110,515390,370590,208790,373380,390040,326800,438360 +Adenylyl cyclase-associated protein 1,S275,33250,39090,31800,38120,14860,27280,22930,40860,31300,43830 +Adenylyl cyclase-associated protein 1,S34,10488,9409,10301,13772,12215,10285,7071,9375,12170,9412 +ADP-ribosylation factor GTPase-activating protein 1,S360; S361,6791,6688,4864,5870,4305,8549,5837,6919,4891,7207 +ADP-ribosylation factor GTPase-activating protein 2,S432,14520,14530,9129,11980,15540,13300,35080,24330,17510,18920 +ADP-ribosylation factor-like protein 2; ARL2-SNX15 readthrough (NMD candidate),S45,11810,10030,13290,6788,11770,11010,9710,8009,14910,9958 +Aftiphilin,S517,84900,59520,67790,48060,74480,48650,79920,57050,75950,53530 +Aftiphilin,T617,26770,56720,11650,34640,8945,39460,34380,61270,17640,37280 +Aftiphilin,S411,20780,18890,24870,20150,33880,15680,25320,17160,22660,23130 +Aftiphilin,S411,10500,8270,7800,7400,7926,5657,7487,7131,5820,7651 +"Alkyldihydroxyacetonephosphate synthase, peroxisomal",S65,7239,5366,8405,4864,8058,6842,8364,7498,6948,5803 +Alpha-adducin,S586,542300,356100,598900,280200,748400,372700,652800,283300,311000,146300 +Alpha-adducin,T11,135920,259000,74900,162320,57250,132180,79010,263000,76100,198290 +Alpha-adducin,S355; S358,113700,99470,193000,134100,76520,70910,151100,128500,129100,96670 +Alpha-adducin,S464; S465,121970,82280,141160,95650,96380,70040,151020,86140,70610,56413 +Alpha-adducin,S358,78720,72140,72270,47520,51520,37610,112600,80740,75010,57700 +Alpha-adducin,S355; S358,59190,60260,85220,68060,60200,51380,73520,65420,72980,75600 +Alpha-adducin,S358,18410,22630,34060,32700,32480,26320,24840,25990,27980,26560 +Alpha-adducin,S355; S358,21909,22665,23557,18021,14398,11439,28621,26954,16856,15209 +Alpha-adducin,S358; T364,8852,7403,10390,7353,5925,5917,9373,8072,6702,8231 +Alpha-endosulfine,S109,80020,151700,97300,154100,57150,127500,180600,128900,107000,169300 +Alpha-enolase; Beta-enolase; Gamma-enolase,S40,4190,1837,3566,1730,3692,1560,2953,2570,2591,3111 +Alpha-soluble NSF attachment protein,S195,84410,63260,83360,47860,70840,43950,87430,66690,70700,53690 +Alpha-synuclein,Y133,1074,1410,1148,1228,1370,50,1426,1470,1058,691.8 +Alpha-synuclein; Beta-synuclein,Y39,7803,11810,9587,11770,7670,14110,11250,14100,9341,14700 +Alpha-taxilin,S514; S515,57420,46410,58790,52480,51650,52240,34180,49200,59010,78930 +Alpha-taxilin,S515,27140,21100,17640,14826,14814,16614,22180,27980,21120,16936 +Alsin,S1464,6076,3589,7249,4482,5834,3515,7285,4722,6438,5898 +Amine oxidase [flavin-containing] B,S465,2541,3201,4219,2025,2289,2202,5303,3997,4384,6468 +AMP deaminase 2,S168,752200,790800,453000,1030000,471500,1069000,550600,1230000,801300,789700 +AMP deaminase 2,S76,280942,311530.4,334173,565391,698351,714315,914344,780822,726354,637965 +AMP deaminase 2,S76,149400,164000,210110,343410,459860,451620,473740,467120,419100,408100 +AMP deaminase 2,S190,44960,75170,38389,64595,21398,52670,55698,76700,59416,92250 +AMP deaminase 2,S134,15866,80580,8768,84290,11455,112770,11154,99720,29980,76580 +AMP deaminase 2,S76,48900,71940,23600,56690,34800,61990,64750,60800,40770,47970 +AMP deaminase 2,S151,21196,43175,23789,50401,22815,58090,12833,41673,14943,40360 +AMP deaminase 2,Y145,3570,15153,4291.1,12299,2891,14091,1666,11100,1870,8086 +Amyloid beta A4 precursor protein-binding family B member 1-interacting protein,S526,59401,59005,79474,93138,128952,135200,94250,77217,121733,125897 +Amyloid-beta A4 precursor protein-binding family A member 2,S283,39500,119700,25250,116900,10560,104200,7298,110500,30230,107100 +Amyloid-beta A4 precursor protein-binding family A member 3,S46; S48,2828,3925,2456,1245,2073,1798,2901,1277,2082,1713 +AN1-type zinc finger protein 2B,T185,16518,32803.9,17104,26011.9,10656,24267,14400.4,24717,19748,24256.6 +Anaphase-promoting complex subunit 2,S470,5137,7602,7316,4681,6464,4116,10990,5005,6774,4573 +Anaphase-promoting complex subunit 4,S777; S779,23190,13690,21390,13000,22730,15580,24660,21500,28040,17940 +Anaphase-promoting complex subunit CDC26,S42,11950,8989,7894,6514,7297.8,4988,14959,9441.2,9744,7853 +Anaphase-promoting complex subunit CDC26,S42,2017,607,1507,1201,1119,50,3104,1360,1676,1031 +Anion exchange protein 2,S144,26940,22280,38870,38800,43670,40760,16970,18600,41310,36910 +Anion exchange protein 2,S132,22664,14020.3,25918,18644,24236,16490.4,21891,16689,22789,17566 +Anion exchange protein 2,S144,20433,19746,20796,19803,15682,17342,19926,18687,22229,20585 +Anion exchange protein 2,S144; T148,1279,2448,2364,2111,1827,1873,1579,1789,1235,1345 +Ankyrin repeat and IBR domain-containing protein 1,S891; S898,1624,4318,1486,2180,1494,1556,2088,3411,1205,3455 +Ankyrin repeat and LEM domain-containing protein 2,S662,12790,9402,12380,8012,17080,8931,11540,10340,8186,4568 +Ankyrin repeat and MYND domain-containing protein 2,S419,19880,17060,24290,13590,25350,20210,19620,18530,21620,11430 +Ankyrin repeat and SAM domain-containing protein 1A,S663,204600,168100,168000,114500,153700,127000,278800,192000,199300,151200 +Ankyrin repeat and SAM domain-containing protein 1A,S663,144600,131800,128600,94810,122700,77930,186600,155800,171700,133800 +Ankyrin repeat and SAM domain-containing protein 1A,S677,17239,11291,20718,10560.9,22448,11454,36658,14405,20086,13888 +Ankyrin repeat and SAM domain-containing protein 1A,S663; S666,11840,7517,18130,12530,15700,10790,18850,11010,14030,9480 +Ankyrin repeat domain-containing protein 13A,S586,56155.2,117463,18954.3,103326.9,9091.1,93618,9533,103376,29286.1,95909 +Ankyrin repeat domain-containing protein 27,T1023,16120,11340,14660,11020,12130,12740,21980,14180,12550,14900 +Ankyrin-1,S1686,135474,88915,138621,76546,141393,56972,161552,91580,105968,59720 +Ankyrin-1,S856,55940,47810,41601,26070,27593.5,19820,61848,59629,40467,35926 +Antithrombin-III,T63,10210,8037,12150,9864,20050,12800,10350,7725,11670,10690 +AP-1 complex subunit sigma-1A,S147,1888,50,1747,1416,3087,1486,1625,2017,2157,717.7 +AP-2 complex subunit alpha-1,T647,12390,7032,11530,6399,12610,5303,15450,7238,13580,8529 +AP-2 complex subunit alpha-1,S655; S657,4029,2437,4406,2383,4850,2329,5579,4095,3061,1834 +AP-3 complex subunit beta-1,S276,83620,72130,72570,48730,69410,38634,86730,42122,72400,67050 +AP2-associated protein kinase 1,T640; S642,90170,75420,115000,79990,110600,90530,71710,66040,91540,67630 +AP2-associated protein kinase 1,T620; S624,108400,70040,98500,47840,104300,55320,114300,52840,78290,47910 +Apolipoprotein B receptor,T565,41050,47900,43320,60000,47600,53330,40070,56130,33900,41430 +Apolipoprotein B-100,S4048,41910,30490,32280,18820,33800,24150,39500,29970,27150,16120 +ARF GTPase-activating protein GIT1,S410,165440,136015,109250,113845,107969,80624,162790,162032,172748,134507 +ARF GTPase-activating protein GIT1,S592,61998,131068,53034,123960,53072,109975,39716,105945,63307,123049 +ARF GTPase-activating protein GIT1,S410; S413,98156,129448,56688,67388,55416,42798,121458,61078,68372,138993 +ARF GTPase-activating protein GIT1,S362; T364,14450,11590,24180,15940,14980,13150,18780,17770,14550,12330 +ARF GTPase-activating protein GIT1,S410; S413; S414,7814,6408,10043,9017,6528,7034,9361,7180,6757,7748 +ARF GTPase-activating protein GIT1,S410; S413,6091.2,6525.4,6156,3486.5,5010.5,2882.5,4495,3479.3,4120.8,5193.9 +ARF GTPase-activating protein GIT1,S592,1655,4354,1710,3555,948.9,2971,1857,4154,2128,4302 +ARF GTPase-activating protein GIT2,S415,36460,26330,46670,41220,61310,33440,103600,43790,52570,36390 +ARF GTPase-activating protein GIT2,S415; S418,7565.2,4796.6,8779,7397,5342.3,6082.7,10190,7510,7010,9400 +ARF GTPase-activating protein GIT2,S418; S421,3642,3336,5577,3736,5976,3098,6372,4378,4390,3124 +"Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 2",S379,158500,112800,177800,112600,180400,122500,151000,115500,175000,114500 +"Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 2",S378; S379,153900,94860,136300,82790,126300,100300,162000,108400,132400,74860 +"Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 2",S384,63710,39410,73010,43160,49630,34330,66550,43300,50330,40289 +"Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 2",S927,26561,50820,21109,50870,15401,52740,21486,56650,22681,49430 +"Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 2",S927; S929,2705,4521,50,3328,649,4526,966.3,4653,1726,4141 +"Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 1",S229,629858,373887.1,664054,385676,589763,402387,732766,438067.4,528156,381605.5 +"Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1",S1008,228300,197600,249900,214000,256700,111800,244800,230200,210500,215300 +"Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1",S717,94610,72990,120310,100920,73836,66805,86490,93700,78418,57587 +"Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1",S1041,52072,42425,91737,106087,67773,126031,20500,72739,94562,66579 +"Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1",S839; S843,65630,89670,43240,74430,40750,84030,42110,88150,50680,71150 +"Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1",T813,18970,60520,18380,80970,18400,95790,14530,65700,21230,63330 +"Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1",S717,68776,46689,82132,57242,10510,8581,90449,55794,13538,8431 +"Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1",S1008,19150,10810,69100,47100,71720,62750,5894,22720,46740,18420 +"Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1",S1027,34630,18600,45060,24510,48090,24180,35810,23050,28140,22450 +"Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1",T1048,30272,26506,24170,25964,26790,25855,18166,27167,23229,29313 +"Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1",S1041; T1048,11780,16580,21280,46990,19460,62040,4125,21780,18830,23180 +"Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1",S843,19970,6006,18580,6263,15200,7046,24720,10010,21910,6594 +"Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1",S766; Y767,5537,3389,5813,4648,7983,5980,4264,4106,5972,4796 +"Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 2",S820,349054,274070,223593,202274,291235,278484,351611,319714,342946,296327 +"Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 2",S701,274511,196047.9,252478,163918.3,285923,179752,311017,235449,296283,192218 +"Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 2",S701,154796,108498,200238,114881,194840,154105,156666,137446,169857,94386 +"Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 2",S701,60850,33597,65590,35010,43590,33690,60810,37060,44220,26207 +"Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 2",S722,7094,13271,10063,31586,8004,27735,6940.7,8224,10888,22296 +"Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 2",S820,15130,11460,15230,9470,17450,11400,13590,10070,18380,13820 +Armadillo repeat-containing X-linked protein 3,S61,19720,11610,18080,9208,18660,12060,15020,8584,13690,8394 +Astrocytic phosphoprotein PEA-15,S116,1127784,1094946,835954,1015303,655864,872749,790944,1111485,1085607,940767 +Astrocytic phosphoprotein PEA-15,S116,760300,367300,875000,371800,684700,344000,701400,333900,721300,344500 +Astrocytic phosphoprotein PEA-15,S116,53020,57870,36570,39160,26390,32910,48360,40530,40710,48080 +AT-rich interactive domain-containing protein 3B,S560,8663,5922,11060,6024,13000,7804,12490,7483,11450,8719 +Ataxin-2,T741,122600,49830,105100,39480,72360,24550,145000,56150,96550,42390 +Ataxin-2-like protein,S238,2755,1677,2303,1480,3338,1464,2774,2787,1825,1760 +Atlastin-1,S10,321934,523322,207828,454293,136536,514223,121129,484956,230172,428574 +Atlastin-1,S22; S23,155200,118600,181000,116200,170300,123300,164600,124800,148400,100800 +"ATP-binding cassette sub-family B member 6, mitochondrial",S755,4373,3171,3087,2053,4306,2711,3243,2768,3343,2052 +ATP-binding cassette sub-family F member 1,S109,321500,232000,268900,192100,266600,144900,314400,249400,291000,215600 +ATP-binding cassette sub-family F member 1,T108; S109,261490,154320,262920,146980,235720,136200,260070,172670,254310,159510 +ATP-binding cassette sub-family F member 1,S109,200252,147876,213018,146583,194196,117516,238962,168095,225698,155299 +ATP-binding cassette sub-family F member 1,S228,209143,157170,197879,138957.5,171960,104112.5,221662,148291.1,195748,172752 +ATP-binding cassette sub-family F member 1,T108; S109,140040,93010,144350,84680,136940,81080,148600,109510,140060,87110 +ATP-citrate synthase,S455,172740,230980,107560,228560,88550,222560,82670,234880,131230,260860 +ATP-dependent RNA helicase DDX3X,S606,1612,3426,1676,2192,1646,3171,3019,5402,3078,3024 +ATP-dependent RNA helicase DHX29,S71; T72,18530,37030,15770,47790,15740,39140,22070,42050,21940,38750 +Autophagy-related protein 2 homolog A,S403,12960,39540,14390,41470,5624,36200,20370,44530,19400,36080 +Autophagy-related protein 2 homolog B,S886,8896,9751,5307,6759,5827,3910,7495,4904,6329,5978 +Autophagy-related protein 9A,S828,260176,155897,161031,103164,163704,91161,247505,143500,157760,114017 +Autophagy-related protein 9A,S14,14320,15940,11600,12990,10480,11380,5489,7889,7912,9446 +Axin-1,S75; S77,45230,28070,50040,31480,54720,31320,39740,35800,44220,29180 +Axin-1,S77; T79,38410,25470,47460,29510,44410,24960,34500,26690,35650,24210 +Axin-1,S75; T79,11454,12306,15008,10409,14506,8971,11206,8374,13659,11732 +B-cell lymphoma/leukemia 10,S141,53450,62590,75070,102400,60560,95320,26300,61580,67970,104700 +B-cell lymphoma/leukemia 10,S138,20600,20070,16360,15690,11890,14470,16880,20050,18320,17170 +B-cell scaffold protein with ankyrin repeats,S542,8733,34340,3261,34650,2765,37260,2838,18220,11060,29160 +Band 4.1-like protein 2,S39,4068,2132,1980,2739,4016,2774,5252,4091,3593,1314 +Basic leucine zipper and W2 domain-containing protein 2,S412,3486,1578.7,4187,1547,3383,50,6708,1903.4,2494,1179 +Basigin,S362,152667,90316,141029,92934,116781,69115,167043,122280,140715,83831 +Bcl2-associated agonist of cell death,S99,52882,61975,54615,59817,62634,69695,54326,63836,63851,64305 +Bcl2-associated agonist of cell death,S25,23850,17510,21490,17090,25060,16380,22730,20810,18970,13770 +Bcl2-associated agonist of cell death,S74; S75,11280,14720,8557,10020,8206,15340,11150,12490,6980,14260 +BCL2/adenovirus E1B 19 kDa protein-interacting protein 2,S114,168800,159200,163700,138400,184000,133500,232400,173900,192100,169200 +BCL2/adenovirus E1B 19 kDa protein-interacting protein 2,Y118,172200,149900,178800,137700,173200,135200,223600,162300,185000,134900 +BET1 homolog,S50,65329,200003,50609,200270,72502,214452,114525,256619,100369,182501 +BET1-like protein,S9,142700,98180,126900,92810,105900,70350,142800,108600,108100,65930 +BET1-like protein,S9,76470,47810,43760,29780,35190,23560,92270,56770,41190,25690 +Beta-1-syntrophin,S87,903322.6,1277714,1030347,1387068,1158646,1376323,823115,1224066,837132,1081721.3 +Beta-1-syntrophin,T214,673637,491185,798079,504324,714905,510424,674116,511644,597180,476698 +Beta-1-syntrophin,T214; S219,335690,274070,357780,299670,308150,283220,271090,260380,322840,296990 +Beta-1-syntrophin,T214,67390,53258,70420,45293,80410,60467,64614,57408,81620,53708 +Beta-1-syntrophin,T214; S219,53762,52026,56459,50672,60954,47488,49750,47659,52382,48168 +Beta-2 adrenergic receptor,S246,1143,2261,50,2136,671.5,1321,50,1868,50,1771 +Beta-adrenergic receptor kinase 1,S670,207400,176800,150400,128900,155600,137600,229800,216200,141700,120900 +Beta-adrenergic receptor kinase 1; Beta-adrenergic receptor kinase 2,S487,1181,1034,815.2,1057,840.7,1056,652.3,1233,1472,1690 +Beta-arrestin-1,S412,179100,130900,200500,119500,207800,136600,199700,143900,214600,154300 +Beta-arrestin-1,Y47,8176,7983,9158,4177,5078,3950,14630,8095,8855,9042 +Beta-arrestin-1,T370,5866,11900,6672,8268,5531,8466,8516,10050,4437,9049 +Beta-arrestin-1,T370,1354,3255,2091,4749,2538,4830,50,2667,1937,2638 +Beta-parvin,S54,50,11080,141352,467278,50,31190,50,50,6516,50 +Beta-parvin,S254,41740,66690,48250,42910,48370,41880,62090,55700,61920,73950 +Bifunctional coenzyme A synthase,S178,96850,62620,102800,47690,100600,55400,119000,85440,95120,61530 +BMP-2-inducible protein kinase,S947; S949,13817,11641,20321,8757,11990,7021,27284,11925,28471,19078 +Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 2,S493,7019,4300,9630,6709,9690,8350,7991,4974,8258,7166 +Breast carcinoma-amplified sequence 3,S886,14323,15788,10116,12254,9744,9504,13562,11076,10991,14117 +Breast carcinoma-amplified sequence 3,S461,948.9,3365,50,2507,50,3213,50,3800,1084,3256 +Brefeldin A-inhibited guanine nucleotide-exchange protein 1,S397,96110,106200,69580,83040,75830,90750,77850,115400,103800,108700 +Brefeldin A-inhibited guanine nucleotide-exchange protein 1,S1569,36140,9477,46130,13110,59330,18070,53280,15190,36000,12350 +Brefeldin A-inhibited guanine nucleotide-exchange protein 1,Y662,3542,8632,1452,5096,2273,2964,4345,5289.1,3357,6704 +Brefeldin A-inhibited guanine nucleotide-exchange protein 1,Y662; S684,2278,5155,1107,4314,1062,3734,1950,5260,1814,4381 +Brefeldin A-inhibited guanine nucleotide-exchange protein 2,S1525,160300,46840,71790,18900,15290,16280,118900,23830,29860,18900 +Brefeldin A-inhibited guanine nucleotide-exchange protein 2,S279,64770,44020,35010,31070,46430,36280,60890,54090,43170,35040 +Bridging integrator 2,S395,12259290,13785590,8350920,13666420,7405620,11447390,5697690,13344220,8015420,12668360 +Bridging integrator 2,S436,12645767,4770196.8,15489213,3897568,14682597,4617680.3,17403426,6442574.4,16168111,5169614.5 +Bridging integrator 2,S259,2369680,6071420,2688350,6428880,3486080,7396250,2998430,7142620,4480910,7220580 +Bridging integrator 2,S451,1092600,2300500,679800,1573200,519800,1226900,697700,2541900,777000,1925800 +Bridging integrator 2,S440; S444; T446,891556,1465654.3,1141088,1459640.7,1130608,1654953.5,886860,1426904.4,952159,1343331.5 +Bridging integrator 2,T423; T438,959871,824641,863685,814576.6,859208,834619.8,667220.3,927358,879354,904851 +Bridging integrator 2,S282; T283,632215,1360709,326113,936715,284275,804423,909889,653782,344709.4,1478034 +Bridging integrator 2,S272; S273,234930,348170,193470,258580,182380,229250,279840,310520,215890,381500 +Bridging integrator 2,S259; S263,111510,446500,104220,447440,104560,517800,50657,356220,90750,350320 +Bridging integrator 2,S369,120941,187474,132615.1,193608,124142,217013,81129,185696,100550,188139 +Bridging integrator 2,S462,167150,229620,66637,117567,43422,79940,120148,181469,59413,142057 +Bridging integrator 2,S395,100760,122500,43025,105690,37833,93840,50085,122540,40402,63779 +Bridging integrator 2,S375,69080,90630,62120,68490,63020,75100,58180,85270,63510,73460 +Bridging integrator 2,T366; S369,63980,42400,78320,42680,91380,37590,93260,43460,48690,30610 \ No newline at end of file diff --git a/tests/countdata_edgeR.R b/tests/countdata_edgeR.R new file mode 100644 index 0000000..e9c4063 --- /dev/null +++ b/tests/countdata_edgeR.R @@ -0,0 +1,13 @@ +app <- ShinyDriver$new("../") +app$snapshotInit("countdata_edgeR") + +app$setInputs(data_file_type = "upload") +app$uploadFile(datafile = "../data/examplecounts_short.csv") # <-- This should be the path to the file, relative to the app's tests/ directory +app$setInputs(upload_data = "click") +app$setInputs(input_collapse_panel = "analysis_panel") +app$setInputs(sel_gene = "ENSMUSG00000008028_1700008O03Rik") +app$setInputs(sel_gene = c("ENSMUSG00000008028_1700008O03Rik", "ENSMUSG00000036151_Tm6sf2")) +app$setInputs(action_heatmaps = "click") +#app$snapshot() +app$setInputs(datafilter_groups = c("group1", "group2")) +app$setInputs(datafilter_groups = c("group1", "group2", "group3")) diff --git a/ui-tab-inputdata.R b/ui-tab-inputdata.R index c5d398c..5993f85 100644 --- a/ui-tab-inputdata.R +++ b/ui-tab-inputdata.R @@ -102,10 +102,12 @@ tabPanel("Input Data", ## ==================================================================================== ## column(8, bsCollapse(id="input_collapse_panel",open="data_panel",multiple = FALSE, - bsCollapsePanel(title="Data Contents: Check Before `Submit`",value="data_panel", + bsCollapsePanel(title="Data Contents: Check Before `Submit`", + value="data_panel", dataTableOutput('countdataDT') ), - bsCollapsePanel(title="Analysis Results: Ready to View Other Tabs",value="analysis_panel", + bsCollapsePanel(title="Analysis Results: Ready to View Other Tabs", + value="analysis_panel", downloadButton('downloadResults_CSV','Save Results as CSV File'), downloadButton('downloadResults_RData', 'Save Results as START RData File for Future Upload',