Skip to content
Open
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1,782 changes: 1,782 additions & 0 deletions 7.collab-data/2.run_model.ipynb

Large diffs are not rendered by default.

846 changes: 846 additions & 0 deletions 7.collab-data/3.pinwheel_plots.ipynb

Large diffs are not rendered by default.

561 changes: 561 additions & 0 deletions 7.collab-data/4.cell-killing-plots.ipynb

Large diffs are not rendered by default.

78,987 changes: 78,987 additions & 0 deletions 7.collab-data/data/PH7MLH-expression-matrix-TPM.tsv

Large diffs are not rendered by default.

66,098 changes: 66,098 additions & 0 deletions 7.collab-data/data/RCK_833_S44_L003_R1_001_genes.fpkm_tracking.sorted

Large diffs are not rendered by default.

325 changes: 325 additions & 0 deletions 7.collab-data/data/cell-killing.csv
Original file line number Diff line number Diff line change
@@ -0,0 +1,325 @@
DIPG10 (WT),3-Deazaneplanocin A (nM),Surviving Fraction,,,
,0,1.02,0.963529,1.016471,
,1,0.942353,1.012941,0.988235,
,3.162278,0.914118,1.058824,0.995294,
,10,0.963529,1.087059,1.027059,
,31.622777,0.991765,1.02,1.034118,
,100,0.963529,1.090588,0.952941,
,316.227766,0.850588,0.967059,1.023529,
,1000,0.695294,0.783529,0.847059,
,3162.27766,0.536471,0.730588,0.642353,
,10000,0.589412,0.667059,0.649412,
,,,,,
,Axitinib (nM),Surviving Fraction,,,
,0,0.986111,0.963384,1.050505,
,1,0.872475,0.917929,1.027778,
,3.162278,0.872475,0.95202,1.186869,
,10,0.717172,0.876263,0.872475,
,31.622777,0.584596,0.77399,0.739899,
,100,0.353535,0.429293,0.402778,
,316.227766,0.224747,0.319444,0.22096,
,1000,0.141414,0.190657,0.160354,
,3162.27766,0.126263,0.137626,0.224747,
,10000,0.099747,0.103535,0.156566,
,,,,,
,Cladribine (nM),Surviving Fraction,,,
,0,0.917184,1.044513,1.038302,
,1,0.824017,0.994824,1.097308,
,3.162278,0.898551,0.935818,0.979296,
,10,0.89234,0.935818,1.174948,
,31.622777,1.001035,1.022774,1.087992,
,100,0.960663,1.041408,1.047619,
,316.227766,0.89234,0.969979,1.063147,
,1000,1.010352,0.917184,0.951346,
,3162.27766,0.780538,0.845756,0.895445,
,10000,0.646998,0.733954,0.730849,
,,,,,
DIPG13 (M),3-Deazaneplanocin A (nM),Surviving Fraction,,,
,0,0.915842,0.965347,1.118812,
,1,0.851485,0.930693,0.955446,
,3.162278,0.935644,0.851485,1.039604,
,10,0.811881,0.881188,0.965347,
,31.622777,0.990099,0.876238,1.034653,
,100,1.084158,1.039604,0.960396,
,316.227766,0.945545,0.99505,0.975248,
,1000,0.935644,0.881188,0.910891,
,3162.27766,0.717822,0.737624,0.747525,
,10000,0.668317,0.594059,0.559406,
,,,,,
,Axitinib (nM),Surviving Fraction,,,
,0,1.085414,0.817346,1.09724,
,1,0.695138,0.537451,0.60841,
,3.162278,0.612352,0.446781,0.486202,
,10,0.458607,0.35611,0.387648,
,31.622777,0.403417,0.26544,0.296978,
,100,0.344284,0.194481,0.202365,
,316.227766,0.320631,0.17477,0.178712,
,1000,0.281209,0.186597,0.170828,
,3162.27766,0.170828,0.135348,0.143233,
,10000,0.277267,0.249671,0.229961,
,,,,,
,Cladribine (nM),Surviving Fraction,,,
,0,1.186555,0.863866,0.94958,
,1,0.994958,0.853782,0.969748,
,3.162278,1.161345,0.954622,0.838655,
,10,1.010084,0.657143,0.87395,
,31.622777,0.87395,0.757983,0.793277,
,100,0.697479,0.642017,0.752941,
,316.227766,0.808403,0.763025,0.652101,
,1000,0.747899,0.742857,0.626891,
,3162.27766,0.702521,0.642017,0.722689,
,10000,0.752941,0.717647,0.828571,
,,,,,
DIPG17 (M),3-Deazaneplanocin A (nM),Surviving Fraction,,,
,0,1.056991,1.027356,0.915653,
,1,0.87462,0.781155,0.949088,
,3.162278,0.787994,0.867021,0.800912,
,10,0.784954,0.93769,0.776596,
,31.622777,0.949848,0.819149,0.786474,
,100,0.93693,0.904255,0.641337,
,316.227766,0.895137,0.643617,0.696049,
,1000,0.477964,0.491641,0.49924,
,3162.27766,0.379179,0.343465,0.306231,
,10000,0.306231,0.266717,0.266717,
,,,,,
,Axitinib (nM),Surviving Fraction,,,
,0,0.901238,1.005474,1.093289,
,1,0.844836,0.848406,0.873394,
,3.162278,0.850547,0.800571,0.796287,
,10,0.722037,0.647787,0.63565,
,31.622777,0.365778,0.413613,0.381485,
,100,0.15445,0.140885,0.166587,
,316.227766,0.047358,0.043789,0.05307,
,1000,0.043075,0.040219,0.031652,
,3162.27766,0.038791,0.039505,0.036649,
,10000,0.055926,0.043075,0.0495,
,,,,,
,Cladribine (nM),Surviving Fraction,,,
,0,1.171141,0.893908,0.934951,
,1,1.14094,0.856737,0.908622,
,3.162278,0.867579,0.884615,0.82731,
,10,0.716572,0.728962,0.748322,
,31.622777,0.397522,0.338668,0.380485,
,100,0.175271,0.194631,0.181466,
,316.227766,0.167527,0.132679,0.149716,
,1000,0.144295,0.130356,0.124161,
,3162.27766,0.109448,0.092411,0.097832,
,10000,0.093185,0.090088,0.105576,
,,,,,
,,,,,
BT245,Axitinib ( nM),,Surviving Fraction,,
,0,0.861199,1.080757,1.058044,
,1,0.830915,1.2,1.177287,
,3.16,1.059937,1.025868,1.156467,
,10,1.025868,0.916088,1.29653,
,31.6,0.694637,1.226498,1.122397,
,100,1.078864,1.198107,1.042902,
,316,0.783596,1.260568,0.942587,
,1000,0.378549,0.450473,0.335016,
,3160,0.249842,0.187382,0.263091,
,10000,0.200631,0.194953,0.198738,
,,,,,
,Cladribine (nM),,Surviving Fraction,,
,0,1.182119,0.884106,0.933775,
,1,1.112583,1.375828,1.120033,
,3.16,1.432947,1.50745,1.333609,
,10,1.398179,1.452815,1.018212,
,31.6,1.259106,1.547185,1.303808,
,100,1.087748,1.20447,1.254139,
,316,0.958609,0.869205,0.96606,
,1000,0.593543,0.568709,0.419702,
,3160,0.496689,0.476821,0.548841,
,10000,0.474338,0.51904,0.494205,
,,,,,
DIPG7,Axitinib ( nM),,Surviving Fraction,,
,0,0.948411,1.23606,0.815529,
,1,1.165711,1.261073,1.121939,
,3.162278,0.843669,1.414278,1.010943,
,10,0.682647,1.25013,0.874935,
,31.622777,0.732673,0.943721,0.645128,
,100,0.399687,0.848359,0.459093,
,316.227766,0.810839,0.885878,0.607608,
,1000,0.4716,0.535696,0.496613,
,3162.27766,0.069828,0.068265,0.077645,
,10000,0.041688,0.083898,0.087024,
,,,,,
,Cladribine (nM),,Surviving Fraction,,
,0,0.97481,0.989068,1.036122,
,1,1.192966,1.155894,1.155894,
,3.162278,1.341255,1.220057,1.509506,
,10,0.953422,0.937738,0.609791,
,31.622777,0.413023,0.581274,0.348859,
,100,0.174905,0.286122,0.077947,
,316.227766,0.046578,0.072243,0.060837,
,1000,0.035171,0.039449,0.046578,
,3162.27766,0.026616,0.030894,0.029468,
,10000,0.020913,0.028042,0.013783,
,,,,,
,,,,,
MAF868 (WT),3-Deazaneplanocin A (nM),Surviving Fraction,,,
,0,1.170994,0.827216,1.001791,
,1,0.870188,0.91316,1.025962,
,3.162278,1.200537,1.042077,0.899731,
,10,1.082363,0.950761,0.918532,
,31.622777,0.848702,0.899731,1.001791,
,100,0.663384,0.566697,0.59624,
,316.227766,0.333035,0.341092,0.443151,
,1000,0.225604,0.136974,0.166517,
,3162.27766,0.110116,0.102059,0.085944,
,10000,0.083259,0.091316,0.077887,
,,,,,
,Axitinib (nM),Surviving Fraction,,,
,0,0.938161,0.916192,1.145647,
,1,0.179007,0.16192,0.188771,
,3.162278,0.117982,0.139951,0.132628,
,10,0.081367,0.105777,0.142392,
,31.622777,0.071603,0.056957,0.08869,
,100,0.037429,0.025224,0.044752,
,316.227766,0.01546,0.003255,0.01546,
,1000,0.027665,0.003255,0.025224,
,3162.27766,0.022783,0.022783,0.010578,
,10000,0.020342,0.032547,0.042311,
,,,,,
,Cladribine (nM),Surviving Fraction,,,
,0,1.030192,0.879231,1.090576,
,1,1.329369,1.36505,1.216834,
,3.162278,1.203111,1.329369,1.323879,
,10,1.408966,1.565416,1.241537,
,31.622777,1.351327,1.005489,1.164684,
,100,0.898445,0.83806,0.769442,
,316.227766,0.591034,0.626715,0.950595,
,1000,0.462031,0.519671,0.500457,
,3162.27766,0.376944,0.549863,0.448307,
,10000,0.36322,0.344007,0.494968,
,,,,,
,,,,,
GBM2 (M),3-Deazaneplanocin A (nM),Surviving Fraction,,,
,0,0.735358,1.093275,1.171367,
,1,0.741866,0.86551,0.995662,
,3.162278,0.605206,0.976139,1.184382,
,10,0.89154,0.956616,1.106291,
,31.622777,0.650759,0.696312,0.774403,
,100,0.872017,0.741866,0.819957,
,316.227766,0.819957,0.650759,0.872017,
,1000,0.845987,0.767896,0.89154,
,3162.27766,0.72885,0.683297,0.657267,
,10000,0.72885,0.72885,0.722343,
,,,,,
,Axitinib (nM),Surviving Fraction,,,
,0,0.942748,0.965649,1.091603,
,1,0.85687,0.919847,0.965649,
,3.162278,0.765267,0.971374,1.045802,
,10,0.685115,0.719466,0.965649,
,31.622777,0.650763,0.553435,0.725191,
,100,0.501908,0.450382,0.622137,
,316.227766,0.341603,0.23855,0.39313,
,1000,0.26145,0.284351,0.23855,
,3162.27766,0.307252,0.278626,0.272901,
,10000,0.347328,0.347328,0.387405,
,,,,,
,Cladribine (nM),Surviving Fraction,,,
,0,1.037113,1.024742,0.938144,
,1,0.826804,0.894845,0.901031,
,3.162278,0.919588,0.863918,0.795876,
,10,0.987629,0.62268,0.659794,
,31.622777,0.579381,0.56701,0.573196,
,100,0.51134,0.523711,0.498969,
,316.227766,0.461856,0.45567,0.740206,
,1000,0.443299,0.381443,0.362887,
,3162.27766,0.449485,0.505155,0.4,
,10000,0.498969,0.517526,0.474227,
,,,,,
,,,,,
GBM1 (WT),3-Deazaneplanocin A (nM),Surviving Fraction,,,
,0,1.006843,1.076989,0.916168,
,1,0.893926,0.84089,0.833191,
,3.162278,0.88195,0.962361,0.887083,
,10,0.901625,0.911035,0.952096,
,31.622777,0.721129,0.829769,0.772455,
,100,0.693755,0.75278,0.706587,
,316.227766,0.446536,0.431993,0.536356,
,1000,0.294269,0.295124,0.374679,
,3162.27766,0.218135,0.218991,0.221557,
,10000,0.143713,0.130026,0.135158,
,,,,,
,Axitinib (nM),Surviving Fraction,,,
,0,0.971492,0.951564,1.076944,
,1,0.12289,0.108774,0.143648,
,3.162278,0.110435,0.092167,0.106283,
,10,0.106283,0.088015,0.106283,
,31.622777,0.066427,0.058954,0.068087,
,100,0.046499,0.052311,0.044008,
,316.227766,0.037365,0.035704,0.032383,
,1000,0.044838,0.032383,0.034874,
,3162.27766,0.039856,0.042347,0.044008,
,10000,0.045668,0.048159,0.052311,
,,,,,
,Cladribine (nM),Surviving Fraction,,,
,0,1.025081,1.032163,0.942756,
,1,1.083505,0.971083,1.044556,
,3.162278,1.010918,0.933904,0.873709,
,10,0.662142,0.731189,0.725878,
,31.622777,0.380643,0.40897,0.371791,
,100,0.213337,0.221304,0.240779,
,316.227766,0.198289,0.200944,0.211567,
,1000,0.186781,0.228386,0.212452,
,3162.27766,0.209796,0.247861,0.254942,
,10000,0.233697,0.260254,0.270876,
,,,,,
BT245,3-Deazaneplanocin A (nM),Surviving Fraction,,,
,0,1.238219895,1.890052356,2.17539267,
,1,2.27486911,3.59947644,3.219895288,
,3.162278,2.518324607,3.45026178,3.235602094,
,10,2.884816754,3.235602094,2.884816754,
,31.622777,2.222513089,2.219895288,2.452879581,
,100,1.952879581,2.222513089,1.845549738,
,316.227766,1.062827225,1.463350785,1.062827225,
,1000,0.816753927,0.997382199,0.706806283,
,3162.27766,1.09947644,0.782722513,0.69895288,
,10000,1.028795812,1.083769634,0.887434555,
,,,,,
DIPG7,3-Deazaneplanocin A (nM),Surviving Fraction,,,
,0,1.02074392,1.063662375,1.08297568,
,1,1.550786838,1.419885551,2.117310443,
,3.162278,1.168812589,1.432761087,1.743919886,
,10,1.010014306,1.383404864,1.576537911,
,31.622777,0.945636624,1.113018598,1.542203147,
,100,1.638769671,1.827610873,1.441344778,
,316.227766,0.724606581,1.164520744,1.271816881,
,1000,0.829756795,0.821173104,1.001430615,
,3162.27766,0.718168813,0.949928469,0.69241774,
,10000,1.040057225,1.063662375,0.896280401,
,,,,,
DIPG4,Axitinib(nM),Surviving Fraction,,,
,0,2.27451,2.745098,1.892157,
,1,2.862745,2.45098,2.156863,
,3.162278,2.862745,2.362745,2.098039,
,10,1.95098,2.27451,2.686275,
,31.622777,1.598039,2.921569,1.098039,
,100,1.480392,2.009804,1.362745,
,316.227766,1.362745,1.009804,1.039216,
,1000,0.980392,0.980392,1.068627,
,3162.27766,1.068627,1.303922,0.77451,
,10000,1.127451,1.127451,0.745098,
,,,,,
DIPG4,Cladribine,Survivng Fraction,,,
,0,2.333333,2.039216,2.362745,
,1,2.892157,2.039216,1.862745,
,3.162278,1.95098,2.27451,1.862745,
,10,1.862745,1.509804,1.686275,
,31.622777,1.480392,1.27451,1.745098,
,316.227766,1.480392,2.27451,1.303922,
,1000,1.215686,1.303922,1.833333,
,3162.27766,1.245098,1.303922,0.921569,
,,,,,
DIPG4,3-Deazaneplanocin A (nM),Surviving Fraction,,,
,0,1.515873,1.396825,1.777778,1.515873
,1,1.515873,1.801587,1.277778,1.277778
,3.162278,1.539683,1.468254,1.253968,0.992063
,10,2.230159,1.134921,1.753968,1.325397
,31.622777,1.468254,1.063492,1.230159,1.111111
,100,1.492063,0.944444,1.301587,1.18254
,316.227766,1.492063,0.992063,1.039683,1.206349
,1000,1.325397,1.063492,1.015873,0.920635
,3162.27766,1.15873,1.111111,0.920635,1.087302
,10000,0.992063,1.134921,0.873016,0.920635
Binary file not shown.
Loading