Multiple kernels can be used in a single a SoS notebook, with the SoS kernel being the super kernel that manages others. You can select kernel of a code cell using the language selection dropdown box at the top right corner or using SoS magics. Prompt areas of code cells belonging to different kernels are marked by different colors. You however might not be able to see the language dropdown box and colors as shown below if you are viewing the notebook with a viewer that does not recognize SoS kernel inormation.
In this example we are converting an MS Excel file to csv format using Python pandas module. We then use R to annotate the gene names and draw some plot. The annotated data will be sent back to Python and write in excel format.
Let us first have a look at the data in SoS using its %preview magic. This magic reads data from the excel file and previews it as a sortable and searchable table. The -n option tells the magic to display the result in the main notebook, not in the SoS side panel.
In [1]:
%preview DEG_list.xlsx
> DEG_list.xlsx (107.4 KiB):
Only the first 200 of the 1184 records are previewed. Use option --limit to set a new limit.
| ensembl_gene_id | baseMean | log2FoldChange | stat | pvalue | padj | |
|---|---|---|---|---|---|---|
| 0 | ENSMUSG00000042816 | 1686.121821 | 3.390100 | -28.589868 | 8.979679e-180 | 7.696034e-176 |
| 1 | ENSMUSG00000031635 | 358.401785 | 3.614133 | -21.471980 | 2.846325e-102 | 8.131476e-99 |
| 2 | ENSMUSG00000020838 | 551.448621 | 2.532469 | -18.878942 | 1.699551e-79 | 2.913201e-76 |
| 3 | ENSMUSG00000021765 | 597.716318 | 2.265537 | -17.571072 | 4.103412e-69 | 5.024042e-66 |
| 4 | ENSMUSG00000027907 | 3236.448003 | 1.306965 | -15.152852 | 7.254873e-52 | 6.908654e-49 |
| 5 | ENSMUSG00000026247 | 744.567819 | 1.999957 | -14.202403 | 8.852428e-46 | 6.897249e-43 |
| 6 | ENSMUSG00000030272 | 3322.013499 | 1.029098 | -13.056674 | 5.821582e-39 | 3.837990e-36 |
| 7 | ENSMUSG00000069793 | 317.952685 | 1.645894 | -12.727226 | 4.174068e-37 | 2.384924e-34 |
| 8 | ENSMUSG00000028494 | 4659.305199 | 1.051199 | -12.102120 | 1.029183e-33 | 5.188595e-31 |
| 9 | ENSMUSG00000059645 | 107.043454 | 1.777720 | -11.629145 | 2.930187e-31 | 1.287855e-28 |
| 10 | ENSMUSG00000026834 | 184.146231 | 1.576185 | -10.924823 | 8.771122e-28 | 3.496414e-25 |
| 11 | ENSMUSG00000069355 | 78.423674 | 1.896248 | -10.639715 | 1.947240e-26 | 7.101625e-24 |
| 12 | ENSMUSG00000024066 | 1207.689222 | 1.287185 | -10.412868 | 2.165954e-25 | 7.279729e-23 |
| 13 | ENSMUSG00000059173 | 2047.297734 | 1.290401 | -10.363868 | 3.620191e-25 | 1.128249e-22 |
| 14 | ENSMUSG00000044626 | 107.545685 | 1.479431 | -9.920675 | 3.384591e-23 | 9.833097e-21 |
| 15 | ENSMUSG00000029552 | 990.570372 | 0.942947 | -9.652480 | 4.798095e-22 | 1.305463e-19 |
| 16 | ENSMUSG00000000278 | 2246.095680 | 0.820046 | -9.477766 | 2.597862e-21 | 6.646262e-19 |
| 17 | ENSMUSG00000023067 | 3740.729262 | 0.935633 | -9.180521 | 4.290090e-20 | 1.035725e-17 |
| 18 | ENSMUSG00000021843 | 8362.210457 | 0.774680 | -8.942443 | 3.806602e-19 | 8.699862e-17 |
| 19 | ENSMUSG00000044258 | 622.236008 | 1.062715 | -8.723723 | 2.692001e-18 | 5.840961e-16 |
| 20 | ENSMUSG00000020205 | 1313.876243 | 1.029466 | -8.587091 | 8.919931e-18 | 1.842127e-15 |
| 21 | ENSMUSG00000037280 | 336.544531 | 1.119365 | -8.342550 | 7.270520e-17 | 1.432460e-14 |
| 22 | ENSMUSG00000027556 | 365.075577 | 1.161261 | -8.021451 | 1.045036e-15 | 1.968457e-13 |
| 23 | ENSMUSG00000031799 | 7421.027362 | 0.624473 | -7.913186 | 2.508835e-15 | 4.526730e-13 |
| 24 | ENSMUSG00000036905 | 1706.843435 | 0.709253 | -7.846027 | 4.294230e-15 | 7.435091e-13 |
| 25 | ENSMUSG00000044667 | 545.471721 | 0.867126 | -7.784684 | 6.988793e-15 | 1.163057e-12 |
| 26 | ENSMUSG00000021125 | 389.752252 | 0.884616 | -7.713982 | 1.219520e-14 | 1.953626e-12 |
| 27 | ENSMUSG00000025351 | 5138.213127 | 0.601866 | -7.593747 | 3.107838e-14 | 4.799230e-12 |
| 28 | ENSMUSG00000032666 | 5242.276743 | 0.592958 | -7.454353 | 9.030998e-14 | 1.346090e-11 |
| 29 | ENSMUSG00000019866 | 554.456799 | 0.850782 | -7.439136 | 1.013460e-13 | 1.459809e-11 |
| 30 | ENSMUSG00000025608 | 1575.642204 | 0.686405 | -7.364919 | 1.772542e-13 | 2.470174e-11 |
| 31 | ENSMUSG00000043336 | 572.398895 | 0.802930 | -7.234809 | 4.661851e-13 | 6.292031e-11 |
| 32 | ENSMUSG00000037940 | 265.079339 | 0.911853 | -7.210731 | 5.565229e-13 | 7.312611e-11 |
| 33 | ENSMUSG00000039364 | 194.167058 | 0.998772 | -6.998846 | 2.580798e-12 | 3.276849e-10 |
| 34 | ENSMUSG00000056749 | 345.920854 | 0.914688 | -6.969709 | 3.175962e-12 | 3.916486e-10 |
| 35 | ENSMUSG00000032802 | 17749.447535 | 0.598266 | -6.892196 | 5.493748e-12 | 6.585198e-10 |
| 36 | ENSMUSG00000024672 | 211.819493 | 0.887656 | -6.825385 | 8.769012e-12 | 1.022515e-09 |
| 37 | ENSMUSG00000010086 | 4098.481132 | -0.572777 | 6.720270 | 1.813879e-11 | 2.059053e-09 |
| 38 | ENSMUSG00000058665 | 29.247691 | 0.967621 | -6.683662 | 2.330438e-11 | 2.577164e-09 |
| 39 | ENSMUSG00000009596 | 58.610232 | 0.944848 | -6.642619 | 3.081587e-11 | 3.301343e-09 |
| 40 | ENSMUSG00000029306 | 515.056424 | 0.913920 | -6.578546 | 4.750698e-11 | 4.965348e-09 |
| 41 | ENSMUSG00000028525 | 1397.491979 | 0.579037 | -6.531912 | 6.493551e-11 | 6.625354e-09 |
| 42 | ENSMUSG00000044060 | 2919.794150 | 0.634026 | -6.424378 | 1.324101e-10 | 1.319559e-08 |
| 43 | ENSMUSG00000021871 | 1033.326078 | 0.621687 | -6.372998 | 1.853679e-10 | 1.805336e-08 |
| 44 | ENSMUSG00000026670 | 4392.649088 | 0.461576 | -6.338069 | 2.326619e-10 | 2.215588e-08 |
| 45 | ENSMUSG00000025723 | 3256.551545 | -0.668514 | 6.308321 | 2.820793e-10 | 2.627783e-08 |
| 46 | ENSMUSG00000058715 | 556.298426 | 0.735078 | -6.194826 | 5.834941e-10 | 5.320039e-08 |
| 47 | ENSMUSG00000000214 | 4138.211600 | -0.610492 | 6.070828 | 1.272524e-09 | 1.136059e-07 |
| 48 | ENSMUSG00000021411 | 477.330006 | 0.732723 | -6.026429 | 1.676222e-09 | 1.465924e-07 |
| 49 | ENSMUSG00000051209 | 145.343991 | 0.822896 | -5.958867 | 2.539931e-09 | 2.176848e-07 |
| 50 | ENSMUSG00000046223 | 471.768674 | 0.710971 | -5.915084 | 3.317058e-09 | 2.787141e-07 |
| 51 | ENSMUSG00000021996 | 6915.461113 | 0.554238 | -5.878588 | 4.137815e-09 | 3.394226e-07 |
| 52 | ENSMUSG00000022582 | 88.869956 | 0.845882 | -5.836138 | 5.342459e-09 | 4.319579e-07 |
| 53 | ENSMUSG00000075225 | 187.970746 | 0.762592 | -5.775902 | 7.654194e-09 | 6.046108e-07 |
| 54 | ENSMUSG00000039910 | 898.929113 | 0.706779 | -5.760166 | 8.403126e-09 | 6.517556e-07 |
| 55 | ENSMUSG00000025348 | 8836.099402 | 0.687449 | -5.706812 | 1.151120e-08 | 8.769487e-07 |
| 56 | ENSMUSG00000028145 | 2209.860304 | 0.477298 | -5.685315 | 1.305714e-08 | 9.773471e-07 |
| 57 | ENSMUSG00000024743 | 12173.281232 | -0.480565 | 5.650580 | 1.599070e-08 | 1.176380e-06 |
| 58 | ENSMUSG00000050315 | 661.302294 | 0.782864 | -5.630019 | 1.801894e-08 | 1.303218e-06 |
| 59 | ENSMUSG00000021565 | 1407.135648 | 0.641439 | -5.608616 | 2.039504e-08 | 1.450587e-06 |
| 60 | ENSMUSG00000053477 | 3221.484564 | 0.476041 | -5.551818 | 2.827136e-08 | 1.977956e-06 |
| 61 | ENSMUSG00000007613 | 1878.831124 | 0.555008 | -5.511270 | 3.562528e-08 | 2.452195e-06 |
| 62 | ENSMUSG00000003872 | 498.277117 | -0.614792 | 5.487667 | 4.072760e-08 | 2.759335e-06 |
| 63 | ENSMUSG00000060002 | 3216.792835 | 0.613103 | -5.473168 | 4.420617e-08 | 2.952715e-06 |
| 64 | ENSMUSG00000030399 | 1621.263042 | 0.200993 | -5.436427 | 5.435973e-08 | 3.556413e-06 |
| 65 | ENSMUSG00000045954 | 1547.190653 | 0.602709 | -5.420474 | 5.944109e-08 | 3.844829e-06 |
| 66 | ENSMUSG00000050730 | 1914.008502 | 0.490603 | -5.411401 | 6.253366e-08 | 3.990567e-06 |
| 67 | ENSMUSG00000024621 | 2058.520289 | 0.561670 | -5.392116 | 6.963283e-08 | 4.356118e-06 |
| 68 | ENSMUSG00000037348 | 2683.166398 | -0.453835 | 5.374706 | 7.670781e-08 | 4.746746e-06 |
| 69 | ENSMUSG00000040552 | 416.790372 | 0.638669 | -5.351247 | 8.735010e-08 | 5.328356e-06 |
| 70 | ENSMUSG00000020326 | 8930.360647 | 0.487337 | -5.334489 | 9.581412e-08 | 5.762631e-06 |
| 71 | ENSMUSG00000038151 | 69.583461 | 0.782195 | -5.311110 | 1.089594e-07 | 6.440249e-06 |
| 72 | ENSMUSG00000036062 | 74983.323382 | -0.453463 | 5.290473 | 1.220002e-07 | 7.112942e-06 |
| 73 | ENSMUSG00000020732 | 2187.919687 | -0.428484 | 5.278700 | 1.301033e-07 | 7.483561e-06 |
| 74 | ENSMUSG00000063889 | 640.069865 | 0.586185 | -5.270856 | 1.357893e-07 | 7.715518e-06 |
| 75 | ENSMUSG00000018845 | 111.480390 | 0.708201 | -5.246122 | 1.553341e-07 | 8.701247e-06 |
| 76 | ENSMUSG00000020099 | 464.164167 | -0.602612 | 5.210926 | 1.879007e-07 | 1.038969e-05 |
| 77 | ENSMUSG00000025318 | 6202.137797 | -0.541901 | 5.195926 | 2.037029e-07 | 1.111997e-05 |
| 78 | ENSMUSG00000026778 | 5643.562480 | -0.371148 | 5.163726 | 2.420823e-07 | 1.304885e-05 |
| 79 | ENSMUSG00000026674 | 3577.461644 | 0.561261 | -5.144960 | 2.675772e-07 | 1.424392e-05 |
| 80 | ENSMUSG00000040990 | 1922.697737 | 0.425620 | -5.124828 | 2.978093e-07 | 1.565874e-05 |
| 81 | ENSMUSG00000042826 | 1061.179181 | 0.541590 | -5.111255 | 3.200253e-07 | 1.662289e-05 |
| 82 | ENSMUSG00000041481 | 4975.589229 | -0.422457 | 5.097114 | 3.448701e-07 | 1.769886e-05 |
| 83 | ENSMUSG00000022902 | 17.415075 | 0.569847 | -5.073514 | 3.905364e-07 | 1.974686e-05 |
| 84 | ENSMUSG00000020798 | 54.631755 | 0.727070 | -5.057038 | 4.258182e-07 | 2.134196e-05 |
| 85 | ENSMUSG00000028072 | 7499.283874 | -0.545480 | 5.040457 | 4.644211e-07 | 2.300764e-05 |
| 86 | ENSMUSG00000025592 | 65.433682 | 0.740815 | -5.026139 | 5.004525e-07 | 2.450930e-05 |
| 87 | ENSMUSG00000022836 | 1330.233343 | 0.623212 | -5.016758 | 5.255078e-07 | 2.544556e-05 |
| 88 | ENSMUSG00000005045 | 3628.388469 | -0.426177 | 4.997166 | 5.817912e-07 | 2.779091e-05 |
| 89 | ENSMUSG00000025090 | 608.762834 | 0.543096 | -4.988483 | 6.085519e-07 | 2.881544e-05 |
| 90 | ENSMUSG00000000416 | 1155.098102 | 0.542034 | -4.956080 | 7.192943e-07 | 3.368695e-05 |
| 91 | ENSMUSG00000062760 | 4008.249143 | -0.416101 | 4.928459 | 8.288085e-07 | 3.839624e-05 |
| 92 | ENSMUSG00000033983 | 902.301269 | 0.462619 | -4.924519 | 8.456817e-07 | 3.875890e-05 |
| 93 | ENSMUSG00000020427 | 1337.503405 | 0.604765 | -4.910723 | 9.074128e-07 | 4.114805e-05 |
| 94 | ENSMUSG00000020737 | 6621.883776 | 0.416878 | -4.885709 | 1.030572e-06 | 4.624356e-05 |
| 95 | ENSMUSG00000037062 | 6076.458447 | 0.420008 | -4.881184 | 1.054506e-06 | 4.682715e-05 |
| 96 | ENSMUSG00000031382 | 45.167336 | 0.406106 | -4.867451 | 1.130467e-06 | 4.968546e-05 |
| 97 | ENSMUSG00000035576 | 464.441725 | -0.592566 | 4.849521 | 1.237598e-06 | 5.384179e-05 |
| 98 | ENSMUSG00000001349 | 148.230383 | 0.660789 | -4.841966 | 1.285610e-06 | 5.536844e-05 |
| 99 | ENSMUSG00000053063 | 392.418630 | 0.679222 | -4.825189 | 1.398703e-06 | 5.978657e-05 |
| 100 | ENSMUSG00000004609 | 275.760166 | 0.673551 | -4.811205 | 1.500234e-06 | 6.333868e-05 |
| 101 | ENSMUSG00000024873 | 562.289469 | -0.581251 | 4.794897 | 1.627581e-06 | 6.804478e-05 |
| 102 | ENSMUSG00000075511 | 1418.494601 | -0.454450 | 4.775298 | 1.794410e-06 | 7.429463e-05 |
| 103 | ENSMUSG00000004031 | 2248.642201 | -0.398909 | 4.753532 | 1.998932e-06 | 8.197055e-05 |
| 104 | ENSMUSG00000028459 | 150.698103 | 0.666142 | -4.738651 | 2.151452e-06 | 8.738872e-05 |
| 105 | ENSMUSG00000031519 | 65.708107 | 0.492228 | -4.719913 | 2.359458e-06 | 9.493774e-05 |
| 106 | ENSMUSG00000019966 | 4772.631620 | 0.423625 | -4.709819 | 2.479374e-06 | 9.883477e-05 |
| 107 | ENSMUSG00000040612 | 1708.813914 | 0.604766 | -4.693462 | 2.686198e-06 | 1.060924e-04 |
| 108 | ENSMUSG00000000682 | 484.846830 | 0.626666 | -4.680273 | 2.864929e-06 | 1.121181e-04 |
| 109 | ENSMUSG00000041653 | 935.219188 | -0.606189 | 4.674512 | 2.946540e-06 | 1.144430e-04 |
| 110 | ENSMUSG00000052921 | 484.158457 | 0.536571 | -4.646985 | 3.368215e-06 | 1.294497e-04 |
| 111 | ENSMUSG00000033350 | 4599.085909 | 0.551091 | -4.635570 | 3.559546e-06 | 1.355870e-04 |
| 112 | ENSMUSG00000078771 | 182.455994 | 0.620041 | -4.625054 | 3.745010e-06 | 1.413947e-04 |
| 113 | ENSMUSG00000030731 | 1060.826544 | -0.542463 | 4.611812 | 3.991747e-06 | 1.493942e-04 |
| 114 | ENSMUSG00000057897 | 2165.501453 | -0.393365 | 4.603239 | 4.159713e-06 | 1.543325e-04 |
| 115 | ENSMUSG00000021376 | 636.677868 | 0.560542 | -4.578840 | 4.675618e-06 | 1.712495e-04 |
| 116 | ENSMUSG00000015484 | 140.888497 | 0.673017 | -4.571208 | 4.849216e-06 | 1.768519e-04 |
| 117 | ENSMUSG00000024256 | 6083.247354 | 0.487655 | -4.557837 | 5.168315e-06 | 1.868989e-04 |
| 118 | ENSMUSG00000040724 | 6615.498840 | -0.317752 | 4.521351 | 6.144612e-06 | 2.203447e-04 |
| 119 | ENSMUSG00000039546 | 56.647051 | 0.667581 | -4.508363 | 6.532977e-06 | 2.327259e-04 |
| 120 | ENSMUSG00000029201 | 1776.636541 | 0.388157 | -4.494057 | 6.987887e-06 | 2.464596e-04 |
| 121 | ENSMUSG00000005220 | 118.438206 | 0.640279 | -4.483429 | 7.345319e-06 | 2.569513e-04 |
| 122 | ENSMUSG00000020458 | 53205.000765 | 0.377116 | -4.476709 | 7.580255e-06 | 2.630226e-04 |
| 123 | ENSMUSG00000048096 | 130.140644 | 0.657768 | -4.470087 | 7.818788e-06 | 2.691202e-04 |
| 124 | ENSMUSG00000075249 | 23.933902 | 0.529569 | -4.458699 | 8.245873e-06 | 2.815588e-04 |
| 125 | ENSMUSG00000062997 | 5890.793347 | 0.390708 | -4.449010 | 8.626681e-06 | 2.922331e-04 |
| 126 | ENSMUSG00000082329 | 27.549398 | -0.316849 | 4.429224 | 9.457291e-06 | 3.178577e-04 |
| 127 | ENSMUSG00000066477 | 457.333336 | -0.552386 | 4.413249 | 1.018310e-05 | 3.389291e-04 |
| 128 | ENSMUSG00000027800 | 1352.981210 | 0.480121 | -4.400013 | 1.082442e-05 | 3.574201e-04 |
| 129 | ENSMUSG00000058070 | 20208.608139 | -0.378708 | 4.392670 | 1.119671e-05 | 3.669653e-04 |
| 130 | ENSMUSG00000026880 | 2706.839047 | 0.449022 | -4.373607 | 1.222106e-05 | 3.967446e-04 |
| 131 | ENSMUSG00000025321 | 10607.677389 | 0.431241 | -4.361491 | 1.291788e-05 | 4.169970e-04 |
| 132 | ENSMUSG00000075270 | 2926.923451 | -0.408322 | 4.352885 | 1.343575e-05 | 4.304715e-04 |
| 133 | ENSMUSG00000058546 | 4217.501963 | 0.452739 | -4.343360 | 1.403199e-05 | 4.462381e-04 |
| 134 | ENSMUSG00000024349 | 492.890523 | 0.468243 | -4.333088 | 1.470324e-05 | 4.641402e-04 |
| 135 | ENSMUSG00000032036 | 1545.213929 | -0.412749 | 4.328413 | 1.501878e-05 | 4.704466e-04 |
| 136 | ENSMUSG00000027313 | 280.148989 | 0.573529 | -4.324163 | 1.531123e-05 | 4.744788e-04 |
| 137 | ENSMUSG00000032249 | 4214.430836 | 0.356434 | -4.319295 | 1.565285e-05 | 4.834333e-04 |
| 138 | ENSMUSG00000002012 | 450.459400 | -0.491098 | 4.310303 | 1.630308e-05 | 4.999127e-04 |
| 139 | ENSMUSG00000043832 | 150.109531 | 0.609018 | -4.307250 | 1.652967e-05 | 5.032594e-04 |
| 140 | ENSMUSG00000027208 | 523.843600 | 0.519336 | -4.297960 | 1.723771e-05 | 5.211139e-04 |
| 141 | ENSMUSG00000048899 | 6744.401771 | -0.349289 | 4.291974 | 1.770918e-05 | 5.316166e-04 |
| 142 | ENSMUSG00000049037 | 155.677742 | 0.608852 | -4.286058 | 1.818718e-05 | 5.427030e-04 |
| 143 | ENSMUSG00000094797 | 18.370489 | 0.358503 | -4.275262 | 1.909123e-05 | 5.651862e-04 |
| 144 | ENSMUSG00000021508 | 142.253613 | 0.629162 | -4.268241 | 1.970204e-05 | 5.801245e-04 |
| 145 | ENSMUSG00000059810 | 3919.962308 | -0.365216 | 4.259339 | 2.050325e-05 | 5.985518e-04 |
| 146 | ENSMUSG00000024789 | 1955.949602 | 0.381019 | -4.251012 | 2.128072e-05 | 6.172130e-04 |
| 147 | ENSMUSG00000032908 | 6283.349406 | -0.377863 | 4.243526 | 2.200346e-05 | 6.338846e-04 |
| 148 | ENSMUSG00000032269 | 5359.788720 | -0.545080 | 4.224672 | 2.392889e-05 | 6.847497e-04 |
| 149 | ENSMUSG00000043795 | 94.737661 | 0.612872 | -4.213025 | 2.519727e-05 | 7.150769e-04 |
| 150 | ENSMUSG00000058600 | 4786.732120 | 0.347805 | -4.204510 | 2.616484e-05 | 7.376506e-04 |
| 151 | ENSMUSG00000054277 | 3590.835421 | -0.344597 | 4.197494 | 2.698853e-05 | 7.556487e-04 |
| 152 | ENSMUSG00000062933 | 384.082182 | -0.592479 | 4.191350 | 2.772993e-05 | 7.716213e-04 |
| 153 | ENSMUSG00000035861 | 22.762075 | 0.528728 | -4.181275 | 2.898784e-05 | 8.014202e-04 |
| 154 | ENSMUSG00000036144 | 704.558374 | 0.482705 | -4.176654 | 2.958290e-05 | 8.126290e-04 |
| 155 | ENSMUSG00000082145 | 18.081713 | -0.315132 | 4.173833 | 2.995175e-05 | 8.175207e-04 |
| 156 | ENSMUSG00000026768 | 134.869847 | 0.609512 | -4.163156 | 3.138793e-05 | 8.512984e-04 |
| 157 | ENSMUSG00000005667 | 1392.797019 | 0.406644 | -4.156987 | 3.224728e-05 | 8.677404e-04 |
| 158 | ENSMUSG00000042895 | 26.892136 | 0.283982 | -4.151201 | 3.307356e-05 | 8.858029e-04 |
| 159 | ENSMUSG00000002908 | 1882.511166 | -0.429813 | 4.138458 | 3.496486e-05 | 9.292971e-04 |
| 160 | ENSMUSG00000026484 | 1079.820043 | 0.433964 | -4.133742 | 3.569035e-05 | 9.440869e-04 |
| 161 | ENSMUSG00000078453 | 407.984339 | 0.498521 | -4.127025 | 3.674860e-05 | 9.661163e-04 |
| 162 | ENSMUSG00000031962 | 393.447395 | -0.482314 | 4.101942 | 4.096965e-05 | 1.070519e-03 |
| 163 | ENSMUSG00000083863 | 82.380427 | 0.606053 | -4.093140 | 4.255705e-05 | 1.104757e-03 |
| 164 | ENSMUSG00000032925 | 1548.604347 | 0.482915 | -4.089063 | 4.331188e-05 | 1.118086e-03 |
| 165 | ENSMUSG00000074207 | 369.574207 | 0.524188 | -4.078387 | 4.534922e-05 | 1.163669e-03 |
| 166 | ENSMUSG00000026435 | 1479.800973 | -0.408509 | 4.071521 | 4.670711e-05 | 1.191379e-03 |
| 167 | ENSMUSG00000022217 | 2659.845733 | -0.437365 | 4.067594 | 4.750108e-05 | 1.204462e-03 |
| 168 | ENSMUSG00000015536 | 3903.413565 | 0.351420 | -4.061839 | 4.868759e-05 | 1.227285e-03 |
| 169 | ENSMUSG00000026981 | 67.297339 | 0.596874 | -4.052241 | 5.072928e-05 | 1.272811e-03 |
| 170 | ENSMUSG00000085905 | 38.615920 | 0.574895 | -4.043564 | 5.264488e-05 | 1.311607e-03 |
| 171 | ENSMUSG00000031245 | 279.135564 | 0.568970 | -4.040085 | 5.343192e-05 | 1.321611e-03 |
| 172 | ENSMUSG00000032253 | 3612.102225 | 0.430972 | -4.031820 | 5.534660e-05 | 1.363069e-03 |
| 173 | ENSMUSG00000025867 | 13926.271701 | -0.334032 | 4.028300 | 5.618151e-05 | 1.375725e-03 |
| 174 | ENSMUSG00000068798 | 2640.796289 | 0.419686 | -4.020269 | 5.813161e-05 | 1.415389e-03 |
| 175 | ENSMUSG00000025290 | 12628.526847 | 0.371852 | -4.011613 | 6.030528e-05 | 1.460018e-03 |
| 176 | ENSMUSG00000094335 | 20.686622 | 0.426406 | -4.003223 | 6.248541e-05 | 1.504301e-03 |
| 177 | ENSMUSG00000045318 | 775.498537 | -0.496834 | 4.000499 | 6.320902e-05 | 1.517205e-03 |
| 178 | ENSMUSG00000096931 | 35.233861 | 0.535329 | -3.994924 | 6.471497e-05 | 1.540666e-03 |
| 179 | ENSMUSG00000022895 | 1134.245840 | 0.410693 | -3.987475 | 6.678019e-05 | 1.581049e-03 |
| 180 | ENSMUSG00000045246 | 509.419290 | -0.491459 | 3.980554 | 6.875477e-05 | 1.618854e-03 |
| 181 | ENSMUSG00000023911 | 370.424747 | -0.492521 | 3.972239 | 7.120036e-05 | 1.667275e-03 |
| 182 | ENSMUSG00000030772 | 6967.211749 | -0.324692 | 3.955762 | 7.629094e-05 | 1.773005e-03 |
| 183 | ENSMUSG00000033306 | 2060.455679 | 0.389209 | -3.951667 | 7.760864e-05 | 1.797689e-03 |
| 184 | ENSMUSG00000031958 | 703.556060 | -0.411147 | 3.941892 | 8.084140e-05 | 1.862503e-03 |
| 185 | ENSMUSG00000049404 | 1872.396770 | -0.387567 | 3.936694 | 8.261182e-05 | 1.893114e-03 |
| 186 | ENSMUSG00000043154 | 1969.194245 | 0.329759 | -3.929912 | 8.497691e-05 | 1.934887e-03 |
| 187 | ENSMUSG00000030357 | 17250.957141 | -0.284794 | 3.909251 | 9.258278e-05 | 2.099155e-03 |
| 188 | ENSMUSG00000062078 | 11057.268805 | 0.433507 | -3.900608 | 9.595139e-05 | 2.161239e-03 |
| 189 | ENSMUSG00000018774 | 332.882443 | 0.506687 | -3.891611 | 9.958079e-05 | 2.234181e-03 |
| 190 | ENSMUSG00000022215 | 18.180890 | 0.263239 | -3.879550 | 1.046500e-04 | 2.333293e-03 |
| 191 | ENSMUSG00000075277 | 254.185811 | -0.483543 | 3.874812 | 1.067069e-04 | 2.369253e-03 |
| 192 | ENSMUSG00000006411 | 969.972500 | -0.377833 | 3.865833 | 1.107106e-04 | 2.445477e-03 |
| 193 | ENSMUSG00000060212 | 2673.217124 | -0.394651 | 3.857940 | 1.143467e-04 | 2.512843e-03 |
| 194 | ENSMUSG00000075602 | 974.623857 | 0.413818 | -3.848100 | 1.190377e-04 | 2.602582e-03 |
| 195 | ENSMUSG00000026305 | 1492.203785 | 0.350318 | -3.843718 | 1.211842e-04 | 2.632723e-03 |
| 196 | ENSMUSG00000021710 | 782.053114 | 0.371730 | -3.840828 | 1.226199e-04 | 2.653823e-03 |
| 197 | ENSMUSG00000026959 | 3255.882216 | -0.388816 | 3.834714 | 1.257103e-04 | 2.707035e-03 |
| 198 | ENSMUSG00000027997 | 313.742234 | 0.485476 | -3.829868 | 1.282120e-04 | 2.748783e-03 |
| 199 | ENSMUSG00000027347 | 11487.058826 | -0.328126 | 3.824952 | 1.307974e-04 | 2.785091e-03 |
Because SoS is based on Python 3.6, we can technically use SoS kernel to read the excel file, but we use a Python 3 kernel anyway:
In [2]:
We can then go to a R kernel and get data from the Python3 kernel
In [3]:
and use the ensembl library from bioconductor to get gene names from the Ensembl names in the data. The %preview magic previews the R variable.
In [4]:
Warning message:
%preview annotated
> annotated:
| ensembl_gene_id | baseMean | log2FoldChange | stat | pvalue | padj | external_gene_name |
|---|---|---|---|---|---|---|
| ENSMUSG00000000214 | 4138.211600 | -0.6104918 | 6.070828 | 1.272524e-09 | 1.136059e-07 | Th |
| ENSMUSG00000000278 | 2246.095680 | 0.8200463 | -9.477766 | 2.597862e-21 | 6.646262e-19 | Scpep1 |
| ENSMUSG00000000308 | 9818.688762 | -0.2338556 | 2.821715 | 4.776759e-03 | 3.975285e-02 | Ckmt1 |
| ENSMUSG00000000320 | 155.787128 | 0.2876111 | -1.986710 | 4.695454e-02 | 1.806179e-01 | Alox12 |
| ENSMUSG00000000416 | 1155.098102 | 0.5420341 | -4.956080 | 7.192943e-07 | 3.368695e-05 | Cttnbp2 |
| ENSMUSG00000000420 | 3554.753276 | 0.2553115 | -3.232391 | 1.227588e-03 | 1.514909e-02 | Galnt1 |
| ENSMUSG00000000627 | 4476.218886 | 0.2718751 | -2.310253 | 2.087415e-02 | 1.067084e-01 | Sema4f |
| ENSMUSG00000000628 | 319.764340 | 0.4280945 | -2.946737 | 3.211462e-03 | 2.997037e-02 | Hk2 |
| ENSMUSG00000000682 | 484.846830 | 0.6266664 | -4.680273 | 2.864929e-06 | 1.121181e-04 | Cd52 |
| ENSMUSG00000000730 | 7.627173 | 0.2362571 | -2.682550 | 7.306328e-03 | NA | Dnmt3l |
| ENSMUSG00000000743 | 4563.611985 | -0.2508448 | 2.641865 | 8.245084e-03 | 5.726458e-02 | Chmp1a |
| ENSMUSG00000000751 | 3874.653413 | -0.2331316 | 2.954892 | 3.127784e-03 | 2.945788e-02 | Rpa1 |
| ENSMUSG00000000794 | 77.932213 | -0.2945470 | 2.003576 | 4.511548e-02 | 1.763317e-01 | Kcnn3 |
| ENSMUSG00000001025 | 17006.747340 | -0.2574028 | 2.833605 | 4.602618e-03 | 3.874925e-02 | S100a6 |
| ENSMUSG00000001280 | 2383.288580 | 0.2246021 | -2.467233 | 1.361619e-02 | 8.035354e-02 | Sp1 |
| ENSMUSG00000001333 | 1162.464914 | -0.2255600 | 2.420478 | 1.550010e-02 | 8.749375e-02 | Sync |
| ENSMUSG00000001349 | 148.230383 | 0.6607889 | -4.841966 | 1.285610e-06 | 5.536844e-05 | Cnn1 |
| ENSMUSG00000001380 | 7918.922528 | 0.1824277 | -2.565276 | 1.030939e-02 | 6.648355e-02 | Hars |
| ENSMUSG00000001415 | 4248.668568 | -0.2422268 | 2.539732 | 1.109373e-02 | 6.998002e-02 | Smg5 |
| ENSMUSG00000001436 | 1263.258383 | -0.2358637 | 2.236040 | 2.534914e-02 | 1.219163e-01 | Slc19a1 |
| ENSMUSG00000001700 | 311.687287 | 0.3393851 | -2.773708 | 5.542144e-03 | 4.412350e-02 | Gramd3 |
| ENSMUSG00000001755 | 1499.568213 | -0.2106140 | 2.275383 | 2.288294e-02 | 1.134287e-01 | Coasy |
| ENSMUSG00000001774 | 4364.573704 | 0.2430831 | -2.494867 | 1.260045e-02 | 7.610440e-02 | Chordc1 |
| ENSMUSG00000001847 | 12823.805954 | 0.1778602 | -2.162103 | 3.061020e-02 | 1.377861e-01 | Rac1 |
| ENSMUSG00000001865 | 509.589410 | 0.4566291 | -3.556262 | 3.761693e-04 | 6.278402e-03 | Cpa3 |
| ENSMUSG00000001870 | 762.307906 | 0.3557346 | -3.267733 | 1.084126e-03 | 1.391985e-02 | Ltbp1 |
| ENSMUSG00000001909 | 1565.248475 | -0.2889704 | 3.250489 | 1.152069e-03 | 1.453099e-02 | Trmt1 |
| ENSMUSG00000001911 | 1633.174086 | 0.2427731 | -2.141406 | 3.224132e-02 | 1.423618e-01 | Nfix |
| ENSMUSG00000001924 | 24575.966751 | -0.2108731 | 2.320610 | 2.030790e-02 | 1.048171e-01 | Uba1 |
| ENSMUSG00000001964 | 1547.844892 | 0.1863153 | -2.199904 | 2.781371e-02 | 1.294123e-01 | Emd |
| ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ |
| ENSMUSG00000094335 | 20.686622 | 0.42640562 | -4.003223 | 6.248541e-05 | 0.0015043012 | Igkv1-117 |
| ENSMUSG00000094546 | 64.161416 | 0.07526115 | -2.260089 | 2.381575e-02 | 0.1167772425 | Ighv1-26 |
| ENSMUSG00000094626 | 22.445892 | 0.27654076 | -2.095705 | 3.610832e-02 | 0.1530875042 | Tmem121b |
| ENSMUSG00000094732 | 3.633133 | 0.14851581 | -3.182034 | 1.462445e-03 | NA | 1500015L24Rik |
| ENSMUSG00000094797 | 18.370489 | 0.35850328 | -4.275262 | 1.909123e-05 | 0.0005651862 | Igkv6-15 |
| ENSMUSG00000095028 | 17.748802 | 0.22071387 | -1.964435 | 4.947964e-02 | 0.1864842910 | Sirpb1b |
| ENSMUSG00000095362 | 1014.129481 | 0.33930276 | -2.507800 | 1.214854e-02 | 0.0741588770 | Gm14325 |
| ENSMUSG00000095918 | 8.390640 | 0.23178587 | -3.035931 | 2.397942e-03 | NA | Gm5861 |
| ENSMUSG00000096403 | 29.135621 | -0.24779867 | 3.079376 | 2.074344e-03 | 0.0222366002 | Gm9825 |
| ENSMUSG00000096459 | 14.669469 | 0.21227296 | -2.909286 | 3.622557e-03 | 0.0327782193 | Ighv9-3 |
| ENSMUSG00000096490 | 51.152757 | 0.07584179 | -3.109132 | 1.876381e-03 | 0.0207369783 | Igkv10-94 |
| ENSMUSG00000096715 | 16.382006 | 0.27253764 | -3.301588 | 9.613918e-04 | 0.0128043637 | Igkv3-4 |
| ENSMUSG00000096780 | 124.903362 | -0.34382425 | 2.328241 | 1.989932e-02 | 0.1034559469 | Tmem181b-ps |
| ENSMUSG00000096847 | 2633.169634 | -0.42194215 | 3.709991 | 2.072666e-04 | 0.0039562996 | Tmem151b |
| ENSMUSG00000096931 | 35.233861 | 0.53532942 | -3.994924 | 6.471497e-05 | 0.0015406656 | Gm26656 |
| ENSMUSG00000096965 | 2.868267 | 0.11022564 | -2.252913 | 2.426467e-02 | NA | 3300005D01Rik |
| ENSMUSG00000097047 | 29.021538 | 0.30269031 | -2.223309 | 2.619498e-02 | 0.1244824421 | 1110020A21Rik |
| ENSMUSG00000097180 | 53.448333 | 0.32390828 | -2.222511 | 2.624878e-02 | 0.1245999453 | 2700038G22Rik |
| ENSMUSG00000097357 | 107.212979 | 0.40217004 | -2.821819 | 4.775216e-03 | 0.0397528498 | Gm16793 |
| ENSMUSG00000097375 | 196.255308 | 0.37877733 | -2.808336 | 4.979819e-03 | 0.0409592491 | 6720427I07Rik |
| ENSMUSG00000097404 | 101.130734 | -0.31233829 | 2.122148 | 3.382527e-02 | 0.1464508726 | Gm10814 |
| ENSMUSG00000097466 | 145.564341 | 0.38068267 | -2.630043 | 8.537396e-03 | 0.0584890902 | D430036J16Rik |
| ENSMUSG00000097576 | 15.619078 | 0.25088628 | -2.140711 | 3.229731e-02 | 0.1424989027 | D930030I03Rik |
| ENSMUSG00000097622 | 63.268414 | -0.47408131 | 3.199273 | 1.377745e-03 | 0.0165030907 | A330033J07Rik |
| ENSMUSG00000097645 | 11.668458 | 0.20785568 | -2.153071 | 3.131308e-02 | NA | Gm26863 |
| ENSMUSG00000097908 | 219.536423 | -0.28505132 | 2.258253 | 2.392987e-02 | 0.1171278958 | 4933404O12Rik |
| ENSMUSG00000098276 | 6.499809 | 0.22822696 | -3.102306 | 1.920195e-03 | NA | Mir6358 |
| ENSMUSG00000098318 | 16.721908 | 0.24041191 | -2.126204 | 3.348625e-02 | 0.1454238144 | Lockd |
| ENSMUSG00000098482 | 192.980606 | 0.35082491 | -2.511948 | 1.200668e-02 | 0.0737129485 | Mir6363 |
| ENSMUSG00000098973 | 3337.553280 | 0.48588812 | -3.340461 | 8.363935e-04 | 0.0114601289 | Mir6236 |
We can also draw some plot and preview the result. Instead of displaying the result directly in the notebook, the R code saves the image in a file (so that it can be shared with others separately) and use the %preview magic to display it in the notebook.
In [5]:
pdf: 2
%preview result.png
> result.png (22.0 KiB):
After we confirm that the result is correct, we can transfer the data back to Python and write in excel format.
In [6]:
As a good practice, a %sessioninfo magic should be used at the end of all SoS Notebooks to show the session information of all kernels involved.
In [7]:
SoS
| SoS Version | 0.16.12 |
|---|
Python3
| Kernel | python3 |
|---|---|
| Language | Python3 |
| Version | 3.6.6 |Anaconda, Inc.| (default, Jun 28 2018, 11:07:29) [GCC 4.2.1 Compatible Clang 4.0.1 (tags/RELEASE_401/final)] |
| pandas | 0.23.4 |
R
| Kernel | ir |
|---|---|
| Language | R |
R version 3.4.2 (2017-09-28) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Sierra 10.12.5 Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_2.34.2 feather_0.3.1 loaded via a namespace (and not attached): [1] Rcpp_0.12.18 pillar_1.3.0 compiler_3.4.2 [4] prettyunits_1.0.2 progress_1.2.0 bitops_1.0-6 [7] base64enc_0.1-3 tools_3.4.2 digest_0.6.15 [10] uuid_0.1-2 bit_1.1-14 jsonlite_1.5 [13] evaluate_0.11 RSQLite_2.1.1 memoise_1.1.0 [16] tibble_1.4.2 pkgconfig_2.0.2 rlang_0.2.2 [19] IRdisplay_0.5.0 DBI_1.0.0 curl_3.2 [22] IRkernel_0.8.12.9000 parallel_3.4.2 httr_1.3.1 [25] repr_0.15.0 stringr_1.3.1 S4Vectors_0.16.0 [28] hms_0.4.2 IRanges_2.12.0 stats4_3.4.2 [31] bit64_0.9-7 Biobase_2.38.0 R6_2.2.2 [34] AnnotationDbi_1.40.0 XML_3.98-1.16 pbdZMQ_0.3-3 [37] blob_1.1.1 magrittr_1.5 htmltools_0.3.6 [40] BiocGenerics_0.24.0 assertthat_0.2.0 stringi_1.2.4 [43] RCurl_1.95-4.11 crayon_1.3.4 |
|