MRCT is a program could find hub structure and coexpression module.
More information related the method, see this link.
For the R codes which could reproduce the result of "MRHCA: A nonparametric statistics based method for hub and co-expression module identification in large gene co-expression network", see this link.
git clone --recursive https://github.com/zy26/mrct.git
cd mrct/
Or, you can just click Clone or download under the repository name, then put the code files of libmrct to lib dir.
You may need g++ version >= 5.40.
g++ -std=c++14 -fopenmp -O3 lib/*.cc src/*.cc
./a.out -i testdata/E_coli_anaerobic.txt -o E_coli_anaerobic.id.txt -e E_coli_anaerobic.mr.txt -t 0.9
Use Visual Studio project file mrct.vcxproj inside. You may need modify the Platform Toolset to the version on your PC (You will need Visual Studio 2019 or higher to allow unsigned int for the OpenMP loop counter).
The Command Arguments should be -i testdata/E_coli_anaerobic.txt -o E_coli_anaerobic.id.txt -e E_coli_anaerobic.mr.txt -t 0.9, or you can use your file name instead.
Warning: Try to avoid Debug mode, it may be very slow.
You will see the content of the first output file (E_coli_anaerobic.id.txt) as below somehow.
1 0 1639 979 b3385
1 0 1589 1232 b0421
1 0 1583 2167 b3649
1 0 1559 535 b0184
1 0 1549 3789 b4557
1 0 1547 2562 b3833
1 0 1532 2777 b0434
1 0 1528 960 b3560
1 0 1520 2837 b0637
1 0 1512 2115 b3704
1 0 1506 3861 b3999
1 0 1501 13 b3255
1 0 1496 1880 b4201
1 0 1481 698 b2610
1 0 1480 2425 b3838
1 0 1462 2112 b0183
1 0 1458 1049 b3997
1 0 1447 496 b3639
1 0 1433 2103 b0953
1 0 1426 1099 b4372
1 0 1417 1335 b3200
1 0 1414 2032 b3620
1 0 1409 2521 b2960
1 0 1406 566 b3640
1 0 1406 2113 b0610
1 0 1406 2133 b3985
1 0 1395 2489 b3035
1 0 1392 2520 b3651
1 0 1386 3769 b3611
1 0 1382 1340 b0179
1 0 1374 3770 b3614
1 0 1365 2066 b3783
1 0 1367 3727 b3499
1 0 1359 992 b3610
1 0 1344 1480 b1782
1 0 1342 2836 b0636
1 0 1340 2176 b3341
1 0 1330 1894 b1831
1 0 1325 1234 b2747
1 0 1315 2183 b3307
1 0 1315 4185 b2792
1 0 1314 2519 b2607
1 0 1314 823 b2748
1 0 1310 2126 b3984
1 0 1305 2134 b3983
1 0 1301 2181 b3342
1 0 1293 1694 b3982
1 0 1289 1305 b2828
1 0 1284 1551 b0923
1 0 1282 801 b0172
1 0 1273 1236 b2746
1 0 1265 197 b3734
1 0 1254 2336 b3641
1 0 1253 203 b3733
1 0 1245 4267 b4212
1 0 1232 204 b3735
1 0 1230 2784 b0471
1 0 1228 1336 b3201
1 0 1234 3746 b3552
1 0 1208 2539 b0170
1 0 1198 3592 b2953
1 0 1200 3104 b1447
1 0 1188 3498 b2643
1 0 1179 4245 b3199
1 0 1175 2204 b0176
1 0 1170 2146 b3318
1 0 1174 2292 b3981
1 0 1162 1828 b3821
1 0 1164 2030 b3619
1 0 1160 1762 b2320
1 0 1171 3606 b2986
1 0 1136 2535 b2745
1 0 1124 846 b3340
1 0 1139 1048 b3804
1 0 1134 2427 b4483
1 0 1119 2849 b0699
1 0 1116 2122 b3643
1 0 1121 2972 b1034
1 0 1101 4243 b3195
1 0 1087 3788 b3705
1 0 1078 1854 b4226
1 0 1077 3285 b1978
1 0 1086 2168 b2830
1 0 1070 3603 b2983
1 0 1068 2932 b0898
1 0 1052 969 b2029
1 0 1077 3231 b1803
1 0 1051 3736 b3527
1 0 1025 4242 b3194
1 0 1016 363 b0624
1 0 1030 1900 b0331
1 0 979 3328 b2122
1 0 977 4175 b2647
1 0 969 3417 b2358
1 139 0 2013 b3700
1 0 972 3416 b2357
1 0 977 2742 b0285
1 0 975 1477 b1175
1 0 937 1158 b2490
1 0 942 277 b1987
1 0 924 4176 b2650
1 0 951 1534 b2113
1 0 932 2528 b1265
1 0 896 2875 b0718
1 0 933 2034 b3842
1 0 876 2060 b3901
1 0 881 2811 b0521
1 0 853 3421 b2362
1 372 0 2233 b1012
1 0 901 1252 b3526
1 0 848 2640 b2047
1 0 840 809 b3897
1 0 836 3536 b2770
1 0 844 4094 b1585
1 0 885 1825 b2648
1 0 865 1253 b1827
1 364 0 3073 b1360
1 131 0 2612 b1914
1 0 834 3032 b1251
1 0 813 340 b2933
1 293 0 2302 b2913
1 0 816 2639 b2050
1 0 849 3835 b3878
1 0 819 1757 b3403
1 0 840 3196 b1724
1 183 0 3244 b1832
1 324 0 2747 b0291
1 135 0 3007 b1179
1 289 0 1570 b0750
1 0 801 2865 b0719
1 308 0 1295 b0075
1 0 805 3190 b1698
1 0 791 2727 b0267
1 0 799 1801 b4105
1 373 0 3535 b2769
1 291 0 1443 b3008
1 0 792 661 b1701
1 357 0 2746 b0290
1 315 0 3418 b2359
1 0 786 3078 b1407
1 0 779 4171 b2547
1 0 781 3629 b3080
1 221 0 2455 b2103
1 288 0 127 b3172
1 0 779 3415 b2356
1 0 781 2307 b1975
1 0 781 3913 b4183
1 0 773 2952 b0941
1 0 784 2467 b0002
1 374 0 1248 b3137
1 371 0 3912 b4182
1 253 0 121 b2818
1 247 0 126 b0273
1 318 0 3385 b2294
1 0 768 2859 b0682
1 368 0 122 b3959
1 0 768 2647 b2061
1 231 0 1194 b0077
1 201 0 123 b3958
1 367 0 1730 b1392
1 211 0 2463 b2104
1 214 0 1290 b0074
1 0 761 153 b0754
1 304 0 1727 b1389
1 0 738 795 b4474
1 346 0 3456 b2506
1 228 0 167 b0860
1 218 0 1193 b0078
1 325 0 7 b1338
1 177 0 1957 b1302
1 0 738 359 b2048
1 254 0 2085 b1066
1 209 0 158 b0112
1 0 736 4017 b4572
1 233 0 1293 b0071
1 207 0 2459 b3990
1 223 0 2526 b1263
1 236 0 1639 b3661
1 219 0 1444 b3829
1 237 0 1292 b0072
1 233 0 3626 b3074
1 210 0 889 b1761
1 239 0 124 b3359
1 309 0 2642 b2044
1 212 0 376 b1040
1 199 0 1441 b4013
1 202 0 1291 b0073
1 206 0 378 b1038
1 224 0 129 b4254
1 220 0 3582 b2930
1 218 0 2523 b1260
1 141 0 2939 b0906
1 136 0 665 b2097
1 131 0 2420 b1519
That means: We find 194 hubs. The second column is the cluster bound of the cluster. The third column is a upper bound of the cluster. The forth column is the index of the original rows in the matrix of the input file. The last column is the row names of the forth column.
We can use the R package fix the thrid column later.
We have another output file, the first column in it is the same as the forth column of the file below. Other columns are the EM values for that row.