TReNA

Fit transcriptional regulatory networks using gene expression, priors, machine learning

Getting Started

To build and test:

  • clone this repository
  • install R 3.2.3 or later; RUnit 0.4.31 or later (see below)
  • install the following solver packages:
  • glmnet R package 2.0.3 or later
  • randomForest
  • vbsr
  • flare
  • lassopv
  • cd TReNA
  • R CMD INSTALL .

The most reliable way to install package dependencies (and other of their dependencies):

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install(c("glmnet", "RUnit"))

Using TReNA

  • open an R session
  • source(“inst/unitTests/test_TReNA.R”)
  • runTests() unitTests perform double duty: they ensure the package performs as (currently) expected; they introduce the package to the user and developer. Thus test_TReNA.R is one entry point into this project.

We have also created a Jupyter Notebook demonstrating use of TReNA with 4 different solvers

Table of BDDS Databases (2017/11/13)

Name Footprints.in.millions Tissue Method Seed
1 adrenal_gland_hint_20 33.5 adrenal_gland hint 20
2 adrenal_gland_hint_16 81.4 adrenal_gland hint 16
3 adrenal_gland_wellington_16 24.3 adrenal_gland wellington 16
4 adrenal_gland_wellington_20 24.8 adrenal_gland wellington 20
5 blood_vessel_hint_20 311.0 blood_vessel hint 20
6 blood_vessel_hint_16 315.7 blood_vessel hint 16
7 blood_vessel_wellington_20 60.0 blood_vessel wellington 20
8 blood_vessel_wellington_16 60.6 blood_vessel wellington 16
9 bone_element_hint_20 33.5 bone_element hint 20
10 bone_element_hint_16 33.8 bone_element hint 16
11 bone_element_wellington_16 7.1 bone_element wellington 16
12 bone_element_wellington_20 7.2 bone_element wellington 20
13 brain_hint_16 839.8 brain hint 16
14 brain_hint_20 865.3 brain hint 20
15 brain_wellington_16 228.4 brain wellington 16
16 brain_wellington_20 248.1 brain wellington 20
17 bronchus_hint_20 33.5 bronchus hint 20
18 bronchus_hint_16 62.8 bronchus hint 16
19 bronchus_wellington_16 13.1 bronchus wellington 16
20 bronchus_wellington_20 7.2 bronchus wellington 20
21 esophagus_hint_16 38.3 esophagus hint 16
22 esophagus_hint_20 55.2 esophagus hint 20
23 esophagus_wellington_20 17.6 esophagus wellington 20
24 esophagus_wellington_16 8.4 esophagus wellington 16
25 extraembryonic_structure_hint_16 386.2 extraembryonic_structure hint 16
26 extraembryonic_structure_hint_20 391.7 extraembryonic_structure hint 20
27 extraembryonic_structure_wellington_16 119.7 extraembryonic_structure wellington 16
28 extraembryonic_structure_wellington_20 122.9 extraembryonic_structure wellington 20
29 eye_hint_20 322.6 eye hint 20
30 eye_hint_16 324.3 eye hint 16
31 eye_wellington_20 81.8 eye wellington 20
32 eye_wellington_16 82.9 eye wellington 16
33 gonad_hint_20 39.9 gonad hint 20
34 gonad_hint_16 72.6 gonad hint 16
35 gonad_wellington_20 22.2 gonad wellington 20
36 gonad_wellington_16 26.0 gonad wellington 16
37 heart_hint_16 250.2 heart hint 16
38 heart_hint_20 295.4 heart hint 20
39 heart_wellington_16 64.5 heart wellington 16
40 heart_wellington_20 80.9 heart wellington 20
41 kidney_hint_20 289.5 kidney hint 20
42 kidney_hint_16 289.5 kidney hint 16
43 kidney_wellington_16 73.6 kidney wellington 16
44 kidney_wellington_20 74.3 kidney wellington 20
45 large_intestine_hint_16 120.7 large_intestine hint 16
46 large_intestine_hint_20 126.0 large_intestine hint 20
47 large_intestine_wellington_16 46.2 large_intestine wellington 16
48 large_intestine_wellington_20 55.6 large_intestine wellington 20
49 liver_hint_16 103.0 liver hint 16
50 liver_hint_20 63.1 liver hint 20
51 liver_wellington_20 22.0 liver wellington 20
52 liver_wellington_16 39.5 liver wellington 16
53 lung_hint_20 252.4 lung hint 20
54 lung_hint_16 255.5 lung hint 16
55 lung_wellington_16 55.1 lung wellington 16
56 lung_wellington_20 56.3 lung wellington 20
57 lymphatic_vessel_hint_20 58.4 lymphatic_vessel hint 20
58 lymphatic_vessel_hint_16 59.0 lymphatic_vessel hint 16
59 lymphatic_vessel_wellington_20 10.2 lymphatic_vessel wellington 20
60 lymphatic_vessel_wellington_16 10.2 lymphatic_vessel wellington 16
61 lymphoblast_hint_16 483.6 lymphoblast hint 16
62 lymphoblast_hint_20 498.0 lymphoblast hint 20
63 lymphoblast_wellington_16 150.0 lymphoblast wellington 16
64 lymphoblast_wellington_20 155.8 lymphoblast wellington 20
65 mammary_gland_hint_20 58.6 mammary_gland hint 20
66 mammary_gland_hint_16 59.0 mammary_gland hint 16
67 mammary_gland_wellington_20 11.0 mammary_gland wellington 20
68 mammary_gland_wellington_16 11.0 mammary_gland wellington 16
69 mouth_hint_20 156.6 mouth hint 20
70 mouth_hint_16 156.7 mouth hint 16
71 mouth_wellington_16 39.7 mouth wellington 16
72 mouth_wellington_20 40.0 mouth wellington 20
73 muscle_organ_hint_16 112.3 muscle_organ hint 16
74 muscle_organ_hint_20 116.7 muscle_organ hint 20
75 muscle_organ_wellington_16 28.4 muscle_organ wellington 16
76 muscle_organ_wellington_20 30.3 muscle_organ wellington 20
77 pancreas_hint_16 63.9 pancreas hint 16
78 pancreas_hint_20 81.1 pancreas hint 20
79 pancreas_wellington_16 25.2 pancreas wellington 16
80 pancreas_wellington_20 36.4 pancreas wellington 20
81 prostate_gland_hint_16 44.6 prostate_gland hint 16
82 prostate_gland_hint_20 49.7 prostate_gland hint 20
83 prostate_gland_wellington_16 12.5 prostate_gland wellington 16
84 prostate_gland_wellington_20 17.7 prostate_gland wellington 20
85 skin_hint_16 1281.2 skin hint 16
86 skin_hint_20 1317.1 skin hint 20
87 skin_wellington_20 0.0 skin wellington 20
88 skin_wellington_16 287.2 skin wellington 16
89 spinal_cord_hint_16 82.2 spinal_cord hint 16
90 spinal_cord_hint_20 87.4 spinal_cord hint 20
91 spinal_cord_wellington_16 20.0 spinal_cord wellington 16
92 spinal_cord_wellington_20 21.2 spinal_cord wellington 20
93 stomach_hint_20 51.4 stomach hint 20
94 stomach_hint_16 52.1 stomach hint 16
95 stomach_wellington_20 16.2 stomach wellington 20
96 stomach_wellington_16 16.4 stomach wellington 16
97 thyroid_gland_hint_20 103.4 thyroid_gland hint 20
98 thyroid_gland_hint_16 93.0 thyroid_gland hint 16
99 thyroid_gland_wellington_16 31.2 thyroid_gland wellington 16
100 thyroid_gland_wellington_20 39.6 thyroid_gland wellington 20
101 tongue_hint_16 98.5 tongue hint 16
102 tongue_hint_20 99.9 tongue hint 20
103 tongue_wellington_16 28.2 tongue wellington 16
104 tongue_wellington_20 28.9 tongue wellington 20
105 urinary_bladder_hint_20 24.0 urinary_bladder hint 20
106 urinary_bladder_hint_16 24.2 urinary_bladder hint 16
107 urinary_bladder_wellington_16 8.1 urinary_bladder wellington 16
108 urinary_bladder_wellington_20 8.2 urinary_bladder wellington 20