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