README.md

In PriceLab/trena-until-01mar2018: Fit transcriptional regulatory networks using gene expression, priors, machine learning

TReNA

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

Direct queries to the footprint databases explained here

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):

source("http://bioconductor.org/biocLite.R")
biocLite(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

PriceLab/trena-until-01mar2018 documentation built on May 25, 2019, 1:22 p.m.