trena/DESCRIPTION at master · PriceLab/trena · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
Package: trena
Type: Package
Title: Fit transcriptional regulatory networks using gene expression, priors, machine learning
Version: 2.0.10
Date: 2023-03-13
Author: Paul Shannon <pshannon@systemsbioloyg.org>, Matthew Richards <mrichard@systemsbiology.org>
Maintainer: Paul Shannon <paul.thurmond.shannon@gmail.com>
Imports:
    RSQLite,
    RMySQL,
    lassopv,
    randomForest,
    xgboost,
    RPostgreSQL,
    methods,
    DBI,
    BSgenome,
    BSgenome.Hsapiens.UCSC.hg38,
    BSgenome.Hsapiens.UCSC.hg19,
    BSgenome.Mmusculus.UCSC.mm10,
    SNPlocs.Hsapiens.dbSNP150.GRCh38,
    org.Hs.eg.db,
    Biostrings,
    GenomicRanges,
    biomaRt,
    AnnotationDbi,
    WGCNA
Depends:
    R (>= 3.5.0),
    R6,
    data.table,
    utils,
    glmnet (>= 2.0.3),
    MotifDb (>= 1.19.17)
Suggests:
    RUnit,
    plyr,
    knitr,
    BiocGenerics,
    rmarkdown,
    formatR,
    markdown,
    BiocParallel,
    BSgenome.Scerevisiae.UCSC.sacCer3,
    BSgenome.Athaliana.TAIR.TAIR9
URL: https://pricelab.github.io/trena/
BugReports: https://github.com/PriceLab/trena/issues
VignetteBuilder:
    knitr, rmarkdown, formatR, markdown
Description: Methods for reconstructing transcriptional regulatory networks, especially in species
    for which genome-wide TF binding site information is available.
License: GPL-3
biocViews: Transcription, GeneRegulation, NetworkInference, FeatureExtraction, Regression,
    SystemsBiology, GeneExpression
Collate:
    'Solver.R'
    'BicorSolver.R'
    'CandidateFilter.R'
    'EnsembleSolver.R'
    'FeatureTable.R'
    'FootprintFinder.R'
    'FootprintFilter.R'
    'GeneOntologyFilter.R'
    'HumanDHSFilter.R'
    'LassoPVSolver.R'
    'LassoSolver.R'
    'MotifMatcher.R'
    'PCAMax.R'
    'PearsonSolver.R'
    'RandomForestSolver.R'
    'RidgeSolver.R'
    'SpearmanSolver.R'
    'Trena.R'
    'VarianceFilter.R'
    'XGBoostSolver.R'
    'help.R'
    'sharedFunctions.R'
    'utils.R'
Encoding: UTF-8
RoxygenNote: 7.2.1