generated from stjude-biohackathon/KIDS24-team
-
Notifications
You must be signed in to change notification settings - Fork 1
/
DESCRIPTION
59 lines (59 loc) · 2.11 KB
/
DESCRIPTION
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
Package: ECLIPSE
Title: Enhancer Calling and Linking with Integrated Profiling and Structure Evaluation
Version: 0.99.0.9000
Authors@R: c(
person("Jared", "Andrews", , "[email protected]", role = c("aut", "cre"),
comment = c(ORCID = "0000-0002-0780-6248")),
person("Alyssa", "Obermayer", role = "aut"),
person("Kelly", "McCastlain", role = "aut"),
person("Jacqueline", "Myers", role = "aut"),
person("Nicolas", "Peterson", role = "aut"),
person("Avery", "Bradley", role = "aut"),
person("Young Lab - Whitehead Institute for Biomedical Research", role = "cph",
comment = "Author of included original ROSE thresholding code."))
Description: ECLIPSE provides a performant implementation of the rank ordering of super enhancers (ROSE) method for identifying super enhancers.
It provides options to increase the robustness of ROSE via signal transformations prior to thresholding and additional thresholding approaches.
It also increases flexibility by exposing parameters hidden in the original implementation.
ECLIPSE additionally contains novel functionality to identify sub-structural changes within enhancer regions between groups via sliding window and binning approaches.
It also contains visualization functions to generate high-quality plots of specific loci alongside arbitrary user-provided data.
URL: https://github.com/stjude-biohackathon/ECLIPSE
BugReports: https://github.com/stjude-biohackathon/ECLIPSE/issues
License: MIT
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Imports:
BiocParallel,
genomation,
GenomicRanges,
graphics,
HelloRanges,
IRanges,
Rsamtools,
rtracklayer,
S4Vectors,
stats
Suggests:
BiocStyle,
knitr,
testthat (>= 3.0.0),
rmarkdown,
ENCODExplorer
Depends:
R (>= 4.4.0)
biocViews:
Software,
Sequencing,
Visualization,
MultipleComparison,
Normalization,
DifferentialPeakCalling,
GeneRegulation,
HistoneModification,
PeakDetection,
Epigenetics,
ShinyApps,
Classification
LazyData: false
Config/testthat/edition: 3
VignetteBuilder: knitr