-
Notifications
You must be signed in to change notification settings - Fork 5
/
DESCRIPTION
81 lines (81 loc) · 1.94 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
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
Package: APL
Type: Package
Title: Association Plots
Version: 1.9.0
Authors@R:
c(person(given = "Clemens",
family = "Kohl",
role = c("cre", "aut"),
email = "kohl.clemens@gmail.com"),
person(given = "Elzbieta",
family = "Gralinska", role = c("aut"),
email = "gralinska@molgen.mpg.de"),
person(given = "Martin",
family = "Vingron",
role = c("aut"),
email = "vingron@molgen.mpg.de"))
Description: APL is a package developed for computation of Association Plots
(AP), a method for visualization and analysis of single cell transcriptomics
data. The main focus of APL is the identification of genes characteristic for
individual clusters of cells from input data. The package performs
correspondence analysis (CA) and allows to identify cluster-specific
genes using Association Plots. Additionally, APL computes the
cluster-specificity scores for all genes which allows to rank the genes by
their specificity for a selected cell cluster of interest.
biocViews:
StatisticalMethod,
DimensionReduction,
SingleCell,
Sequencing,
RNASeq,
GeneExpression
License: GPL (>= 3)
Encoding: UTF-8
RoxygenNote: 7.3.1
VignetteBuilder: knitr
Imports:
reticulate,
ggrepel,
ggplot2,
viridisLite,
plotly,
Seurat,
SingleCellExperiment,
magrittr,
SummarizedExperiment,
topGO,
methods,
stats,
utils,
org.Hs.eg.db,
org.Mm.eg.db,
rlang,
Matrix
Depends: R (>= 4.2)
Suggests:
BiocStyle,
knitr,
rmarkdown,
scRNAseq,
scater,
scran,
testthat
Config/testthat/edition: 3
Collate:
'constructor.R'
'CA.R'
'apl.R'
'convert.R'
'generic_methods.R'
'import_packages.R'
'plot.R'
'utils-pipe.R'
Config/reticulate:
list(
packages = list(
list(package = "numpy"),
list(package = "torch")
)
)
SystemRequirements: python, pytorch, numpy
URL: https://vingronlab.github.io/APL/