scCancer/DESCRIPTION at master · czythu/scCancer · 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
Package: scCancer
Type: Package
Title: Supervised and in-depth annotations of the tumor microenvironment
Version: 2.3.0
Author: G-Lab
Maintainer: Wenbo Guo <gwb17@tsinghua.org.cn>, Zeyu Chen <chenzy22@mails.tsinghua.edu.cn>
Description: The package 'scCancer' is focuses on processing and analyzing
    scRNA-seq data for cancer research. Except routine data processing steps,
    it also integrates several cancer-specific analyses. For example,
    more comprehensive quality control, cancer microenvironment cell types
    prediction, cell malignancy estimation, gene set signature scores calculation,
    and expression programs identification. After all steps, the package can
    generate a user-friendly graphic report.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.2.3
Suggests:
    rmarkdown,
    DropletUtils
VignetteBuilder: knitr
Imports:
	Biobase,
    cowplot,
    dplyr,
    ggExtra,
    ggplot2,
	ggpubr,
    grid,
    gridExtra,
    GSVA,
    knitr,
    markdown,
    Matrix,
    methods,
    NNLM,
    pheatmap,
	ComplexHeatmap,
    R.utils,
	hdf5r,
	RcppArmadillo,
	RcppProgress,
    reshape2,
    scds,
    Seurat (>= 3.0),
    SingleCellExperiment,
    SoupX,
    stringr,
    survival,
    survminer,
    harmony,
    rliger,
	monocle,
	edgeR,
	DESeq2,
	DelayedArray,
	DelayedMatrixStats,
	org.Hs.eg.db,
	org.Mm.eg.db,
	garnett,
	xgboost
Depends: R (>= 3.5.0)
biocViews: