-
Notifications
You must be signed in to change notification settings - Fork 7
/
README.Rmd
56 lines (37 loc) · 2.43 KB
/
README.Rmd
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
---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, echo = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "README-"
)
```
# `tcgsaseq`
<!-- badges: start -->
[](https://cran.r-project.org/package=tcgsaseq)
[](https://github.com/denisagniel/tcgsaseq/actions)
[](https://coveralls.io/github/denisagniel/tcgsaseq)
[](https://www.r-pkg.org/pkg/tcgsaseq)
<!-- badges: end -->
<img src="man/figures/lifecycle-deprecated.svg" width="20%" />
## WARNING: deprecation
`tcgsaseq` capabilities and features have been incorporated into the [`Bioconductor` package `dearseq`](https://bioconductor.org/packages/release/bioc/html/dearseq.html).
`tcgsaseq` is the legacy companion package of the 2017 Agniel & Hejblum [*Biostatistics*](https://academic.oup.com/biostatistics/article-abstract/18/4/589/3065599) article.
It has been archived on CRAN and will not be further developped or extended.
If you are interested in using tcgsaseq, you should probably rather look into the newer and more comprehensive `dearseq` package.
## Overview
`tcgsaseq` is a package for analyzing RNA-seq data. The 2 main functions of the package are `varcompseq` and `tcgsa_seq`:
* **Gene-wise Differential Analysis of RNA-seq data** can be performed using the function `varcompseq`.
* **Gene Set Analysis of RNA-seq data** can be performed using the function `tcgsa_seq`.
The method implemented in this package is detailed in the following article:
> Agniel D & Hejblum BP (2017). Variance component score test for time-course gene set analysis of longitudinal RNA-seq data, 2017, [*Biostatistics*](https://academic.oup.com/biostatistics/article-abstract/18/4/589/3065599), 18(4):589-604. [arXiv:1605.02351](https://arxiv.org/abs/1605.02351v4) [DOI: 10.1093/biostatistics/kxx005](https://doi.org/10.1093/biostatistics/kxx005)
## Installation
The easiest way to get `tcgsaseq` is to install it from [GitHub](https://github.com/denisagniel/tcgsaseq):
```{r GitHub-install, eval=FALSE}
#install.packages("devtools")
devtools::install_github("denisagniel/tcgsaseq")
```
-- Denis Agniel and Boris Hejblum