elelab / eif4a3_rnaseq Goto Github PK

Computational Biology Laboratory, Danish Cancer Society Research Center, Strandboulevarden 49, 2100, Copenhagen, Denmark.

This GitHub repository is associated with the publication

eIF4A3 regulates the TFEB-mediated transcriptional response via GSK3B to control autophagy. Sakellariou D, Tiberti M, Kleiber TH, Blazquez L, López AR, Abildgaard MH, Lubas M, Bartek J, Papaleo E, Frankel LB. Cell Death Differ. 2021 Dec;28(12):3344-3356. doi: 10.1038/s41418-021-00822-y.

reference person for repository: elenap-at-cancer.dk

The repository was made with the intent of openly sharing both the raw input data used at the time of the analyses and the R-scripts employed to carry out the study.

Please see the content of each folder for more details.

PLEASE, CITE THE PUBLICATION ABOVE IF YOU USE THE CONTENT OF THIS REPOSITORY FOR YOUR OWN RESEARCH.

The program files (R scripts - files with extension .R) in this repository are licensed under the terms of the GNU General Public License (see LICENSE file). You can redistribute them and/or modify them under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. These programs are distributed in the hope that they will be useful,but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see https://www.gnu.org/licenses/.

## Required software to run

The scripts in this repository are written for R 3.6.2

Used packages and versions are:

from CRAN:

ggplot2 3.2.1 RColorBrewer 1.1-2 plyr 1.8.4 testit 0.11 circlize 0.4.7 factoextra 1.0.6 dplyr 0.8.3 scales 1.0.0 stringr 1.4.0 tidyr 1.0.2 VennDiagram 1.6.20 viridis 0.5.1

from Bioconductor:

SummarizedExperiment limma enrichR 2.1 ComplexHeatmap 2.0.0 TCGAbiolinks 2.12.6_dev0