Computational Biology Laboratory, Danish Cancer Society Research Center, Strandboulevarden 49, 2100, Copenhagen, Denmark.
Repository associated with the publication:
High-throughput proteomics of breast cancer interstitial fluid: identification of tumor subtype-specific serologically relevant biomarkers. Terkelsen T, Pernemalm M, Gromov P, Børresen-Dale AL, Krogh A, Haakensen VD, Lethiö J, Papaleo E, Gromova I. Mol Oncol. 2021 Feb;15(2):429-461. doi: 10.1002/1878-0261.12850.
Reference contact for repository: Elena Papaleo, elenap-at-cancer.dk
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/.
This repository contains proteomics data from tumour interstitial fluids obtained from a cohort of patients with breast cancer. The repository was made with intent of openly sharing both data and R-scripts used for analysis in relation to the publication.
The repository contains X folders:
(1) Data: Proteomics data and patient metadata. These are the data used as the starting point for our analyses.
(2) Backgrounds_and_Databases: Databases and files used for the analysis, KEGG pathways maps, i2d database etc.
(3) R-scripts: A collection of R-scripts that recapitulate the work.
Requirements:
R version 4.0.0 or higher
Rstudio version 1.2.5019 or higher
Although R-packages should automatically be installed and errors raised if they cannot be, we here provide the user with the list of required packages for manual installation:
CRAN:
pamr
openxlsx
ggplot2
dendextend
heatmap.plus
reshape
VennDiagram
RColorBrewer
stringr
caTools
plyr
gplots
corrplot
fitdistrplus
randomForest
glmnet
e1071
caret
varSelRF
Bioconductor:
limma
sva
topGO
GOSim
gdata
UpSetR
biomaRt
WGCNA
viridis
gprofiler2