diff --git a/.RData b/.RData
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index 0000000000000000000000000000000000000000..929ce29797a1ac33cd52ab858bd1ae9ed17de8f0
Binary files /dev/null and b/.RData differ
diff --git a/.Rhistory b/.Rhistory
new file mode 100644
index 0000000000000000000000000000000000000000..2aed2d46480910b29baa911033fad5b39146a869
--- /dev/null
+++ b/.Rhistory
@@ -0,0 +1,201 @@
+shiny::runApp('corplot')
+shiny::runApp('corplot')
+c
+tumor_expression_plot_Christoffer <- read.delim("~/tumor_expression_plot_Christoffer.txt", row.names=1)
+View(tumor_expression_plot_Christoffer)
+cormat<-signif(cor(tumor_expression_plot_Christoffer),2)
+cormat
+View(cormat)
+col<- colorRampPalette(c("blue", "white", "red"))(20)
+heatmap(cormat, col=col, symm=TRUE)
+cormat<-signif(cor(tumor_expression_plot_Christoffer),1)
+View(cormat)
+cormat<-signif(cor(1,tumor_expression_plot_Christoffer))
+cormat<-signif(1,cor(tumor_expression_plot_Christoffer))
+View(cormat)
+cormat<-signif(cor(tumor_expression_plot_Christoffer))
+View(cormat)
+dist(tumor_expression_plot_Christoffer)
+cor(tumor_expression_plot_Christoffer)
+cor(tumor_expression_plot_Christoffer,2)
+cor(tumor_expression_plot_Christoffer),2
+cor(tumor_expression_plot_Christoffer)
+runApp('corplot')
+runApp('Downloads/shinyCorrplot-gh-pages')
+shiny::runApp('corplot')
+runApp('corplot')
+runApp('corplot')
+runApp('corplot')
+runApp('corplot')
+runApp('corplot')
+runApp('corplot')
+runApp('corplot')
+shiny::runApp('corplot')
+shiny::runApp('corplot')
+shiny::runApp('corplot')
+runApp('corplot')
+shiny::runApp('corplot')
+install.packages("h5")
+shiny::runApp('corplot')
+shiny::runApp('publication/corplot')
+?cormat
+?cormap2
+shiny::runApp('publication/corplot')
+shiny::runApp('publication/corplot')
+?cormap2
+runApp('publication/corplot')
+library(coreheat)
+?cormap2
+shiny::runApp('publication/corplot')
+runApp('publication/corplot')
+?citation
+citation(package = "ggcorrplot")
+library(ggcorrplot)
+install.packages("ggcorrplot")
+library(ggcorrplot)
+citation(package = "ggcorrplot")
+install.packages("graphics")
+install.packages("graphics")
+install.packages("graphics")
+install.packages("graphics")
+install.packages("graphics")
+library(graphics)
+??graphics
+?graphics
+install.packages("dataSet")
+install.packages("grDevices")
+install.packages("grDevices")
+install.packages("grDevices")
+library(grDevices)
+?grDevices
+library(grid)
+?grid
+install.packages("dataset")
+install.packages("altset")
+q
+quit
+exit
+citation()
+citation(package = "ggally")
+install.packages("ggally")
+install.packages("GGally")
+library(GGally)
+citation(package = "GGally")
+citation(package = "corrplot")
+citation(package = "GGally")
+citation()
+citation(package = "ggcorrplot")
+citation(package = "shiny")
+library("coreheat")
+?cormap2
+shiny::runApp('publication/corplot')
+library(corrplot)
+library(coreheat)
+?coreheat
+library(coreheat)
+?coreheat
+library(heatmapGen2)
+?heatmapGen2
+.libPaths()
+.libPaths()
+myLibraryLocation <- .libPaths()[1]
+cranPackages <- c("shinyBS", "shinythemes", "knitr", "rmarkdown", "shinyjs", "plyr", "RColorBrewer", "R.utils", "gdata", "data.table", "foreach", "ggplot2", "scales", "curl", "openssl", "httr", "Rcurl", "XML", "WGCNA")
+sapply(cranPackages, install.packages, lib = myLibraryLocation)
+bioConPackages <- c("AnnotationDbi", "biomaRt", "org.Hs.eg.db", "org.Mm.eg.db", "Heatplus", "genefilter", "impute", "preprocessCore", "Go.db")
+if (!requireNamespace("BiocManager", quietly = TRUE))
+install.packages("BiocManager")
+BiocManager::install(bioConPackages)
+install.packages("/home/dhajam/publication/corplot/packages/coreheat_0.1.0_R_x86_64-pc-linux-gnu.tar.gz", repos = NULL, type="source")
+library(coreheat)
+install.packages('rsconnect')
+rsconnect::setAccountInfo(name='biocpr',
+token='D7412524543BF89B036143D3FB9F8A57',
+secret='<SECRET>')
+rsconnect::setAccountInfo(name='biocpr',
+token='D7412524543BF89B036143D3FB9F8A57',
+secret='SHRyvzmyM0DRFzfxbuChXTZq7uxP7qcGdO3kw+XX')
+rsconnect::setAccountInfo(name='biocpr',
+token='D7412524543BF89B036143D3FB9F8A57',
+secret='SHRyvzmyM0DRFzfxbuChXTZq7uxP7qcGdO3kw+XX')
+lucid$currentUser()
+library(rsconnect)
+rsconnect::setAccountInfo(name='biocpr',
+token='D7412524543BF89B036143D3FB9F8A57',
+secret='SHRyvzmyM0DRFzfxbuChXTZq7uxP7qcGdO3kw+XX')
+rsconnect::setAccountInfo(name='biocpr',
+token='D7412524543BF89B036143D3FB9F8A57',
+secret='SHRyvzmyM0DRFzfxbuChXTZq7uxP7qcGdO3kw+XX')
+shiny::runApp('publication/corplot')
+runApp('publication/corplot')
+runApp('publication/corplot')
+runApp('/home/dhajam/publication/corplot')
+library(rsconnect)
+rsconnect::deployApp('/home/dhajam/publication/corplot')
+shiny::runApp('publication/corplot')
+shiny::runApp('publication/corplot')
+rsconnect::deployApp('/home/dhajam/publication/corplot')
+runApp('publication/corplot')
+runApp('publication/corplot')
+shiny::runApp()
+runApp()
+rsconnect::deployApp('/home/dhajam/publication/corplot')
+rsconnect::deployApp('/home/dhajam/publication/corplot')
+allPackages <- installed.packages()
+allPackages <- allPackages[ is.na(allPackages[,4]), 1]
+sapply(allPackages, remove.packages)
+shiny::runApp()
+runApp()
+rsconnect::deployApp('/home/dhajam/publication/corplot')
+install.packages("rsconnect")
+install.packages("rsconnect")
+rsconnect::deployApp('/home/dhajam/publication/corplot')
+rsconnect::deployApp('/home/dhajam/publication/corplot')
+rsconnect::deployApp('/home/dhajam/publication/corplot')
+rsconnect::appDependencies('/home/dhajam/publication/corplot')
+if (!requireNamespace("BiocManager", quietly = TRUE))
+install.packages("BiocManager")
+installed.packages()
+devtools::install_github("cancer-genetics-utu/readR")
+install
+install.packages("devtools")
+devtools::install_github("cancer-genetics-utu/readR")
+rsconnect::deployApp('/home/dhajam/publication/corplot')
+devtools::install_github("cancer-genetics-utu/medseqr")
+devtools::install_github("cancer-genetics-utu/coreheat")
+devtools::install_github("cancer-genetics-utu/genRal")
+devtools::install_github("cancer-genetics-utu/heatmapGen")
+devtools::install_github("cancer-genetics-utu/heatmapGen2")
+devtools::install_github("cancer-genetics-utu/PAMhm")
+cran_packages <- c("R.methodsS3", "R.oo", "R.utils", "RColorBrewer", "RCurl", "XML", "clipr", "cluster", "curl", "data.table","devtools", "digest", "foreach", "gdata", "ggplot2", "httr", "knitr", "openssl", "plyr", "rmarkdown", "scales", "shiny", "shinyBS", "shinyjs", "shinythemes", "WGCNA")
+bio_packages <- c("AnnotationDbi", "Biobase", "BiocGenerics", "GO.db", "Heatplus", "IRanges", "S4Vectors", "biomaRt", "genefilter", "impute", "latticeExtra", "org.Hs.eg.db", "org.Mm.eg.db", "preprocessCore")
+sapply(cran_packages, install.packages)
+if (!requireNamespace("BiocManager", quietly = TRUE))
+install.packages("BiocManager")
+BiocManager::install(bio_packages)
+install.packages("impute")
+BiocManager::install("impute")
+install.packages("WGCNA")
+rsconnect::deployApp('/home/dhajam/publication/corplot')
+devtools::install_github("cancer-genetics-utu/readR")
+devtools::install_github("cancer-genetics-utu/medseqr")
+devtools::install_github("cancer-genetics-utu/coreheat")
+devtools::install_github("cancer-genetics-utu/genRal")
+devtools::install_github("cancer-genetics-utu/heatmapGen")
+devtools::install_github("cancer-genetics-utu/heatmapGen2")
+devtools::install_github("cancer-genetics-utu/PAMhm")
+devtools::install_github("cancer-genetics-utu/medseqr")
+rsconnect::deployApp('/home/dhajam/publication/corplot')
+BiocManager::install("Heatplus")
+rsconnect::deployApp('/home/dhajam/publication/corplot')
+options(repos = BiocManager::repositories())
+getOption("repos")
+rsconnect::deployApp('/home/dhajam/publication/corplot')
+options(repos="https://CRAN.R-project.org")
+getOption("repos")
+options(repos = BiocManager::repositories())
+getOption("repos")
+rsconnect::deployApp('/home/dhajam/publication/corplot')
+options(repos = "https://CRAN.R-project.org")
+getOption("repos")
+options(repos = BiocManager::repositories())
+rsconnect::deployApp('/home/dhajam/publication/corplot')
diff --git a/data/PrCaTCGASample.pdf b/data/PrCaTCGASample.pdf
new file mode 100644
index 0000000000000000000000000000000000000000..78d283a6ff91d0274e7c418e00b5cf4814bf09fe
Binary files /dev/null and b/data/PrCaTCGASample.pdf differ
diff --git a/data/PrCaTCGASample.txt b/data/PrCaTCGASample.txt
new file mode 100644
index 0000000000000000000000000000000000000000..134a5e4fcca81b9ec10a2176cbb9b576f040f38a
--- /dev/null
+++ b/data/PrCaTCGASample.txt
@@ -0,0 +1,27 @@
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+TMPRSS2	0.3886	0.0313	-0.403	0.038	0.7692	0.7087	1.3773	0.2734	-0.7227	-0.1155	0.4707	-0.7945	-0.1692	0.4148	0.842	0.2611	0.0976	-0.6155	0.1894	-0.5631	-0.6828	-1.1365	-0.5439	-0.6547	-0.3057	1.0775	0.7059	-0.2284	-0.5945	0.2372	0.7255	-0.2568	0.7217	0.1927	-0.1003	0.3677	-2.3486	0.959	-2.055	0.1159	0.7428	0.1247	-0.6565	0.151	0.1945	0.6446	0.336	1.1894	-0.6831	-0.2578	-0.1408	0.3444	0.8938	0.0278	0.0758	-1.6545	0.9554	-1.7663	0.604	0.5407	0.0718	-0.2132	0.3149	-0.2745	-2.0049	0.0391	0.0951	-1.032	0.2867	0.5056	-0.0423	0.7835	0.8283	1.2937	0.9172	0.1408	-1.406	0.5439	0.3214	-0.3369	-0.211	-1.2733	0.2572	0.5719	0.6075	0.8346	0.3554	-2.5981	-0.3435	0.712	-0.5987	-0.0258	0.4257	0.2258	0.8715	0.3071	0.7735	-0.0122	-2.6913	0.5496	-0.0527	0.7389	0.1952	1.3508	0.1528	0.7234	-0.0949	0.9611	1.3177	0.9619	0.4152	-0.4257	0.4319	0.6015	0.9817	0.392	0.0854	0.9366	-0.2565	0.3197	-0.0522	-0.2365	0.5813	1.0153	-0.2268	-2.757	0.2233	0.2784	-0.0556	0.4233	0.6924	0.2142	0.2218	-0.3611	-0.4049	-0.7028	-1.0411	1.3138	0.8979	0.3226	-0.1777	-0.408	-0.0464	0.0989	0.1599	1.1433	0.5296	0.6852	0.2314	0.6477	0.5562	-1.293	0.6495	0.8056	-0.4122	0.4534	-2.1637	0.9427	-0.4186	0.1522	1.305	0.4417	0.3748	0.1707	-0.3778	-0.289	-0.5859	0.5055	1.2239	1.277	0.6478	0.8053	-0.3832	-0.3753	-0.0138	0.8385	0.3065	-0.2284	0.7061	-1.3005	0.4731	1.0279	0.8145	0.3061	0.5495	0.6912	0.7142	0.1198	0.5053	0.4591	-0.2695	-0.3841	0.5768	0.7897	0.7817	0.2928	-0.1413	0.7836	-1.9338	-0.7772	0.1589	-0.5168	-4.0982	-0.1987	0.3896	-0.5858	-0.952	0.1138	0.232	0.3535	-0.3032	1.0869	0.8048	-2.1814	-0.2916	0.3866	-0.302	0.7566	0.1689	-1.2026	-0.2024	-0.839	-0.1553	0.2306	-1.3024	0.5731	-0.1744	-0.0504	0.099	0.1262	-0.3614	-0.3468	-0.1503	0.2659	-0.4641	0.3633	-3.2143	0.8087	0.2399	1.0151	-2.1365	0.7868	-1.5091	-0.4627	0.5755	0.8561	-0.6745	-0.566	-0.0973	-0.0194	0.059	1.0054	-0.0091	0.487	-0.2494	-0.0834	0.035	1.0723	-0.3053	-0.2703	0.5283	1.0134	0.3201	-0.16	0.6251	-0.6189	0.5945	0.7997	0.2909	0.3909	0.2174	0.5519	0.7134	-2.9342	-1.2159	-0.1456	0.0559	-1.3378	-9.1487	-4.2336	1.0769	-0.0613	0.5323	-0.5551	0.1526	-1.2376	-1.7438	-0.2611	-0.0409	-0.1633	0.8682	-0.7093	0.5564	0.3216	0.7782	0.5795	-0.7916	0.6129	0.7428	0.7404	1.2307	-1.0936	-0.7124	-1.1055	-0.5148	0.3545	1.6123	-1.2971	-1.68	-0.8756	0.1774	0.2937	0.9544	1.5897	0.0874	0.3902	-0.2336	-1.792	0.3936	-0.4807	0.0747	0.2432	-0.0654	0.1494	0.8878	1.0759	-0.4062	1.0987	0.3787	0.007	0.344	0.3057	-0.4294
+ERG	0.8645	-0.857	1.2964	1.2673	-1.739	-0.8118	-0.918	-0.6939	1.2359	1.2075	1.5014	-0.3	1.2787	1.0622	-1.2435	-1.0063	-0.5042	1.272	-1.1703	1.1286	-0.6702	-0.8788	-0.7535	1.3272	1.4388	0.4709	-1.1872	1.3414	0.8591	-0.5473	-0.6166	-1.2665	0.1268	1.437	1.1119	-0.5653	1.311	-0.9005	0.8899	1.5576	1.0917	0.9956	0.9361	-1.0932	0.6248	0.1763	-0.5381	-1.2437	-0.1016	1.2459	0.9666	-0.7545	-0.8413	-0.8997	0.8426	-0.5625	-1.0708	1.289	-0.8539	-0.3381	-0.6561	1.0642	1.2367	1.3129	1.0467	1.2631	1.0232	1.3966	-0.8704	-0.8346	1.2345	-0.7291	-0.8898	-0.9588	-1.2443	0.4218	0.9064	-1.0381	-1.2061	1.5393	1.1918	1.0487	-0.7555	-0.7152	-1.0374	-0.7782	1.1956	1.0754	1.2843	-0.9547	-0.6482	-0.8897	-0.5703	-0.4963	1.02	-0.8596	1.4684	-0.7509	1.3313	-0.8368	1.6096	-0.4819	0.9437	-0.8234	-0.1819	-1.3853	1.2715	-1.351	-1.0033	-1.1214	-0.6925	1.4901	-0.6728	-0.8559	-1.1605	-0.0102	-0.9025	-0.8466	-1.5385	-0.695	0.7203	-0.7485	-1.5988	-1.228	-1.2814	1.1174	-1.0509	0.575	1.3331	-0.5587	0.8768	0.4105	0.524	1.2413	0.923	1.0229	0.9376	-1.0995	-1.1348	-0.8475	-1.2045	0.7671	-0.9223	1.0733	0.39	-0.9722	-1.055	-0.6143	-1.0102	-0.8167	0.7223	-0.2487	-0.8763	-1.4287	0.7063	-0.5972	-0.5999	-0.8743	1.2122	1.186	-0.601	-0.3212	1.3635	1.4605	1.1764	1.2944	1.0647	-0.8643	-0.7119	-0.3933	-0.6907	-0.799	1.0347	0.6231	1.0933	-0.6605	-0.7959	0.4488	0.9595	0.7079	1.2484	-0.8383	-1.2568	1.214	-0.9649	0.9265	-0.9084	1.011	-0.4505	-0.9441	-0.6101	1.2077	-0.6161	-1.1015	1.4062	-0.7251	1.4157	-1.3281	0.943	1.0204	-0.586	-0.5449	1.163	1.1894	-0.6946	0.6901	0.7786	-0.5744	1.2706	1.3335	1.1483	-0.9695	1.1097	1.0799	1.2218	-0.4676	1.0441	-0.7616	-0.0961	-0.7912	0.5132	0.7857	1.1869	-1.0103	1.1793	-0.9698	-1.0686	-0.497	-1.1608	1.2557	-0.6493	1.025	-0.8997	1.3348	1.4545	-0.7025	1.3436	-1.5453	1.2482	-0.7068	1.1497	-0.567	1.271	0.9329	0.6963	0.3946	1.0987	-0.0671	1.1517	-0.6947	1.0031	-1.1675	-1.4476	-0.579	1.0709	1.2649	-0.8305	-1.0255	-0.7954	-1.3092	-0.582	-0.8214	-0.9587	1.2321	-0.7625	-0.2171	-0.507	-0.6831	-0.7723	-0.9779	-0.3427	-0.9014	-0.8559	1.2195	-0.56	0.4545	-1.0874	-0.3807	0.8658	1.0799	-0.9759	-1.0804	-0.5544	1.0178	-0.7169	0.7171	1.2965	1.392	-0.2916	1.061	-0.8982	0.9522	1.6291	-0.5835	-1.0228	-1.164	1.4859	-0.9964	-1.3537	-1.3642	-1.1515	0.6731	0.1304	-1.3997	1.1947	-0.8379	-1.2317	1.3473	1.2149	1.5772	-1.1453	-0.534	-0.7821	-1.4803	1.3336	-0.6758	-1.0182	1.2579	-0.675	-0.6885	-0.6481	1.639	-0.753	1.105	-0.7089	-0.3753	-1.0791	-1.2057	-0.5854	-0.7816	-1.3315	-0.6531	0.8968
diff --git a/data/README.md b/data/README.md
index 08cb03e73148651aab2be1946d5898e01eef75a7..e9db0d821d30623a24318afaa7911aa283a119ba 100644
--- a/data/README.md
+++ b/data/README.md
@@ -1,3 +1,3 @@
 ### Example dataset
 
-Example datasets can be found at `biocpr\data\` or can be obtained from [gitlab](https://gitlab.utu.fi/biocpr/corplot/tree/master/Data). The datasets have been downloaded from GEO database (DataSet Record GDS5072) and formatted so that they can be used with BioCPR. For more information on the dataset format, please refer `FAQ`.
+Example datasets can be found at `biocpr\data\` or can be obtained from [gitlab](https://gitlab.utu.fi/dhajam/biocpr/-/tree/master/data). The dataset has been downloaded from The Cancer Genome Atlas (TCGA) dataset consisting of [333 patients with primary prostate cancer](https://www.cbioportal.org/study/summary?id=prad_tcga_pub). The dataset was obtained via the cBioPortal for Cancer Genomics and a subset of the data was created to contain genes commonly associated with cancer. The subset named "PrCaTCGASample.txt" is provided in the data repository.For more information on the dataset format, please refer `FAQ`.
diff --git a/data/subset_GDS5072.tsv b/data/subset_GDS5072.tsv
deleted file mode 100644
index 227a6b271dac80544c0358f383318d29b50c2d82..0000000000000000000000000000000000000000
--- a/data/subset_GDS5072.tsv
+++ /dev/null
@@ -1,19 +0,0 @@
-IDENTIFIER	GSM1095883	GSM1095886	GSM1095877	GSM1095878	GSM1095879	GSM1095880	GSM1095881	GSM1095882	GSM1095884	GSM1095885
-APC	787.8	783.3	508.8	635.1	603.3	535.8	686.2	677.5	516.9	919.9
-ATM	41.7	6.6	26.5	80.7	34.2	133.1	75.9	4.4	10.2	32.5
-BRAF	1440.4	2108.8	1061.8	868	1155.4	1438.9	2179.1	1065.3	999	14487.9
-BRCA1	79.9	364.3	384.7	182.7	353.3	498.7	911	416.2	328.7	535.2
-BRCA2	23	3.2	58.3	2.1	23.5	21.9	2.5	3.5	8.8	45.5
-CHD1	1299.1	946.9	588.9	1135.2	1386.3	938.7	594.7	1070.7	82.4	875.4
-GNAS-AS1	74.7	23.2	13.6	20.2	14.4	67.4	8.6	105.2	44.9	61.1
-ISG15	455.2	11685.6	968.2	8783.9	414.9	7630.3	17259	11813.4	1009.4	441.2
-KMT2D	40.6	1.9	82.5	49	11.9	30.8	11.7	8.9	11.8	4.4
-MYC	5012.4	2449.9	2327.5	3745.1	2382.7	1218.8	1977.5	4913.6	3260.4	1374.3
-PIK3CA	239.3	180.2	236.8	134.4	291	282.1	459.8	52	454.6	327.9
-PIK3CB	2308.7	2341.6	4040.1	3848	3987.7	3738.5	2004.6	3553.1	3001.7	4471.4
-PTEN	1424.4	1656.8	1729.7	1188.8	256.3	1595.2	1471.2	1637.1	2416.7	3078.1
-RAF1	152.4	319.5	646.7	988.3	2248.6	731.3	326.9	647.3	218.4	255.9
-RB1	2704.4	3149.6	1567.8	3025	2565.6	1861.8	1962.3	3355.1	1313.6	3976.5
-RSPO2	39.5	3.9	3.5	14.1	1.6	10.7	6.7	12.5	3.5	7.5
-SPOP	1720.9	1331.5	1805.3	1456.7	1256.4	1213	1907.2	1980	1985.4	988.1
-TP53	779.7	784.5	490.4	207.5	548.6	364	377.3	426.8	594.8	333.3
diff --git a/markdown/README.md b/markdown/README.md
index 1ea15922a574494265fa28d86d99d4ccc15ff352..fd381b65ddbc5ac8c3c62dfcd28a19064ee85197 100755
--- a/markdown/README.md
+++ b/markdown/README.md
@@ -12,8 +12,8 @@ The source code and installation instructions can be obtained from [gitlab](http
 
 ### Required Software
 
-BioCPR requires additional in-house R packages in-order to run. The required packages can be obtained from this [link](https://gitlab.utu.fi/dhajam/biocpr).
+BioCPR requires additional in-house R packages in-order to run. The required packages can be obtained from this [link](https://gitlab.utu.fi/dhajam/biocpr/blob/master/packages) or can be installed from github.
 
 ### Frequently asked questions  
 
-Please refer to the [FAQ](https://gitlab.utu.fi/dhajam/biocpr/blob/master/Markdown/FAQ.md) here.
+Please refer to the [FAQ](https://gitlab.utu.fi/dhajam/biocpr/blob/master/markdown/FAQ.md) here.
diff --git a/markdown/usage_instructions.pdf b/markdown/usage_instructions.pdf
new file mode 100644
index 0000000000000000000000000000000000000000..c8da8f7e9b7825deea8dcccc07c76c0d5f8d125f
Binary files /dev/null and b/markdown/usage_instructions.pdf differ
diff --git a/rsconnect/shinyapps.io/biocpr/corplot.dcf b/rsconnect/shinyapps.io/biocpr/corplot.dcf
new file mode 100644
index 0000000000000000000000000000000000000000..9665cde30ebc9911d47dee2ba07174b7bb35b767
--- /dev/null
+++ b/rsconnect/shinyapps.io/biocpr/corplot.dcf
@@ -0,0 +1,10 @@
+name: corplot
+title:
+username:
+account: biocpr
+server: shinyapps.io
+hostUrl: https://api.shinyapps.io/v1
+appId: 2285412
+bundleId: 3220865
+url: https://biocpr.shinyapps.io/corplot/
+when: 1591145681.80498
diff --git a/server.R b/server.R
index 403b4a9de8ff6a552c5ce66aae8a7293f5add96e..e3ae9dbfbce3330869a4e35e577aa2947125dcad 100755
--- a/server.R
+++ b/server.R
@@ -1,18 +1,39 @@
 ## Required libraries ##
+# cran_packages <- c("R.methodsS3", "R.oo", "R.utils", "RColorBrewer", "RCurl", "XML", "clipr", "cluster", "curl", "data.table","devtools", "digest", "foreach", "gdata", "ggplot2", "httr", "knitr", "openssl", "plyr", "rmarkdown", "scales", "shiny", "shinyBS", "shinyjs", "shinythemes")
+# bio_packages <- c("AnnotationDbi", "Biobase", "BiocGenerics", "GO.db", "Heatplus","impute", "IRanges", "S4Vectors", "biomaRt", "genefilter", "impute", "latticeExtra", "org.Hs.eg.db", "org.Mm.eg.db", "preprocessCore")
+# 
+# sapply(cran_packages, install.packages)
+# 
+# if (!requireNamespace("BiocManager", quietly = TRUE))
+#   install.packages("BiocManager")
+# BiocManager::install(bio_packages)
+# 
+# BiocManager::install("Heatplus")
+# install.packages("WGCNA")
+# devtools::install_github("cancer-genetics-utu/readR")
+# devtools::install_github("cancer-genetics-utu/medseqr")
+# devtools::install_github("cancer-genetics-utu/coreheat")
+# devtools::install_github("cancer-genetics-utu/genRal")
+# devtools::install_github("cancer-genetics-utu/heatmapGen")
+# devtools::install_github("cancer-genetics-utu/heatmapGen2")
+# devtools::install_github("cancer-genetics-utu/PAMhm")
 
 library(shiny)
 library(shinyBS)
 library(plyr)
 library(RColorBrewer)
+library(genefilter)
+library(DT)
+library(digest)
 library(readR)
 library(medseqr)
+library(coreheat)
+library(genRal)
+library(heatmapGen)
 library(heatmapGen2)
-library(genefilter)
-library(DT)
 library(PAMhm)
-library(coreheat)
-library(digest)
-options(shiny.maxRequestSize = 40 * 1024 ^ 2)#increase maximum upload size for fileInput() to 40 MB
+
+options(shiny.maxRequestSize = 52 * 1024 ^ 2)#increase maximum upload size for fileInput() to 40 MB
 #library(shinysky)
 
 
diff --git a/ui.R b/ui.R
index 9598a284c18cff5a617b46d54a20d7c57cf680e6..e3fa648bb6e25c451ecb68682eb778334385dd0a 100755
--- a/ui.R
+++ b/ui.R
@@ -104,15 +104,15 @@ navbarPage(
              tabPanel("About",
                       h4("About"),
                       hr(),
-                      includeMarkdown("Markdown/README.md")),
+                      includeMarkdown("markdown/README.md")),
              tabPanel("FAQ",
                       h4("Frequently Asked Quesitons"),
                       hr(),
-                      includeMarkdown("Markdown/FAQ.md")),
+                      includeMarkdown("markdown/FAQ.md")),
              tabPanel("Session Information",
                       h4("R session information"),
                       hr(),
-                      includeMarkdown("Markdown/RSessionInfo.Rmd"))
+                      includeMarkdown("markdown/RSessionInfo.Rmd"))
              ),
   id='mainNavbarPage', footer=list(tags$hr(), tags$table(style="width: 100%; ", tags$tbody(tags$tr(tags$th(style="text-align: center; ", tags$label(style="font-family: Verdana; font-size: 12pt; font-weight: normal; color: grey; ", "This app has been created and is maintained by the Institute of Biomedicine, University of Turku."))))))
 )