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planemo upload commit 13e28726551f8751007f28a3c6cd5d00ba278056 |
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netboxr_r.R netboxr_xml.xml test-data/community.membership.txt test-data/localModel_histogram.pdf test-data/neighbor_data.txt test-data/netbox2010_data.txt test-data/network.sif test-data/network_plot.pdf test-data/nodeType.txt tool_conf.xml |
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| diff -r 000000000000 -r 785ed8621503 netboxr_r.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/netboxr_r.R Wed Aug 24 08:27:40 2022 +0000 |
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| @@ -0,0 +1,117 @@ +# Set up R error handling to go to stderr +options(show.error.messages = FALSE, + error = function() { + cat(geterrmessage(), file = stderr()) + q("no", 1, FALSE)}) +# Avoid crashing Galaxy with an UTF8 error on German LC settings +loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") +# Import required libraries and data +suppressPackageStartupMessages({ + library(netboxr) + library(igraph) + library(RColorBrewer) +}) + +data(netbox2010) +args <- commandArgs(TRUE) +# Vars +gene_list <- scan(args[2], what = character(), sep = "\n") +cutoff <- args[4] +community <- args[6] +global_model <- args[8] +global_iterations <- args[10] +global_number <- args[12] +local_model <- args[14] +local_iterations <- args[16] + +network_plot <- args[18] +plot_width <- args[20] +output_sif <- args[22] +neighbor_list <- args[24] +modmem <- args[26] +nt <- args[28] + +sink("metadata.txt") +sink(stdout(), type = "message") +# Network analysis as described in netboxr vignette +sif_network <- netbox2010$network +graph_reduced <- networkSimplify(sif_network, directed = FALSE) +threshold <- cutoff +results <- print(geneConnector(geneList = gene_list, networkGraph = graph_reduced, + directed = FALSE, pValueAdj = "BH", pValueCutoff = threshold, + communityMethod = community, keepIsolatedNodes = FALSE)) + +# Check the p-value of the selected linker +linker_df <- results$neighborData +linker_df[linker_df$pValueFDR < threshold, ] +graph_layout <- layout_with_fr(results$netboxGraph) + +# Global Network Null Model +if (global_model) { + global_test <- globalNullModel(netboxGraph = results$netboxGraph, networkGraph = graph_reduced, + iterations = global_iterations, numOfGenes = global_number) + global_test +} + +# Local Network Null Model +if (local_model) { + local_test <- localNullModel(netboxGraph = results$netboxGraph, iterations = local_iterations) + local_test +} + +## Output +# Plot the edge annotated graph +if (network_plot) { + + edges <- results$netboxOutput + interaction_type <- unique(edges[, 2]) + interaction_type_color <- brewer.pal(length(interaction_type), name = "Spectral") + edge_colors <- data.frame(interaction_type, interaction_type_color, stringsAsFactors = FALSE) + colnames(edge_colors) <- c("INTERACTION_TYPE", "COLOR") + netbox_graph_annotated <- annotateGraph(netboxResults = results, edgeColors = + edge_colors, directed = FALSE, linker = TRUE) + pdf("network_plot.pdf", width = plot_width) + plot(results$netboxCommunity, netbox_graph_annotated, layout = graph_layout, + vertex.size = 10, vertex.shape = V(netbox_graph_annotated)$shape, edge.color + = E(netbox_graph_annotated)$interactionColor, edge.width = 3) + + # Add interaction type annotations + legend(x = -1.8, y = -1, legend = interaction_type, col = + interaction_type_color, lty = 1, lwd = 2, bty = "n", cex = 1) + dev.off() +} + +# Local Network Null Model +if (local_model) { + pdf("localModel_histogram.pdf") + h <- hist(local_test$randomModularityScore, breaks = 35, plot = FALSE) + h$density <- h$counts / sum(h$counts) + plot(h, freq = FALSE, ylim = c(0, 0.1), xlim = c(0.1, 0.6), col = "lightblue") + abline(v = local_test$modularityScoreObs, col = "red") + dev.off() +} + +# NetBox algorithm output in SIF format. +if (output_sif) { + write.table(results$netboxOutput, file = "network.sif", sep = "\t", quote = FALSE, + col.names = FALSE, row.names = FALSE) +} + +# Save neighbor data +if (neighbor_list) { + write.table(results$neighborData, file = "neighbor_data.txt", sep = "\t", + quote = FALSE, col.names = TRUE, row.names = FALSE) +} + +#Save identified pathway module numbers +if (modmem) { + write.table(results$moduleMembership, file = "community.membership.txt", sep = "\t", + quote = FALSE, col.names = FALSE, row.names = FALSE) +} + +# Save file that indicates whether the node is a 'linker' or 'candidate' +if (nt) { + write.table(results$nodeType, file = "nodeType.txt", sep = "\t", quote = FALSE, col.names = FALSE, + row.names = FALSE) +} +sink(NULL) |
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| diff -r 000000000000 -r 785ed8621503 netboxr_xml.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/netboxr_xml.xml Wed Aug 24 08:27:40 2022 +0000 |
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| b'@@ -0,0 +1,151 @@\n+<tool id="netboxr" name="netboxr" version="1.6.0">\n+ <description>enables automated discovery of biological process modules by network analysis.</description>\n+ <requirements>\n+ <requirement type="package" version="1.6.0">bioconductor-netboxr</requirement>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[\n+Rscript \'$__tool_directory__/netboxr_r.R\'\n+--geneList \'$geneList\'\n+--cutoff \'$cutoff\'\n+--community $community\n+--globalModel $globalModel\n+--globalIterations \'$globalIterations\'\n+--globalNumber \'$globalNumber\'\n+--localModel $localModel\n+--localIterations \'$localIterations\'\n+--networkPlot $networkPlot\n+--plotWidth \'$plotWidth\'\n+--outputSIF $outputSIF\n+--neighborList $neighborList\n+--modmem $modmem\n+--nt $nt\n+\t]]></command>\n+ <inputs>\n+ <param argument="--geneList" type="data" format="txt" label="Gene list" help="A newline-delimited text file that contains a list of genes of interest" />\n+ <param argument="--cutoff" type="float" value="0.05" label="P-Value Cut-Off" help="The corrected p-value (or q-value) cut-off to apply for the graph output. Default: 0.05" />\n+ <param argument="--community" type="select" label="Community detection method" help="Community detection methods include edge betweenness score (EBC), leading eigenvector method (LEC), Louvain method (LOUV), or Leiden method (LEID). Default: EBC">\n+ <option value="ebc">EBC</option>\n+ <option value="lec">LEC</option>\n+ <option value="louvain">LOUV</option>\n+ <option value="leiden">LEID</option>\n+ </param>\n+ <param argument="--globalModel" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Global network null model" help="Perform global network null model analysis. The global network null model calculates the empirical p-value as the number of times (over a set of iterations) the size of the largest connected component (the giant component) in the network coming from the same number of randomly selected genes equals or exceeds the size of the largest connected component in the observed network. Default: Yes" />\n+ <param argument="--globalIterations" type="integer" value="10" label="Global network null model iterations" help="Global network null model iterations. Recommended: 1000" />\n+ <param argument="--globalNumber" type="integer" value="274" label="Global network model number of genes" help="Global network null model number of genes." />\n+ <param argument="--localModel" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Local network null model" help="Perform local network null model analysis. The local network null model evaluates the deviation of modularity in the observed network from modularity distribution in the random network. Default: Yes" />\n+ <param argument="--localIterations" type="integer" value="10" label="Local network null model iterations" help="Local network null model iterations. Recommended: 1000" />\n+ <param argument="--networkPlot" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Network plot" help="Output the annotated graph of netboxr output. Default: Yes" />\n+ <param argument="--plotWidth" type="integer" value="8" label="Network plot width" help="Plot width. Recommended: 9" />\n+ <param argument="--outputSIF" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Network in SIF format" help="Output the network in SIF format. Default: Yes" />\n+ <param argument="--neighborList" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Neighbor list" help="Output a table containing the information of all neighbor nodes. Default: Yes" />\n+ <param argument="--modmem" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Module membership" help="Output a table containing the identified pathway module numbers. Default: Yes" />\n+ <'..b'eType" format="tabular" from_work_dir="nodeType.txt" label="${tool.name} on ${on_string}: Node type">\n+ <filter>nodeType is True</filter>\n+ </data>\n+ <data name="metadata" format="txt" from_work_dir="metadata.txt" label="${tool.name} on ${on_string}: Metadata" />\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="geneList" value="netbox2010_data.txt" />\n+ <param name="cutoff" value="0.05" />\n+ <param name="community" value="ebc" />\n+ <param name="globalModel" value="True" />\n+ <param name="globalIterations" value="10" />\n+ <param name="globalNumber" value="274" />\n+ <param name="localModel" value="True" />\n+ <param name="localIterations" value="10" />\n+ <param name="networkPlot" value="True" />\n+ <param name="plotWidth" value="8" />\n+ <param name="outputSIF" value="True" />\n+ <param name="neighborList" value="True" />\n+ <param name="modmem" value="True" />\n+ <param name="nt" value="True" />\n+ <output name="output_pdf" file="network_plot.pdf" compare="sim_size" />\n+ <output name="localModel_pdf" file="localModel_histogram.pdf" compare="sim_size" />\n+ <output name="output_sif" file="network.sif">\n+ <assert_contents>\n+ <has_text_matching expression="CBL\\tPP\\tPIK3R1" />\n+ <has_text_matching expression="PIK3R1\\tIN_SAME_COMPONENT\\tAGAP2" />\n+ </assert_contents>\n+ </output>\n+ <output name="output_neighbor" file="neighbor_data.txt">\n+ <assert_contents>\n+ <has_text_matching expression="idx\\tname\\tlocalDegree\\tglobalDegree\\tpValueRaw\\toddsRatio\\tpValueFDR" />\n+ <has_text_matching expression="1712\\tCRK\\t11\\t81\\t2.39208791593171e-05\\t1.70873218314362\\t0.0186673141177578" />\n+ <has_text_matching expression="6187\\tRPS27\\t2\\t186\\t0.975923212389053\\t-0.825808759394024\\t0.975923212389053" />\n+ </assert_contents>\n+ </output>\n+ <output name="moduleMembership" file="community.membership.txt">\n+ <assert_contents>\n+ <has_text_matching expression="CBL\\t1" />\n+ <has_text_matching expression="CCT6A\\t10" />\n+ </assert_contents>\n+ </output>\n+ <output name="nodeType" file="nodeType.txt">\n+ <assert_contents>\n+ <has_text_matching expression="CDKN2B\\tcandidate" />\n+ <has_text_matching expression="PTPN11\\tlinker" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+\n+NetBox is a network-based approach that combines prior knowledge with a\n+network clustering algorithm. The algorithm allows for the identification\n+of functional modules and allows for combining multiple data types, such as\n+mutations and copy number alterations. NetBox performs network analysis on\n+human interaction networks, and comes pre-loaded with a Human Interaction\n+Network (HIN) derived from four literature curated data sources, including\n+the Human Protein Reference Database (HPRD), Reactome, NCI-Nature Pathway\n+Interaction (PID) Database, and the MSKCC Cancer Cell Map.\n+\n+-----\n+\n+**INPUTS**\n+\n+**Gene list**\n+A newline-delimited text file that contains a list of genes of interest is\n+required.\n+\n+Example of text file contents:\n+\n+EGFR\n+TP53\n+ACTB\n+GAPDH\n+\n+**Cutoff value**\n+The corrected p-value (or q-value) cut-off to apply for the graph output.\n+The default p-value is 0.05.\n+\n+\n+**OUTPUTS**\n+\n+* A PDF with a plot of the edge annotated graph (optional)\n+\n+* A text file with tabular data containing information of all neighbor nodes (optional)\n+\n+ \t]]></help>\n+ <citations>\n+ <citation type="doi">10.1371/journal.pone.0234669</citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r 785ed8621503 test-data/community.membership.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/community.membership.txt Wed Aug 24 08:27:40 2022 +0000 |
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| @@ -0,0 +1,72 @@ +CBL 1 +ADAM12 1 +PIK3R1 1 +PTPN11 1 +KIT 1 +MPDZ 1 +KDR 1 +ERBB2 1 +SPRY2 1 +FRS2 1 +TEK 1 +GAB1 1 +PDGFRA 1 +IFNG 1 +VLDLR 1 +DOCK1 1 +EGFR 1 +JAK2 1 +CRK 1 +PIK3C2B 1 +PTPRB 1 +PTEN 1 +SH3GL2 1 +FGF23 1 +MAPK11 1 +PIK3CA 1 +HLA-DRA 1 +AVIL 1 +AGAP2 1 +TBP 2 +RB1 2 +TAF1 2 +CDK6 2 +CDKN2A 2 +TP53 2 +HSPA1A 2 +RBBP5 2 +SNAPC3 2 +MDM4 2 +MDM2 2 +KLF6 2 +CDKN2C 2 +CDK4 2 +PIM1 2 +BNC2 2 +EPHA3 2 +CCND2 2 +CDKN2B 2 +IFNW1 3 +IFNA2 3 +IFNB1 3 +IFNAR1 3 +IFNA1 3 +KCNA5 4 +PTPRD 4 +PTPRE 4 +CNTN2 5 +NCAM1 5 +NUP50 6 +THOC4 6 +NUP107 6 +SNRPE 6 +DCTN2 7 +TUBGCP2 7 +FGFR1OP 7 +TUBGCP6 7 +A2M 8 +LYZ 8 +PPARA 9 +STAC3 9 +CCT2 10 +CCT6A 10 |
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| Binary file test-data/localModel_histogram.pdf has changed |
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| diff -r 000000000000 -r 785ed8621503 test-data/neighbor_data.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/neighbor_data.txt Wed Aug 24 08:27:40 2022 +0000 |
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| b'@@ -0,0 +1,893 @@\n+idx\tname\tlocalDegree\tglobalDegree\tpValueRaw\toddsRatio\tpValueFDR\n+1712\tCRK\t11\t81\t2.39208791593171e-05\t1.70873218314362\t0.0186673141177578\n+4546\tIFNAR1\t6\t23\t4.18549643895914e-05\t2.51872572932126\t0.0186673141177578\n+20\tCBL\t14\t140\t6.50546994954036e-05\t1.3610568890526\t0.0193429306499667\n+500\tGAB1\t8\t57\t0.000248319689968565\t1.75112196905105\t0.0488782736525554\n+414\tCDK6\t5\t21\t0.000300851540057881\t2.40690610751877\t0.0488782736525554\n+84\tPTPN11\t14\t163\t0.000328777625465619\t1.19140466680817\t0.0488782736525554\n+883\tNRCAM\t3\t6\t0.000479055427005265\t3.49957222828438\t0.0610453486983852\n+1589\tEGF\t8\t67\t0.00075960357041191\t1.56599925702267\t0.0623864456740024\n+723\tE4F1\t3\t7\t0.000820026182632156\t3.24814652197521\t0.0623864456740024\n+2002\tUBE2A\t3\t7\t0.000820026182632156\t3.24814652197521\t0.0623864456740024\n+2011\tCCNG1\t3\t7\t0.000820026182632156\t3.24814652197521\t0.0623864456740024\n+9028\tSH3BGRL3\t2\t2\t0.000871691877932093\t5.10566742579647\t0.0623864456740024\n+1075\tIFNAR2\t6\t39\t0.000909219499733219\t1.86759645259685\t0.0623864456740024\n+3417\tCCND1\t7\t55\t0.0011040563656313\t1.64273421305669\t0.0703441627245085\n+152\tSOS1\t10\t109\t0.00140677841553983\t1.26617116982172\t0.0788613246697833\n+5758\tYES1\t5\t30\t0.00169479306853121\t1.97058463576423\t0.0788613246697833\n+475\tFES\t5\t30\t0.00169479306853121\t1.97058463576423\t0.0788613246697833\n+6824\tIL1B\t5\t30\t0.00169479306853121\t1.97058463576423\t0.0788613246697833\n+1514\tEPB41L1\t4\t19\t0.00204257619053189\t2.26516348792102\t0.0788613246697833\n+95\tCRKL\t7\t62\t0.00224497452402098\t1.50713186104734\t0.0788613246697833\n+2777\tMAP2K3\t5\t32\t0.00228227989570501\t1.89485396857421\t0.0788613246697833\n+188\tGRB2\t16\t245\t0.00248499401989919\t0.890626990123815\t0.0788613246697833\n+4\tGRB7\t4\t20\t0.00249450743931036\t2.20253170411913\t0.0788613246697833\n+6547\tNUMA1\t4\t20\t0.00249450743931036\t2.20253170411913\t0.0788613246697833\n+13\tERRFI1\t2\t3\t0.002563877147336\t4.00694389623609\t0.0788613246697833\n+6366\tTRIAP1\t2\t3\t0.002563877147336\t4.00694389623609\t0.0788613246697833\n+485\tTIE1\t2\t3\t0.002563877147336\t4.00694389623609\t0.0788613246697833\n+1027\tKCNE4\t2\t3\t0.002563877147336\t4.00694389623609\t0.0788613246697833\n+6197\tCELSR2\t2\t3\t0.002563877147336\t4.00694389623609\t0.0788613246697833\n+469\tPDGFRB\t7\t67\t0.00350325776782824\t1.42031176303995\t0.104163530963426\n+30\tSHB\t4\t23\t0.00425236950480855\t2.03514326447932\t0.118016403072892\n+5820\tRAP1A\t6\t54\t0.00497475252068343\t1.49590202180316\t0.118016403072892\n+5794\tIL1R1\t4\t24\t0.00498597603079399\t1.98502136739822\t0.118016403072892\n+5506\tBTC\t2\t4\t0.00502760461521287\t3.49600701920192\t0.118016403072892\n+4450\tZNHIT1\t2\t4\t0.00502760461521287\t3.49600701920192\t0.118016403072892\n+5888\tNQO1\t2\t4\t0.00502760461521287\t3.49600701920192\t0.118016403072892\n+92\tPTPRO\t2\t4\t0.00502760461521287\t3.49600701920192\t0.118016403072892\n+6017\tECM1\t2\t4\t0.00502760461521287\t3.49600701920192\t0.118016403072892\n+302\tSH3KBP1\t5\t39\t0.00551594038987694\t1.6672993555707\t0.126159457122314\n+1259\tRAD54B\t3\t13\t0.00587280182975435\t2.40018073325415\t0.128668086485739\n+7\tPIK3R2\t5\t40\t0.0061548531624999\t1.63861431990281\t0.128668086485739\n+890\tSTAT5B\t5\t40\t0.0061548531624999\t1.63861431990281\t0.128668086485739\n+109\tPTK2\t9\t113\t0.00620260955032151\t1.11272217001549\t0.128668086485739\n+44\tSOCS1\t6\t57\t0.00649453744645887\t1.43554846037083\t0.131661986414575\n+1663\tITGB4\t5\t41\t0.00684405330209209\t1.61072308010184\t0.135664345454803\n+2718\tANGPT2\t3\t14\t0.00731280617614375\t2.30909759027298\t0.140937424013585\n+32\tTEC\t4\t27\t0.0076830666388411\t1.84811132829167\t0.140937424013585\n+9027\tPIK3C2A\t2\t5\t0.00821608301424488\t3.15942351693386\t0.140937424013585\n+2681\tSERTAD1\t2\t5\t0.00821608301424488\t3.15942351693386\t0.140937424013585\n+5515\tMAGEB18\t2\t5\t0.00821608301424488\t3.15942351693386\t0.140937424013585\n+5889\tMTSS1\t2\t5\t0.00821608301424488\t3.15942351693386\t0.140937424013585\n+5669\tGTPBP3\t2\t5\t0.00821608301424488\t3.15942351693386\t0.140937424013585\n+497\tPIK3CB\t3\t15\t0.00894359163891158\t2.225604604155\t0.145048795307439\n+662\tSNX6\t3\t15\t0.00894359163891158\t2.225604604155\t0.145048795307439\n+4988\tPHB\t3\t15\t0.00894359163891158\t2.225604604155\t0.'..b'3\t0.813738704638071\t-0.218836844469312\t0.847756374911252\n+7327\tHNRNPD\t2\t103\t0.813738704638071\t-0.218836844469312\t0.847756374911252\n+7328\tHNRNPF\t2\t103\t0.813738704638071\t-0.218836844469312\t0.847756374911252\n+7329\tHNRNPH1\t2\t103\t0.813738704638071\t-0.218836844469312\t0.847756374911252\n+7330\tHNRNPH2\t2\t103\t0.813738704638071\t-0.218836844469312\t0.847756374911252\n+7331\tHNRNPL\t2\t103\t0.813738704638071\t-0.218836844469312\t0.847756374911252\n+7332\tHNRNPM\t2\t103\t0.813738704638071\t-0.218836844469312\t0.847756374911252\n+7333\tHNRNPR\t2\t103\t0.813738704638071\t-0.218836844469312\t0.847756374911252\n+7334\tHNRNPU\t2\t103\t0.813738704638071\t-0.218836844469312\t0.847756374911252\n+7335\tHNRNPUL1\t2\t103\t0.813738704638071\t-0.218836844469312\t0.847756374911252\n+7446\tPCF11\t2\t103\t0.813738704638071\t-0.218836844469312\t0.847756374911252\n+7459\tPHF5A\t2\t103\t0.813738704638071\t-0.218836844469312\t0.847756374911252\n+7555\tSF3B14\t2\t103\t0.813738704638071\t-0.218836844469312\t0.847756374911252\n+7556\tSF3B5\t2\t103\t0.813738704638071\t-0.218836844469312\t0.847756374911252\n+7557\tSF4\t2\t103\t0.813738704638071\t-0.218836844469312\t0.847756374911252\n+7586\tSNRNP200\t2\t103\t0.813738704638071\t-0.218836844469312\t0.847756374911252\n+7587\tSNRNP40\t2\t103\t0.813738704638071\t-0.218836844469312\t0.847756374911252\n+6329\tATP5J2\t2\t104\t0.81795993658245\t-0.22875334948814\t0.847756374911252\n+5496\tRBM5\t2\t104\t0.81795993658245\t-0.22875334948814\t0.847756374911252\n+7487\tPRPF8\t2\t104\t0.81795993658245\t-0.22875334948814\t0.847756374911252\n+2695\tRPL5\t2\t105\t0.822095587778289\t-0.238574681196091\t0.847756374911252\n+2087\tSF3A3\t2\t105\t0.822095587778289\t-0.238574681196091\t0.847756374911252\n+2424\tSNRPB2\t2\t105\t0.822095587778289\t-0.238574681196091\t0.847756374911252\n+2473\tTXNL4A\t2\t105\t0.822095587778289\t-0.238574681196091\t0.847756374911252\n+2816\tCSTF1\t2\t105\t0.822095587778289\t-0.238574681196091\t0.847756374911252\n+3365\tCCAR1\t2\t105\t0.822095587778289\t-0.238574681196091\t0.847756374911252\n+4595\tSF3B2\t2\t105\t0.822095587778289\t-0.238574681196091\t0.847756374911252\n+6192\tEFTUD2\t2\t105\t0.822095587778289\t-0.238574681196091\t0.847756374911252\n+1486\tPAPOLA\t2\t106\t0.826147005130104\t-0.248302670138155\t0.848989779465498\n+1691\tCD2BP2\t2\t106\t0.826147005130104\t-0.248302670138155\t0.848989779465498\n+2422\tSF3A2\t2\t106\t0.826147005130104\t-0.248302670138155\t0.848989779465498\n+1766\tSF3A1\t2\t107\t0.830115531036522\t-0.257939094556514\t0.849154878078644\n+3059\tPRPF4\t2\t107\t0.830115531036522\t-0.257939094556514\t0.849154878078644\n+3517\tPABPN1\t2\t107\t0.830115531036522\t-0.257939094556514\t0.849154878078644\n+7326\tHNRNPC\t2\t107\t0.830115531036522\t-0.257939094556514\t0.849154878078644\n+4297\tSF3B3\t2\t108\t0.834002502480785\t-0.267485682364305\t0.852153759693998\n+2988\tPCBP2\t2\t109\t0.837809250178602\t-0.276944113027159\t0.855063902928276\n+4468\tSF3B4\t2\t110\t0.841537097780771\t-0.286316019357612\t0.857886961394797\n+665\tSF3B1\t2\t111\t0.845187361128093\t-0.295602989227195\t0.860624573203492\n+3964\tPTBP1\t2\t113\t0.85226035524807\t-0.31392825609699\t0.865849928110796\n+439\tVIM\t2\t113\t0.85226035524807\t-0.31392825609699\t0.865849928110796\n+3919\tRPS7\t2\t115\t0.859038577822236\t-0.33193177808228\t0.870752740247085\n+287\tSMAD1\t2\t115\t0.859038577822236\t-0.33193177808228\t0.870752740247085\n+2815\tCSTF2\t2\t117\t0.865532209448699\t-0.349624797847373\t0.876339081530352\n+2801\tLSM2\t2\t118\t0.868675436084772\t-0.358358223296043\t0.878524363931538\n+3442\tSMC1A\t2\t121\t0.877705505480484\t-0.384121445080123\t0.886651541210183\n+3825\tPCBP1\t2\t122\t0.88058634707523\t-0.392567559856226\t0.888555454288581\n+677\tRPS3A\t2\t124\t0.886161358114687\t-0.409254341477723\t0.89317054399808\n+683\tBUB3\t2\t134\t0.910596051541953\t-0.488854243172278\t0.916762616225081\n+2675\tBUB1B\t2\t138\t0.918923494761648\t-0.51904788356207\t0.924103446817801\n+4732\tMAD2L1\t2\t139\t0.920888734702681\t-0.526460135724721\t0.925036882156297\n+1684\tCDC20\t2\t142\t0.926519520852894\t-0.548382633000971\t0.928601587191889\n+4003\tEEF1G\t2\t142\t0.926519520852894\t-0.548382633000971\t0.928601587191889\n+4955\tEEF1A1\t2\t168\t0.961736895547538\t-0.721112630716305\t0.962816286002699\n+6187\tRPS27\t2\t186\t0.975923212389053\t-0.825808759394024\t0.975923212389053\n' |
| b |
| diff -r 000000000000 -r 785ed8621503 test-data/netbox2010_data.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/netbox2010_data.txt Wed Aug 24 08:27:40 2022 +0000 |
| b |
| @@ -0,0 +1,517 @@ +CDKN2B +EGFR +CDKN2A +MTAP +PTEN +TP53 +SEC61G +LANCL2 +DMRTA1 +IFNE +IFNA1 +ELAVL2 +IFNA8 +IFNA2 +IFNA13 +IFNA6 +KLHL9 +IFNA5 +IFNA14 +CYP27B1 +IFNA10 +IFNA16 +IFNA7 +IFNW1 +IFNA21 +CDK4 +TSPAN31 +VOPP1 +MARCH9 +VSTM2A +KIAA1797 +AGAP2 +METTL1 +TSFM +FAM119B +AVIL +MLLT3 +PTPLAD2 +IFNB1 +CTDSP2 +HLA-DRA +NF1 +XRCC6BP1 +MDM2 +OS9 +GSX2 +SLC24A2 +RPL21P44 +PDGFRA +CHIC2 +SEPT14 +NME7 +RB1 +C9orf82 +MARS +SLC35E3 +DTX3 +PLAA +CPM +MBD6 +PIP4K2C +SLC26A10 +LRRC19 +KIT +ZNF713 +B4GALNT1 +TEK +IFT74 +DDIT3 +GEFT +KIF5A +LINGO2 +C9orf11 +MOBKL2B +NUP107 +DCTN2 +FKBP9 +IFNK +PTPRD +PAOX +ERBB2 +PIK3R1 +GLI1 +CPSF6 +ARHGAP9 +PIK3CA +FRS2 +LYZ +INHBC +C9orf72 +INHBE +YEATS4 +LNX1 +LRIG3 +MDM4 +ECHS1 +KDR +KISS1 +GBAS +RAB3IP +PLEKHA6 +CCT2 +ETNK2 +MRPS17 +LRRN2 +REN +PPP1R15B +SOX13 +LRRC10 +PIK3C2B +GOLT1A +C1orf157 +CLRN3 +C10orf90 +HMGA2 +PPM1H +TYRP1 +TPD52L3 +DOCK1 +LAX1 +NPS +FAM196A +hCG_1757335 +BEST3 +FOXI2 +PRELP +TCERG1L +SNRPE +SRD5A3 +CCT6A +TMEM165 +GRIP1 +RAP1B +ATP2B4 +PSPH +EBF3 +GLRX3 +PTPRE +SLC16A7 +ZC3H11A +OPTC +ADAM12 +FIP1L1 +C9orf150 +NFASC +MKI67 +R3HDM2 +PSIP1 +NKX6-2 +C9orf93 +RCL1 +INSL6 +PPAPDC2 +CNOT2 +AK3 +ERMP1 +AVPR1A +NOTUM +KIAA2026 +CD274 +RANBP6 +KIAA1432 +MLANA +MON2 +RASL11B +CCND2 +SCFD2 +INSL4 +BNIP3 +GLDC +ATAD1 +EPHA3 +KCNV2 +MGMT +STAC3 +SNAPC3 +DUX4 +HELB +JAK2 +GLIS3 +FRG2B +LRRC66 +LRRC27 +KDM4C +CAND1 +USP15 +DCUN1D4 +SGCB +CDC37L1 +BNC2 +PPP2R2D +SRGAP1 +LMO7 +FMOD +TTC39B +FAM19A2 +FREM1 +ZDHHC21 +KLRC3 +C10orf92 +SUMF2 +STK32C +C10orf91 +C9orf123 +SPATA18 +C12orf61 +PDCD1LG2 +RFX3 +USP46 +KIAA0020 +NFIB +TDRD3 +C9orf68 +PWWP2B +CNTLN +RLN2 +SH3GL2 +IL33 +JAKMIP3 +MPDZ +C10orf93 +RNLS +KCNMB4 +INPP5A +ACER2 +VLDLR +SLC1A1 +DPYSL4 +CLOCK +CER1 +SMARCA2 +TMEM5 +DST +PHKG1 +CHCHD2 +UHRF2 +CHIT1 +IRAK3 +MYO3A +CELSR1 +PRAP1 +C22orf9 +ZNF511 +GAD2 +PANX2 +ADAMTSL1 +RIBC2 +NCRNA00168 +GTSE1 +TSPO +KIAA1644 +PIP4K2A +SLC12A6 +GALNT8 +LPHN3 +CALY +MDM1 +TMEM19 +DYRK4 +RAPGEF3 +C12orf66 +SMC1B +ZBED4 +C22orf40 +BIK +PARVG +ARID2 +PKDREJ +MSRB3 +TMEM81 +TAF1 +CRELD2 +OR6C74 +MCAT +CDKN2C +DACH1 +KCNQ1 +EDNRB +SLC6A12 +RAD51AP1 +TSPAN9 +A2BP1 +DENND4C +RP3-474I12.5 +MIOX +SBF1 +ENO1 +DIAPH3 +CCR6 +UCHL3 +DSTYK +GRAMD4 +PARP11 +TBC1D4 +RPAP3 +BTG2 +NUP50 +HDAC10 +RPS6 +WDR27 +CACNA1C +PHF21B +PIBF1 +BRD1 +RBBP5 +EFCAB4B +NMU +IL26 +TTC38 +PNPLA5 +ZFC3H1 +CERK +PNPLA3 +WIF1 +NDUFA9 +SLC2A5 +LDOC1L +ATAD2B +NTF3 +TBK1 +SLFN11 +PHACTR3 +NDFIP2 +SLAIN1 +FGF6 +PITRM1 +RASSF4 +LARP4B +HAUS6 +KLF5 +DOCK5 +DIP2C +PFKP +SLITRK1 +TUBGCP2 +UPK3A +DMRT2 +C12orf4 +C12orf56 +UNC93A +KCNA1 +ARHGAP8 +RRAGA +C6orf124 +RERE +RAB21 +PIM1 +PCDH9 +HSPA1A +CTNNA3 +DMRT3 +PIM3 +TTLL2 +PHF10 +GTSF1 +HDAC7 +APBB1IP +RNASET2 +C13orf37 +AKR1E2 +SLITRK5 +KLF12 +PTPRR +IFNG +GTPBP4 +FGF23 +PRMT8 +TYMP +SPRY2 +MAPK8IP2 +SFT2D1 +LLPH +C13orf34 +PLIN2 +DYRK2 +MAPK12 +KLHDC7B +WDR37 +SLITRK6 +KCTD12 +ADM2 +MLC1 +PDCL2 +OR10A7 +PDCD2 +XPOT +C6orf70 +TBC1D22A +T +EXOC1 +AKR1C3 +TCTE3 +SAPS2 +VDR +LARP4 +NCKAP1L +FAM116B +AKR1C1 +CNTN2 +NDUFA4L2 +AKR1C4 +BCL11A +KLHL1 +SCEL +ADORA1 +SLC45A1 +SLC2A7 +DMRT1 +SPAG6 +MYCBP2 +C12orf5 +FAM118A +A2M +FBXL3 +OMG +PLXNB2 +PSMB1 +RAB11FIP4 +RBM26 +FAM154A +ATXN10 +PCDH17 +GNS +TRABD +FBLN1 +ARSA +CLN5 +SLC48A1 +PARVB +KLF6 +PAPSS2 +COMMD6 +TBC1D15 +DACT2 +PTPRB +CHI3L1 +CDC123 +CHKB +BBS10 +TBP +C12orf64 +GPR157 +AKR1CL1 +EVI2B +DNAJC1 +MYBPH +KCNA5 +FGFR1OP +THAP2 +ADAMTS20 +IDI2 +RASSF3 +MPPED1 +TMBIM4 +ALG12 +RPS6KA2 +MOV10L1 +FAM120B +CPT1B +THOC4 +ADARB2 +ODF3B +C10orf10 +PRR18 +RNF219 +SLFN13 +ZNF479 +IL17REL +LMF2 +TTLL8 +PDE10A +C22orf26 +TTLL12 +SLFN12 +TRMU +ADAM8 +C10orf125 +AKR1C2 +NCAM1 +COMMD3 +IDI1 +ZMYND11 +FAF1 +CA6 +TUBGCP6 +TCP10 +C6orf120 +THBS2 +PPARA +P11 +FAM19A5 +PRR5 +IL22 +SULT4A1 +DIS3 +MAPK11 +ST7 +DLL1 +BRP44L +BMI1 +CTRB1 +AKAP3 +SCUBE1 +GPR31 +PTPRZ1 +SAMM50 +WNT7B +SCO2 +LEMD3 +POU4F1 +NCAPH2 +EFCAB6 +KCNA6 +RP3-402G11.5 +RABL2B +PCDH20 +LOC553158 |
| b |
| diff -r 000000000000 -r 785ed8621503 test-data/network.sif --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/network.sif Wed Aug 24 08:27:40 2022 +0000 |
| b |
| @@ -0,0 +1,152 @@ +CBL PP PIK3R1 +ADAM12 PP PIK3R1 +CBL PP PTPN11 +PIK3R1 PP PTPN11 +CBL PP KIT +PIK3R1 PP KIT +PTPN11 PP KIT +KIT PP MPDZ +CBL PP KDR +PIK3R1 STATE_CHANGE KDR +PTPN11 PP KDR +TBP PP RB1 +PIK3R1 PP RB1 +TBP PP TAF1 +RB1 PP TAF1 +PIK3R1 PP ERBB2 +PTPN11 PP ERBB2 +CBL PP SPRY2 +PTPN11 PP SPRY2 +CBL PP FRS2 +PIK3R1 STATE_CHANGE FRS2 +PTPN11 PP FRS2 +KDR PP FRS2 +RB1 PP CDK6 +CDK6 PP CDKN2A +PIK3R1 PP TEK +PTPN11 PP TEK +PIK3R1 PP GAB1 +PTPN11 PP GAB1 +KIT STATE_CHANGE GAB1 +KDR STATE_CHANGE GAB1 +FRS2 PP GAB1 +CBL PP PDGFRA +PIK3R1 PP PDGFRA +PTPN11 PP PDGFRA +CBL STATE_CHANGE IFNG +PTPN11 STATE_CHANGE IFNG +PDGFRA INTERACTS_WITH IFNG +TBP PP TP53 +TP53 PP HSPA1A +PIK3R1 IN_SAME_COMPONENT VLDLR +CBL CO_CONTROL_INDEPENDENT_SIMILAR DOCK1 +PIK3R1 CO_CONTROL_INDEPENDENT_SIMILAR DOCK1 +RB1 PP RBBP5 +TBP IN_SAME_COMPONENT SNAPC3 +RB1 PP SNAPC3 +RB1 PP MDM4 +TP53 PP MDM4 +TBP PP MDM2 +RB1 PP MDM2 +TAF1 PP MDM2 +CDKN2A PP MDM2 +TP53 PP MDM2 +MDM4 PP MDM2 +CBL PP EGFR +PIK3R1 PP EGFR +PTPN11 PP EGFR +ERBB2 PP EGFR +GAB1 PP EGFR +IFNG CO_CONTROL_INDEPENDENT_ANTI EGFR +CBL STATE_CHANGE JAK2 +PIK3R1 PP JAK2 +PTPN11 PP JAK2 +KIT PP JAK2 +ERBB2 PP JAK2 +GAB1 STATE_CHANGE JAK2 +IFNG IN_SAME_COMPONENT JAK2 +EGFR PP JAK2 +CBL PP CRK +PIK3R1 PP CRK +KIT PP CRK +KDR PP CRK +FRS2 PP CRK +TEK STATE_CHANGE CRK +GAB1 PP CRK +PDGFRA PP CRK +DOCK1 PP CRK +EGFR PP CRK +TP53 PP KLF6 +KCNA5 PP PTPRE +PTPRD PP PTPRE +ERBB2 PP PIK3C2B +EGFR PP PIK3C2B +TEK PP PTPRB +PIK3R1 CO_CONTROL_INDEPENDENT_ANTI PTEN +GAB1 CO_CONTROL_INDEPENDENT_SIMILAR PTEN +TP53 PP PTEN +CBL IN_SAME_COMPONENT SH3GL2 +EGFR IN_SAME_COMPONENT SH3GL2 +CBL STATE_CHANGE FGF23 +CDK6 PP CDKN2C +CDKN2A PP CDKN2C +TP53 PP CDKN2C +CNTN2 IN_SAME_COMPONENT NCAM1 +RB1 PP CDK4 +CDK6 IN_SAME_COMPONENT CDK4 +CDKN2A PP CDK4 +CDKN2C PP CDK4 +NUP50 STATE_CHANGE THOC4 +PIK3R1 STATE_CHANGE MAPK11 +KDR STATE_CHANGE MAPK11 +NUP50 IN_SAME_COMPONENT NUP107 +THOC4 STATE_CHANGE NUP107 +DCTN2 IN_SAME_COMPONENT TUBGCP2 +PIK3R1 PP IFNAR1 +PTPN11 PP IFNAR1 +IFNW1 PP IFNAR1 +IFNA2 PP IFNAR1 +IFNB1 PP IFNAR1 +IFNG METABOLIC_CATALYSIS IFNAR1 +PTPN11 METABOLIC_CATALYSIS A2M +RB1 PP BNC2 +TP53 PP EPHA3 +CRK PP EPHA3 +PIM1 PP EPHA3 +RB1 PP CCND2 +CDK6 PP CCND2 +CDK4 PP CCND2 +CDK4 PP CDKN2B +PPARA PP STAC3 +IFNAR1 PP IFNA1 +CBL CO_CONTROL_INDEPENDENT_SIMILAR PIK3CA +PIK3R1 PP PIK3CA +PTPN11 IN_SAME_COMPONENT PIK3CA +KDR STATE_CHANGE PIK3CA +FRS2 STATE_CHANGE PIK3CA +TEK STATE_CHANGE PIK3CA +GAB1 IN_SAME_COMPONENT PIK3CA +VLDLR IN_SAME_COMPONENT PIK3CA +DOCK1 CO_CONTROL_INDEPENDENT_SIMILAR PIK3CA +EGFR IN_SAME_COMPONENT PIK3CA +JAK2 CO_CONTROL_INDEPENDENT_SIMILAR PIK3CA +CRK CO_CONTROL_INDEPENDENT_SIMILAR PIK3CA +PTEN CO_CONTROL_INDEPENDENT_ANTI PIK3CA +MAPK11 STATE_CHANGE PIK3CA +A2M PP LYZ +CBL IN_SAME_COMPONENT HLA-DRA +PTPN11 STATE_CHANGE HLA-DRA +IFNG METABOLIC_CATALYSIS HLA-DRA +JAK2 CO_CONTROL_INDEPENDENT_SIMILAR HLA-DRA +CRK PP AVIL +CCT2 IN_SAME_COMPONENT CCT6A +DCTN2 IN_SAME_COMPONENT FGFR1OP +TUBGCP2 IN_SAME_COMPONENT FGFR1OP +NUP50 STATE_CHANGE SNRPE +THOC4 IN_SAME_COMPONENT SNRPE +NUP107 STATE_CHANGE SNRPE +DCTN2 IN_SAME_COMPONENT TUBGCP6 +TUBGCP2 IN_SAME_COMPONENT TUBGCP6 +FGFR1OP IN_SAME_COMPONENT TUBGCP6 +PIK3R1 IN_SAME_COMPONENT AGAP2 +PIK3CA IN_SAME_COMPONENT AGAP2 |
| b |
| diff -r 000000000000 -r 785ed8621503 test-data/network_plot.pdf |
| b |
| Binary file test-data/network_plot.pdf has changed |
| b |
| diff -r 000000000000 -r 785ed8621503 test-data/nodeType.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/nodeType.txt Wed Aug 24 08:27:40 2022 +0000 |
| b |
| @@ -0,0 +1,280 @@ +CDKN2B candidate +EGFR candidate +CDKN2A candidate +MTAP candidate +PTEN candidate +TP53 candidate +SEC61G candidate +IFNA1 candidate +ELAVL2 candidate +IFNA8 candidate +IFNA2 candidate +KLHL9 candidate +IFNA5 candidate +CYP27B1 candidate +IFNW1 candidate +CDK4 candidate +AGAP2 candidate +METTL1 candidate +AVIL candidate +MLLT3 candidate +IFNB1 candidate +CTDSP2 candidate +HLA-DRA candidate +NF1 candidate +XRCC6BP1 candidate +MDM2 candidate +OS9 candidate +PDGFRA candidate +CHIC2 candidate +NME7 candidate +RB1 candidate +C9orf82 candidate +MARS candidate +DTX3 candidate +PLAA candidate +CPM candidate +MBD6 candidate +KIT candidate +TEK candidate +DDIT3 candidate +KIF5A candidate +MOBKL2B candidate +NUP107 candidate +DCTN2 candidate +PTPRD candidate +PAOX candidate +ERBB2 candidate +PIK3R1 candidate +GLI1 candidate +CPSF6 candidate +ARHGAP9 candidate +PIK3CA candidate +FRS2 candidate +LYZ candidate +INHBC candidate +INHBE candidate +YEATS4 candidate +LNX1 candidate +MDM4 candidate +ECHS1 candidate +KDR candidate +KISS1 candidate +RAB3IP candidate +CCT2 candidate +ETNK2 candidate +REN candidate +PPP1R15B candidate +SOX13 candidate +PIK3C2B candidate +HMGA2 candidate +TYRP1 candidate +TPD52L3 candidate +DOCK1 candidate +LAX1 candidate +PRELP candidate +SNRPE candidate +CCT6A candidate +GRIP1 candidate +RAP1B candidate +ATP2B4 candidate +PTPRE candidate +ZC3H11A candidate +OPTC candidate +ADAM12 candidate +FIP1L1 candidate +NFASC candidate +MKI67 candidate +R3HDM2 candidate +PSIP1 candidate +CNOT2 candidate +AVPR1A candidate +KIAA2026 candidate +CD274 candidate +RASL11B candidate +CCND2 candidate +BNIP3 candidate +GLDC candidate +EPHA3 candidate +KCNV2 candidate +MGMT candidate +STAC3 candidate +SNAPC3 candidate +HELB candidate +JAK2 candidate +GLIS3 candidate +CAND1 candidate +SGCB candidate +CDC37L1 candidate +BNC2 candidate +PPP2R2D candidate +SRGAP1 candidate +LMO7 candidate +FMOD candidate +ZDHHC21 candidate +KLRC3 candidate +SUMF2 candidate +RFX3 candidate +KIAA0020 candidate +NFIB candidate +RLN2 candidate +SH3GL2 candidate +IL33 candidate +MPDZ candidate +INPP5A candidate +VLDLR candidate +SLC1A1 candidate +DPYSL4 candidate +CLOCK candidate +CER1 candidate +SMARCA2 candidate +DST candidate +PHKG1 candidate +UHRF2 candidate +IRAK3 candidate +MYO3A candidate +CELSR1 candidate +C22orf9 candidate +GAD2 candidate +PANX2 candidate +RIBC2 candidate +TSPO candidate +SLC12A6 candidate +TMEM19 candidate +RAPGEF3 candidate +SMC1B candidate +BIK candidate +PARVG candidate +ARID2 candidate +TAF1 candidate +CRELD2 candidate +CDKN2C candidate +DACH1 candidate +KCNQ1 candidate +EDNRB candidate +SLC6A12 candidate +RAD51AP1 candidate +SBF1 candidate +ENO1 candidate +DIAPH3 candidate +CCR6 candidate +UCHL3 candidate +PARP11 candidate +TBC1D4 candidate +BTG2 candidate +NUP50 candidate +HDAC10 candidate +RPS6 candidate +CACNA1C candidate +BRD1 candidate +RBBP5 candidate +EFCAB4B candidate +NMU candidate +WIF1 candidate +NDUFA9 candidate +NTF3 candidate +TBK1 candidate +PHACTR3 candidate +NDFIP2 candidate +FGF6 candidate +RASSF4 candidate +KLF5 candidate +PFKP candidate +TUBGCP2 candidate +UPK3A candidate +KCNA1 candidate +ARHGAP8 candidate +RRAGA candidate +RERE candidate +PIM1 candidate +HSPA1A candidate +CTNNA3 candidate +PIM3 candidate +PHF10 candidate +HDAC7 candidate +APBB1IP candidate +KLF12 candidate +PTPRR candidate +IFNG candidate +GTPBP4 candidate +FGF23 candidate +PRMT8 candidate +TYMP candidate +SPRY2 candidate +MAPK8IP2 candidate +C13orf34 candidate +DYRK2 candidate +MAPK12 candidate +WDR37 candidate +MLC1 candidate +PDCL2 candidate +PDCD2 candidate +XPOT candidate +EXOC1 candidate +AKR1C3 candidate +SAPS2 candidate +VDR candidate +CNTN2 candidate +NDUFA4L2 candidate +AKR1C4 candidate +BCL11A candidate +KLHL1 candidate +SCEL candidate +ADORA1 candidate +SPAG6 candidate +MYCBP2 candidate +A2M candidate +OMG candidate +PLXNB2 candidate +PSMB1 candidate +RAB11FIP4 candidate +ATXN10 candidate +PCDH17 candidate +FBLN1 candidate +ARSA candidate +PARVB candidate +KLF6 candidate +COMMD6 candidate +PTPRB candidate +TBP candidate +DNAJC1 candidate +MYBPH candidate +KCNA5 candidate +FGFR1OP candidate +RPS6KA2 candidate +FAM120B candidate +CPT1B candidate +THOC4 candidate +C10orf10 candidate +PDE10A candidate +NCAM1 candidate +COMMD3 candidate +ZMYND11 candidate +FAF1 candidate +CA6 candidate +TUBGCP6 candidate +TCP10 candidate +THBS2 candidate +PPARA candidate +IL22 candidate +DIS3 candidate +MAPK11 candidate +ST7 candidate +DLL1 candidate +BRP44L candidate +BMI1 candidate +CTRB1 candidate +AKAP3 candidate +SCUBE1 candidate +PTPRZ1 candidate +SAMM50 candidate +WNT7B candidate +LEMD3 candidate +POU4F1 candidate +RABL2B candidate +CRK linker +IFNAR1 linker +CBL linker +GAB1 linker +CDK6 linker +PTPN11 linker |
| b |
| diff -r 000000000000 -r 785ed8621503 tool_conf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_conf.xml Wed Aug 24 08:27:40 2022 +0000 |
| b |
| @@ -0,0 +1,24 @@ +<?xml version="1.0"?> +<tool_dependency> +<package name="R" version="4.0.0"> +<repository name="package_r_4_0_0" owner="iuc" /> +</package> +<package name="netboxr" version="1.6.0"> +<install version="1.0"> +<actions> +<action type="setup_r_environment"> +<repository name="package_r_3_2_1" owner="iuc"> +<package name="R" version="3.2.1" /> +</repository> +<package name = "igraph"> +https://cran.r-project.org/src/contrib/igraph_1.3.0.tar.gz +</package> +<package name = "netboxr"> +https://www.bioconductor.org/packages/release/bioc/src/contrib/netboxr_1.6. +0.tar.gz +</package> +</action> +</actions> +</install> +</package> +</tool_dependency> |