# HG changeset patch
# User bgruening
# Date 1661329660 0
# Node ID 785ed86215037fee2f89fb2387449c030dd575d5
planemo upload commit 13e28726551f8751007f28a3c6cd5d00ba278056
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
@@ -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)
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
@@ -0,0 +1,151 @@
+
+ enables automated discovery of biological process modules by network analysis.
+
+ bioconductor-netboxr
+
+
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+
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+
+
+
+
+
+ output_pdf is True
+
+
+ localModel is True
+
+
+ outputSIF is True
+
+
+ output_neighbor is True
+
+
+ moduleMembership is True
+
+
+ nodeType is True
+
+
+
+
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+
+
+ 10.1371/journal.pone.0234669
+
+
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
@@ -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
diff -r 000000000000 -r 785ed8621503 test-data/localModel_histogram.pdf
Binary file test-data/localModel_histogram.pdf has changed
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
@@ -0,0 +1,893 @@
+idx name localDegree globalDegree pValueRaw oddsRatio pValueFDR
+1712 CRK 11 81 2.39208791593171e-05 1.70873218314362 0.0186673141177578
+4546 IFNAR1 6 23 4.18549643895914e-05 2.51872572932126 0.0186673141177578
+20 CBL 14 140 6.50546994954036e-05 1.3610568890526 0.0193429306499667
+500 GAB1 8 57 0.000248319689968565 1.75112196905105 0.0488782736525554
+414 CDK6 5 21 0.000300851540057881 2.40690610751877 0.0488782736525554
+84 PTPN11 14 163 0.000328777625465619 1.19140466680817 0.0488782736525554
+883 NRCAM 3 6 0.000479055427005265 3.49957222828438 0.0610453486983852
+1589 EGF 8 67 0.00075960357041191 1.56599925702267 0.0623864456740024
+723 E4F1 3 7 0.000820026182632156 3.24814652197521 0.0623864456740024
+2002 UBE2A 3 7 0.000820026182632156 3.24814652197521 0.0623864456740024
+2011 CCNG1 3 7 0.000820026182632156 3.24814652197521 0.0623864456740024
+9028 SH3BGRL3 2 2 0.000871691877932093 5.10566742579647 0.0623864456740024
+1075 IFNAR2 6 39 0.000909219499733219 1.86759645259685 0.0623864456740024
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+13 ERRFI1 2 3 0.002563877147336 4.00694389623609 0.0788613246697833
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+7556 SF3B5 2 103 0.813738704638071 -0.218836844469312 0.847756374911252
+7557 SF4 2 103 0.813738704638071 -0.218836844469312 0.847756374911252
+7586 SNRNP200 2 103 0.813738704638071 -0.218836844469312 0.847756374911252
+7587 SNRNP40 2 103 0.813738704638071 -0.218836844469312 0.847756374911252
+6329 ATP5J2 2 104 0.81795993658245 -0.22875334948814 0.847756374911252
+5496 RBM5 2 104 0.81795993658245 -0.22875334948814 0.847756374911252
+7487 PRPF8 2 104 0.81795993658245 -0.22875334948814 0.847756374911252
+2695 RPL5 2 105 0.822095587778289 -0.238574681196091 0.847756374911252
+2087 SF3A3 2 105 0.822095587778289 -0.238574681196091 0.847756374911252
+2424 SNRPB2 2 105 0.822095587778289 -0.238574681196091 0.847756374911252
+2473 TXNL4A 2 105 0.822095587778289 -0.238574681196091 0.847756374911252
+2816 CSTF1 2 105 0.822095587778289 -0.238574681196091 0.847756374911252
+3365 CCAR1 2 105 0.822095587778289 -0.238574681196091 0.847756374911252
+4595 SF3B2 2 105 0.822095587778289 -0.238574681196091 0.847756374911252
+6192 EFTUD2 2 105 0.822095587778289 -0.238574681196091 0.847756374911252
+1486 PAPOLA 2 106 0.826147005130104 -0.248302670138155 0.848989779465498
+1691 CD2BP2 2 106 0.826147005130104 -0.248302670138155 0.848989779465498
+2422 SF3A2 2 106 0.826147005130104 -0.248302670138155 0.848989779465498
+1766 SF3A1 2 107 0.830115531036522 -0.257939094556514 0.849154878078644
+3059 PRPF4 2 107 0.830115531036522 -0.257939094556514 0.849154878078644
+3517 PABPN1 2 107 0.830115531036522 -0.257939094556514 0.849154878078644
+7326 HNRNPC 2 107 0.830115531036522 -0.257939094556514 0.849154878078644
+4297 SF3B3 2 108 0.834002502480785 -0.267485682364305 0.852153759693998
+2988 PCBP2 2 109 0.837809250178602 -0.276944113027159 0.855063902928276
+4468 SF3B4 2 110 0.841537097780771 -0.286316019357612 0.857886961394797
+665 SF3B1 2 111 0.845187361128093 -0.295602989227195 0.860624573203492
+3964 PTBP1 2 113 0.85226035524807 -0.31392825609699 0.865849928110796
+439 VIM 2 113 0.85226035524807 -0.31392825609699 0.865849928110796
+3919 RPS7 2 115 0.859038577822236 -0.33193177808228 0.870752740247085
+287 SMAD1 2 115 0.859038577822236 -0.33193177808228 0.870752740247085
+2815 CSTF2 2 117 0.865532209448699 -0.349624797847373 0.876339081530352
+2801 LSM2 2 118 0.868675436084772 -0.358358223296043 0.878524363931538
+3442 SMC1A 2 121 0.877705505480484 -0.384121445080123 0.886651541210183
+3825 PCBP1 2 122 0.88058634707523 -0.392567559856226 0.888555454288581
+677 RPS3A 2 124 0.886161358114687 -0.409254341477723 0.89317054399808
+683 BUB3 2 134 0.910596051541953 -0.488854243172278 0.916762616225081
+2675 BUB1B 2 138 0.918923494761648 -0.51904788356207 0.924103446817801
+4732 MAD2L1 2 139 0.920888734702681 -0.526460135724721 0.925036882156297
+1684 CDC20 2 142 0.926519520852894 -0.548382633000971 0.928601587191889
+4003 EEF1G 2 142 0.926519520852894 -0.548382633000971 0.928601587191889
+4955 EEF1A1 2 168 0.961736895547538 -0.721112630716305 0.962816286002699
+6187 RPS27 2 186 0.975923212389053 -0.825808759394024 0.975923212389053
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
@@ -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
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
@@ -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
diff -r 000000000000 -r 785ed8621503 test-data/network_plot.pdf
Binary file test-data/network_plot.pdf has changed
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
@@ -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
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
@@ -0,0 +1,24 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+https://cran.r-project.org/src/contrib/igraph_1.3.0.tar.gz
+
+
+https://www.bioconductor.org/packages/release/bioc/src/contrib/netboxr_1.6.
+0.tar.gz
+
+
+
+
+
+