Mercurial > repos > ppericard > viscorvar
changeset 5:88c1fd2ac110 draft default tip
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 21d09ff286a496ff475f32626d88dd42423ae663"
| author | ppericard |
|---|---|
| date | Tue, 07 Sep 2021 10:40:08 +0000 |
| parents | d4e9f7546dfa |
| children | |
| files | data/block_Y.tsv data/meta_sample.tsv data/metadata_mirna.tsv data/metadata_mrna.tsv data/metadata_protein.tsv data/mirna.tsv data/mrna.tsv data/param_integration_mixOmics.txt data/protein.tsv data/response_var.tsv data/var_interest.tsv macros_mixomics.xml macros_viscorvar.xml mixomics_blocksplsda.R mixomics_blocksplsda.xml mixomics_plotindiv.xml mixomics_plotvar.xml viscorvar_circlecor.xml viscorvar_computematsimilarity.xml viscorvar_matcoraddvar.xml viscorvar_networkvar.R viscorvar_networkvar.xml |
| diffstat | 22 files changed, 1426 insertions(+), 118 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/block_Y.tsv Tue Sep 07 10:40:08 2021 +0000 @@ -0,0 +1,151 @@ + Basal Her2 LumA +A0FJ 1 0 0 +A13E 1 0 0 +A0G0 1 0 0 +A0SX 1 0 0 +A143 1 0 0 +A0DA 1 0 0 +A0B3 1 0 0 +A0I2 1 0 0 +A0RT 1 0 0 +A131 1 0 0 +A124 1 0 0 +A1B6 1 0 0 +A1AZ 1 0 0 +A0YM 1 0 0 +A04P 1 0 0 +A04T 1 0 0 +A0AT 1 0 0 +A0AL 1 0 0 +A0CE 1 0 0 +A07R 1 0 0 +A0FL 1 0 0 +A150 1 0 0 +A0E0 1 0 0 +A0U4 1 0 0 +A0XU 1 0 0 +A0AV 1 0 0 +A0AR 1 0 0 +A0RX 1 0 0 +A0D2 1 0 0 +A0CM 1 0 0 +A0WX 1 0 0 +A0T0 1 0 0 +A0T2 1 0 0 +A04U 1 0 0 +A0JL 1 0 0 +A147 1 0 0 +A0B9 1 0 0 +A1AI 1 0 0 +A14X 1 0 0 +A12V 1 0 0 +A1AY 1 0 0 +A0D0 1 0 0 +A0SK 1 0 0 +A128 1 0 0 +A04D 1 0 0 +A0A7 0 1 0 +A094 0 1 0 +A12L 0 1 0 +A0I9 0 1 0 +A0EE 0 1 0 +A135 0 1 0 +A152 0 1 0 +A18P 0 1 0 +A18R 0 1 0 +A08X 0 1 0 +A0TX 0 1 0 +A09X 0 1 0 +A1AT 0 1 0 +A12Q 0 1 0 +A12T 0 1 0 +A0RH 0 1 0 +A07I 0 1 0 +A04W 0 1 0 +A12P 0 1 0 +A0EQ 0 1 0 +A0D1 0 1 0 +A09G 0 1 0 +A1B0 0 1 0 +A14P 0 1 0 +A0T1 0 1 0 +A137 0 1 0 +A13Z 0 1 0 +A08L 0 1 0 +A0IK 0 1 0 +A12D 0 1 0 +A0XN 0 0 1 +A0B0 0 0 1 +A18S 0 0 1 +A0CS 0 0 1 +A0EI 0 0 1 +A0IO 0 0 1 +A0T6 0 0 1 +A1AU 0 0 1 +A07Z 0 0 1 +A0XS 0 0 1 +A1BD 0 0 1 +A08T 0 0 1 +A12Y 0 0 1 +A0J5 0 0 1 +A18F 0 0 1 +A0AS 0 0 1 +A0DV 0 0 1 +A140 0 0 1 +A0SU 0 0 1 +A12A 0 0 1 +A0RM 0 0 1 +A0AZ 0 0 1 +A0EW 0 0 1 +A0XW 0 0 1 +A12B 0 0 1 +A0BP 0 0 1 +A0RG 0 0 1 +A0T7 0 0 1 +A08A 0 0 1 +A0DK 0 0 1 +A0SH 0 0 1 +A18N 0 0 1 +A06P 0 0 1 +A15L 0 0 1 +A0YL 0 0 1 +A1AL 0 0 1 +A133 0 0 1 +A086 0 0 1 +A0I8 0 0 1 +A0EA 0 0 1 +A09A 0 0 1 +A0DS 0 0 1 +A1B1 0 0 1 +A0X0 0 0 1 +A1AP 0 0 1 +A0W5 0 0 1 +A0JF 0 0 1 +A1AV 0 0 1 +A0RO 0 0 1 +A08Z 0 0 1 +A0RV 0 0 1 +A0DP 0 0 1 +A0EX 0 0 1 +A15R 0 0 1 +A0FD 0 0 1 +A0ES 0 0 1 +A0BM 0 0 1 +A0EU 0 0 1 +A12X 0 0 1 +A146 0 0 1 +A0CD 0 0 1 +A0BQ 0 0 1 +A04A 0 0 1 +A0CT 0 0 1 +A0TZ 0 0 1 +A03L 0 0 1 +A1AK 0 0 1 +A0E1 0 0 1 +A0H7 0 0 1 +A0FS 0 0 1 +A0BS 0 0 1 +A08O 0 0 1 +A12H 0 0 1 +A15E 0 0 1 +A0W4 0 0 1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/meta_sample.tsv Tue Sep 07 10:40:08 2021 +0000 @@ -0,0 +1,151 @@ + Y +A0FJ Basal +A13E Basal +A0G0 Basal +A0SX Basal +A143 Basal +A0DA Basal +A0B3 Basal +A0I2 Basal +A0RT Basal +A131 Basal +A124 Basal +A1B6 Basal +A1AZ Basal +A0YM Basal +A04P Basal +A04T Basal +A0AT Basal +A0AL Basal +A0CE Basal +A07R Basal +A0FL Basal +A150 Basal +A0E0 Basal +A0U4 Basal +A0XU Basal +A0AV Basal +A0AR Basal +A0RX Basal +A0D2 Basal +A0CM Basal +A0WX Basal +A0T0 Basal +A0T2 Basal +A04U Basal +A0JL Basal +A147 Basal +A0B9 Basal +A1AI Basal +A14X Basal +A12V Basal +A1AY Basal +A0D0 Basal +A0SK Basal +A128 Basal +A04D Basal +A0A7 Her2 +A094 Her2 +A12L Her2 +A0I9 Her2 +A0EE Her2 +A135 Her2 +A152 Her2 +A18P Her2 +A18R Her2 +A08X Her2 +A0TX Her2 +A09X Her2 +A1AT Her2 +A12Q Her2 +A12T Her2 +A0RH Her2 +A07I Her2 +A04W Her2 +A12P Her2 +A0EQ Her2 +A0D1 Her2 +A09G Her2 +A1B0 Her2 +A14P Her2 +A0T1 Her2 +A137 Her2 +A13Z Her2 +A08L Her2 +A0IK Her2 +A12D Her2 +A0XN LumA +A0B0 LumA +A18S LumA +A0CS LumA +A0EI LumA +A0IO LumA +A0T6 LumA +A1AU LumA +A07Z LumA +A0XS LumA +A1BD LumA +A08T LumA +A12Y LumA +A0J5 LumA +A18F LumA +A0AS LumA +A0DV LumA +A140 LumA +A0SU LumA +A12A LumA +A0RM LumA +A0AZ LumA +A0EW LumA +A0XW LumA +A12B LumA +A0BP LumA +A0RG LumA +A0T7 LumA +A08A LumA +A0DK LumA +A0SH LumA +A18N LumA +A06P LumA +A15L LumA +A0YL LumA +A1AL LumA +A133 LumA +A086 LumA +A0I8 LumA +A0EA LumA +A09A LumA +A0DS LumA +A1B1 LumA +A0X0 LumA +A1AP LumA +A0W5 LumA +A0JF LumA +A1AV LumA +A0RO LumA +A08Z LumA +A0RV LumA +A0DP LumA +A0EX LumA +A15R LumA +A0FD LumA +A0ES LumA +A0BM LumA +A0EU LumA +A12X LumA +A146 LumA +A0CD LumA +A0BQ LumA +A04A LumA +A0CT LumA +A0TZ LumA +A03L LumA +A1AK LumA +A0E1 LumA +A0H7 LumA +A0FS LumA +A0BS LumA +A08O LumA +A12H LumA +A15E LumA +A0W4 LumA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/metadata_mirna.tsv Tue Sep 07 10:40:08 2021 +0000 @@ -0,0 +1,185 @@ +Variable metadata_var1 metadata_var2 metadata_var3 +hsa-let-7a-1 182 79 44 +hsa-let-7a-2 137 151 74 +hsa-let-7a-3 53 136 136 +hsa-let-7b 32 168 147 +hsa-let-7c 169 33 78 +hsa-let-7d 114 21 160 +hsa-let-7e 43 4 22 +hsa-let-7f-1 58 152 67 +hsa-let-7f-2 128 148 85 +hsa-let-7g 30 70 69 +hsa-let-7i 141 90 125 +hsa-mir-100 118 45 6 +hsa-mir-101-1 13 57 165 +hsa-mir-101-2 34 38 176 +hsa-mir-103-1 183 23 138 +hsa-mir-103-2 105 142 54 +hsa-mir-106a 150 51 58 +hsa-mir-106b 9 94 37 +hsa-mir-107 39 66 168 +hsa-mir-10a 173 122 79 +hsa-mir-10b 135 87 96 +hsa-mir-125a 107 117 10 +hsa-mir-125b-1 22 140 42 +hsa-mir-126 87 83 104 +hsa-mir-127 140 35 33 +hsa-mir-128-1 104 62 49 +hsa-mir-128-2 18 183 150 +hsa-mir-1287 84 49 68 +hsa-mir-1301 47 14 173 +hsa-mir-1307 152 120 52 +hsa-mir-130a 171 126 31 +hsa-mir-130b 2 113 64 +hsa-mir-132 181 44 157 +hsa-mir-134 78 170 134 +hsa-mir-139 90 81 117 +hsa-mir-140 149 16 9 +hsa-mir-141 127 143 124 +hsa-mir-142 67 89 180 +hsa-mir-143 25 77 115 +hsa-mir-144 161 131 162 +hsa-mir-145 88 95 100 +hsa-mir-146a 79 160 83 +hsa-mir-146b 126 133 21 +hsa-mir-148a 155 86 172 +hsa-mir-148b 24 177 155 +hsa-mir-149 177 153 93 +hsa-mir-150 21 121 95 +hsa-mir-151 6 132 41 +hsa-mir-152 89 149 179 +hsa-mir-155 35 141 169 +hsa-mir-15a 71 93 99 +hsa-mir-15b 180 124 146 +hsa-mir-16-1 131 43 3 +hsa-mir-16-2 10 156 63 +hsa-mir-17 166 13 40 +hsa-mir-181a-1 85 169 129 +hsa-mir-181a-2 44 61 182 +hsa-mir-181b-1 73 182 32 +hsa-mir-181c 157 80 183 +hsa-mir-181d 49 67 159 +hsa-mir-182 76 129 61 +hsa-mir-183 178 139 56 +hsa-mir-185 167 114 65 +hsa-mir-186 146 109 62 +hsa-mir-191 40 40 181 +hsa-mir-192 125 63 16 +hsa-mir-193a 109 172 94 +hsa-mir-193b 17 96 116 +hsa-mir-194-1 162 32 102 +hsa-mir-194-2 176 99 122 +hsa-mir-195 86 157 119 +hsa-mir-196a-1 119 30 97 +hsa-mir-196b 3 104 88 +hsa-mir-197 83 58 178 +hsa-mir-199a-1 12 123 82 +hsa-mir-199a-2 158 52 142 +hsa-mir-199b 145 173 2 +hsa-mir-19b-2 168 17 77 +hsa-mir-200a 69 54 127 +hsa-mir-200b 14 39 53 +hsa-mir-200c 70 84 143 +hsa-mir-203 136 130 7 +hsa-mir-205 142 73 76 +hsa-mir-20a 100 36 98 +hsa-mir-21 94 176 51 +hsa-mir-210 27 102 109 +hsa-mir-214 110 105 174 +hsa-mir-218-2 91 27 50 +hsa-mir-22 160 98 91 +hsa-mir-221 138 69 151 +hsa-mir-222 116 92 73 +hsa-mir-223 16 137 43 +hsa-mir-2355 20 100 152 +hsa-mir-23a 54 3 11 +hsa-mir-23b 72 178 158 +hsa-mir-24-1 45 85 34 +hsa-mir-24-2 147 134 105 +hsa-mir-25 123 25 133 +hsa-mir-26a-2 64 101 30 +hsa-mir-26b 7 107 118 +hsa-mir-27a 101 150 17 +hsa-mir-27b 46 180 60 +hsa-mir-28 112 15 167 +hsa-mir-29a 36 64 1 +hsa-mir-29b-1 59 22 19 +hsa-mir-29b-2 74 179 101 +hsa-mir-29c 98 106 144 +hsa-mir-3065 134 159 46 +hsa-mir-3074 93 46 166 +hsa-mir-30a 143 181 114 +hsa-mir-30b 38 147 156 +hsa-mir-30c-2 1 76 111 +hsa-mir-30d 42 47 84 +hsa-mir-30e 172 71 57 +hsa-mir-32 15 55 48 +hsa-mir-320a 57 5 170 +hsa-mir-324 33 184 175 +hsa-mir-328 144 37 29 +hsa-mir-330 56 115 8 +hsa-mir-331 95 8 18 +hsa-mir-337 108 108 149 +hsa-mir-338 97 19 163 +hsa-mir-339 175 175 66 +hsa-mir-340 99 2 72 +hsa-mir-342 120 12 123 +hsa-mir-345 164 48 71 +hsa-mir-34a 81 145 70 +hsa-mir-3607 174 24 135 +hsa-mir-361 63 125 137 +hsa-mir-3613 68 34 154 +hsa-mir-3647 111 111 161 +hsa-mir-365-1 92 72 4 +hsa-mir-365-2 52 146 139 +hsa-mir-3653 102 118 80 +hsa-mir-374a 26 166 27 +hsa-mir-374b 37 6 14 +hsa-mir-375 31 127 20 +hsa-mir-378 29 56 103 +hsa-mir-379 55 154 140 +hsa-mir-381 139 112 132 +hsa-mir-409 5 116 55 +hsa-mir-423 65 161 15 +hsa-mir-424 122 164 36 +hsa-mir-425 66 165 145 +hsa-mir-429 41 138 87 +hsa-mir-451 129 88 112 +hsa-mir-452 117 59 184 +hsa-mir-454 62 60 106 +hsa-mir-455 106 7 121 +hsa-mir-484 133 53 126 +hsa-mir-486 170 171 75 +hsa-mir-497 61 155 38 +hsa-mir-500a 130 31 59 +hsa-mir-501 179 163 81 +hsa-mir-505 159 162 26 +hsa-mir-532 50 11 110 +hsa-mir-539 165 74 107 +hsa-mir-542 51 135 24 +hsa-mir-574 4 174 25 +hsa-mir-576 8 103 120 +hsa-mir-582 184 65 47 +hsa-mir-584 60 10 141 +hsa-mir-589 132 28 130 +hsa-mir-590 163 26 153 +hsa-mir-625 82 110 5 +hsa-mir-628 154 42 35 +hsa-mir-629 153 29 113 +hsa-mir-660 75 18 86 +hsa-mir-664 103 119 28 +hsa-mir-7-1 96 9 108 +hsa-mir-708 28 97 23 +hsa-mir-744 23 20 177 +hsa-mir-769 115 158 148 +hsa-mir-874 124 91 90 +hsa-mir-9-1 11 144 89 +hsa-mir-9-2 19 41 39 +hsa-mir-92a-1 80 78 45 +hsa-mir-92a-2 121 75 12 +hsa-mir-92b 113 128 164 +hsa-mir-93 77 1 171 +hsa-mir-96 48 68 92 +hsa-mir-98 156 50 131 +hsa-mir-99a 151 167 13 +hsa-mir-99b 148 82 128
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/metadata_mrna.tsv Tue Sep 07 10:40:08 2021 +0000 @@ -0,0 +1,201 @@ +Variable metadata_var1 metadata_var2 metadata_var3 +RTN2 67 127 139 +NDRG2 18 110 40 +CCDC113 117 72 99 +FAM63A 77 190 113 +ACADS 94 80 186 +GMDS 149 14 178 +HLA-H 140 21 168 +SEMA4A 80 124 126 +ETS2 107 178 11 +LIMD2 35 68 71 +NME3 85 45 92 +ZEB1 188 139 63 +CDCP1 198 13 169 +GIYD2 84 2 97 +RTKN2 180 168 54 +MANSC1 153 99 32 +TAGLN 152 93 195 +IFIT3 108 196 101 +ARL4C 66 151 112 +HTRA1 157 121 125 +KIF13B 130 3 110 +CPPED1 113 97 167 +SKAP2 150 30 114 +ASPM 128 108 34 +KDM4B 40 157 145 +TBXAS1 55 39 127 +MT1X 189 5 21 +MED13L 135 173 157 +SNORA8 71 174 182 +RGS1 28 200 161 +CBX6 133 96 84 +WWC2 184 152 67 +TNFRSF12A 169 140 53 +ZNF552 21 164 42 +MAPRE2 193 23 131 +SEMA5A 109 106 83 +STAT5A 174 182 64 +FLI1 43 60 116 +COL15A1 127 134 93 +C7orf55 74 177 85 +ASF1B 45 114 78 +FUT8 38 141 98 +LASS4 60 16 100 +SQLE 115 166 138 +GPC4 53 65 88 +AKAP12 196 90 152 +AGL 69 95 61 +ADAMTS4 156 57 29 +EPHB3 90 183 189 +MAP3K1 23 123 107 +PRNP 70 181 4 +PROM2 111 59 190 +SLCO3A1 175 150 46 +SNHG1 47 191 187 +PRKCDBP 119 180 103 +MXI1 32 70 102 +CSF1R 110 103 143 +TANC2 129 78 24 +SLC19A2 7 9 177 +RHOU 36 128 95 +C4orf34 75 40 165 +LRIG1 39 149 133 +DOCK8 167 18 65 +BOC 98 67 25 +C11orf52 100 34 86 +S100A16 116 44 183 +NRARP 179 87 81 +TTC23 14 189 69 +TBC1D4 103 63 119 +DEPDC6 3 81 59 +ILDR1 9 85 111 +SDC1 143 98 106 +STC2 64 86 197 +DTWD2 166 47 159 +TCF4 105 69 38 +ITPR2 65 154 129 +DPYD 82 112 141 +NME1 178 109 41 +EGLN3 102 135 68 +CD302 120 105 58 +AHR 41 58 77 +LAPTM4B 126 83 188 +OCLN 185 144 149 +HIST1H2BK 139 61 37 +HDAC11 57 15 57 +C18orf1 132 148 27 +C6orf192 89 53 50 +AMPD3 29 38 122 +COL6A1 68 94 6 +RAB3IL1 146 24 22 +APBB1IP 10 8 135 +PSIP1 1 74 163 +EIF2AK2 144 33 171 +CSRP2 104 35 62 +EIF4EBP3 138 119 180 +LYN 172 120 153 +WDR76 87 175 51 +SAMD9L 34 115 150 +ASPH 173 130 176 +RBL1 134 101 105 +SLC43A3 8 158 28 +HN1 123 84 200 +TTC39A 114 50 146 +MTL5 42 54 74 +NES 124 22 90 +APOD 187 37 192 +RIN3 177 143 3 +ALCAM 15 12 140 +C1orf38 25 170 158 +PLCD3 197 28 26 +BSPRY 11 41 47 +NTN4 2 165 55 +IL1R1 192 75 147 +EMP3 81 167 70 +ZKSCAN1 162 169 166 +FMNL2 54 142 162 +OGFRL1 194 153 173 +IRF5 19 25 87 +IGSF3 168 145 118 +DBP 44 160 104 +CNN2 181 10 94 +CAMK2D 195 185 196 +SIGIRR 163 64 185 +AKAP9 155 29 79 +ICA1 101 126 91 +FGD5 141 104 155 +DSG2 4 199 132 +E2F1 6 195 80 +QSOX1 142 27 179 +TOB1 160 198 128 +CSF3R 176 192 44 +SHROOM3 161 36 72 +CCDC80 165 32 20 +FRMD6 12 136 31 +CXCL12 79 197 18 +CCNA2 16 176 144 +TIGD5 20 71 193 +ALDH6A1 24 162 73 +POSTN 86 4 198 +FZD4 17 43 174 +NCAPG2 171 62 39 +SDC4 106 76 136 +SNED1 5 49 10 +PLEKHA4 93 6 175 +KCNAB2 78 117 19 +SH3KBP1 76 51 12 +IGSF9 159 194 17 +DNLZ 151 11 82 +S1PR3 186 100 36 +PTPRE 63 161 134 +FLJ23867 46 19 30 +PLSCR1 125 66 109 +LMO4 131 111 14 +IFITM2 48 125 120 +LRRC25 121 52 164 +TST 72 133 160 +NCF4 97 118 181 +NCOA7 51 156 89 +IL4R 200 122 148 +CCDC64B 154 42 56 +SGPP1 13 46 172 +RUNX3 122 48 123 +SLC5A6 199 56 121 +IFIH1 164 107 191 +PREX1 27 91 15 +PLAUR 95 179 124 +CDK18 136 163 170 +SLC43A2 148 20 108 +GK 96 186 1 +ICAM2 145 132 13 +YPEL2 191 146 151 +CBR1 37 82 199 +MEX3A 183 17 115 +ZNRF3 147 26 184 +PTPRM 30 88 194 +C1orf162 137 171 7 +GAS6 58 89 33 +C1QB 59 129 35 +PVRL4 26 7 117 +CTSK 88 184 137 +MRVI1 83 159 8 +LEF1 91 172 52 +PLCD4 52 102 130 +ZNF37B 49 55 16 +MEGF9 33 113 43 +GINS2 170 79 142 +FAM13A 92 31 23 +CPT1A 182 193 5 +SNX10 31 187 60 +TRIM45 158 188 48 +ELP2 61 116 2 +ALOX5 112 138 66 +AMN1 73 92 49 +CERCAM 22 1 156 +SEMA3C 56 77 96 +KRT8 99 147 76 +TP53INP2 62 131 75 +JAM3 118 137 9 +ZNF680 190 155 45 +PBX1 50 73 154
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/metadata_protein.tsv Tue Sep 07 10:40:08 2021 +0000 @@ -0,0 +1,143 @@ +Variable metadata_var1 metadata_var2 metadata_var3 +14-3-3_epsilon 99 58 121 +4E-BP1 66 91 11 +4E-BP1_pS65 112 4 123 +4E-BP1_pT37 119 93 53 +4E-BP1_pT70 127 85 83 +53BP1 76 70 77 +A-Raf_pS299 134 104 69 +ACC1 22 32 78 +ACC_pS79 59 72 14 +AMPK_alpha 142 27 47 +AMPK_pT172 4 8 138 +ANLN 113 63 59 +AR 138 79 124 +ARID1A 7 6 57 +ASNS 42 15 106 +ATM 135 50 24 +Akt 35 140 4 +Akt_pS473 120 42 30 +Akt_pT308 23 20 42 +Annexin_I 14 122 140 +B-Raf 118 87 109 +Bak 11 54 117 +Bax 20 130 75 +Bcl-2 79 2 27 +Bcl-xL 124 16 21 +Beclin 39 83 112 +Bid 86 113 136 +Bim 54 31 37 +C-Raf 98 129 139 +C-Raf_pS338 65 137 41 +CD31 94 88 16 +CD49b 41 103 1 +CDK1 133 40 86 +Caspase-7_cleavedD198 52 107 74 +Caveolin-1 53 46 3 +Chk1 88 51 40 +Chk1_pS345 63 77 36 +Chk2 61 71 107 +Chk2_pT68 110 33 58 +Claudin-7 12 62 33 +Collagen_VI 78 97 94 +Cyclin_B1 89 56 93 +Cyclin_D1 96 123 17 +Cyclin_E1 111 78 82 +DJ-1 123 94 98 +Dvl3 58 116 38 +E-Cadherin 45 10 26 +EGFR 57 121 22 +EGFR_pY1068 31 76 71 +EGFR_pY1173 139 68 18 +ER-alpha 8 111 29 +ER-alpha_pS118 141 18 44 +ERK2 47 90 66 +FOXO3a 9 49 128 +Fibronectin 104 99 20 +GAB2 130 55 119 +GATA3 10 37 115 +GSK3-alpha-beta 136 12 88 +GSK3-alpha-beta_pS21_S9 131 13 51 +HER2 74 119 105 +HER2_pY1248 85 65 118 +HER3 132 48 129 +HER3_pY1289 29 26 110 +HSP70 137 75 7 +IGFBP2 122 73 15 +INPP4B 38 23 46 +IRS1 43 34 81 +JNK2 26 118 104 +JNK_pT183_pT185 93 115 68 +K-Ras 103 139 70 +Ku80 95 39 61 +LBK1 77 66 50 +Lck 64 38 134 +MAPK_pT202_Y204 82 95 91 +MEK1 34 112 142 +MEK1_pS217_S221 102 127 64 +MIG-6 69 25 87 +Mre11 116 132 116 +N-Cadherin 25 101 56 +NF-kB-p65_pS536 17 74 10 +NF2 37 120 97 +Notch1 16 64 80 +P-Cadherin 5 45 31 +PAI-1 128 24 72 +PCNA 62 9 25 +PDCD4 81 134 52 +PDK1_pS241 107 81 48 +PI3K-p110-alpha 21 86 19 +PKC-alpha 72 114 125 +PKC-alpha_pS657 70 14 54 +PKC-delta_pS664 15 47 100 +PR 50 60 35 +PRAS40_pT246 101 125 132 +PRDX1 36 96 76 +PTEN 115 53 127 +Paxillin 55 100 133 +Pea-15 83 135 9 +RBM3 1 30 23 +Rad50 108 17 113 +Rb_pS807_S811 129 11 62 +S6 13 19 43 +S6_pS235_S236 91 52 135 +S6_pS240_S244 46 44 65 +SCD1 80 141 96 +STAT3_pY705 44 1 84 +STAT5-alpha 100 67 6 +Shc_pY317 114 84 126 +Smad1 126 59 90 +Smad3 51 109 8 +Smad4 30 80 92 +Src 18 5 131 +Src_pY416 60 28 63 +Src_pY527 109 89 13 +Stathmin 19 22 45 +Syk 67 98 39 +Transglutaminase 28 142 95 +Tuberin 105 41 12 +VEGFR2 48 61 99 +XBP1 56 29 28 +XRCC1 87 108 85 +YAP_pS127 3 138 122 +YB-1 27 82 2 +YB-1_pS102 24 124 5 +alpha-Catenin 73 7 32 +beta-Catenin 68 92 55 +c-Kit 2 131 60 +c-Met_pY1235 140 105 34 +c-Myc 40 133 79 +eEF2 49 110 141 +eEF2K 71 3 49 +eIF4E 92 21 67 +mTOR 125 69 102 +mTOR_pS2448 33 102 120 +p27 6 43 111 +p27_pT157 97 117 130 +p27_pT198 90 106 108 +p38_MAPK 32 126 137 +p38_pT180_Y182 84 128 103 +p53 106 36 101 +p70S6K 121 35 114 +p70S6K_pT389 75 57 89 +p90RSK_pT359_S363 117 136 73
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/mirna.tsv Tue Sep 07 10:40:08 2021 +0000 @@ -0,0 +1,185 @@ + A0FJ A13E A0G0 A0SX A143 A0DA A0B3 A0I2 A0RT A131 A124 A1B6 A1AZ A0YM A04P A04T A0AT A0AL A0CE A07R A0FL A150 A0E0 A0U4 A0XU A0AV A0AR A0RX A0D2 A0CM A0WX A0T0 A0T2 A04U A0JL A147 A0B9 A1AI A14X A12V A1AY A0D0 A0SK A128 A04D A0A7 A094 A12L A0I9 A0EE A135 A152 A18P A18R A08X A0TX A09X A1AT A12Q A12T A0RH A07I A04W A12P A0EQ A0D1 A09G A1B0 A14P A0T1 A137 A13Z A08L A0IK A12D A0XN A0B0 A18S A0CS A0EI A0IO A0T6 A1AU A07Z A0XS A1BD A08T A12Y A0J5 A18F A0AS A0DV A140 A0SU A12A A0RM A0AZ A0EW A0XW A12B A0BP A0RG A0T7 A08A A0DK A0SH A18N A06P A15L A0YL A1AL A133 A086 A0I8 A0EA A09A A0DS A1B1 A0X0 A1AP A0W5 A0JF A1AV A0RO A08Z A0RV A0DP A0EX A15R A0FD A0ES A0BM A0EU A12X A146 A0CD A0BQ A04A A0CT A0TZ A03L A1AK A0E1 A0H7 A0FS A0BS A08O A12H A15E A0W4 +hsa-let-7a-1 11.835815644832 12.8979316315316 12.3077264364518 12.0392931397056 13.3909710853051 12.3403716402942 12.4376972179566 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/param_integration_mixOmics.txt Tue Sep 07 10:40:08 2021 +0000 @@ -0,0 +1,9 @@ +Nombre de variables à sélectionner : +mrna 50 +mirna 40 +protein 40 + +ncomp = 2 + + +
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-0.753121614133206 0.197358871901196 -0.11029060468985 -0.23058471285409 -0.0167941039826035 -0.131859069194122 -0.142454191572913 -0.240619902083831 -0.456026783573473 -0.115758687472636 0.120209139314941 0.169955766448218 0.408111725209331 -0.238331593788539 -0.129847965244069 -0.133541704949751 0.0675045774388183 0.611913958337335 0.174902264298335 0.00292919392416219 -0.223947651138999 -0.363831591673215 -0.423511193750844 0.430174651585807 -0.0500570485844045 0.278655327903113 0.35704216515922 0.140726667446533 -0.0646879570248517 -0.0476114837371859 0.0973145489728668 -0.29474058971041 -0.0317919084424805 -0.201291885326395 0.331266886972276 -0.361543973894197 -0.456916525374331 -0.420486230769741 0.0565524609621154 -0.534364831076986 -0.477963887502463 -0.111135593558034 -0.336545756741778 0.39402165635646 -0.557989882486459 0.210415326066138 0.153776778632895 -0.592049600135786 0.248457626350141 -0.265291778295264 0.114093691624581 0.0730677977129317 0.277484232815996 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/response_var.tsv Tue Sep 07 10:40:08 2021 +0000 @@ -0,0 +1,3 @@ +Basal +Her2 +LumA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/var_interest.tsv Tue Sep 07 10:40:08 2021 +0000 @@ -0,0 +1,6 @@ +NDRG2 +CCDC113 +hsa-let-7a-1 +hsa-let-7a-2 +14-3-3_epsilon +4E-BP1
--- a/macros_mixomics.xml Tue Nov 17 13:01:44 2020 +0000 +++ b/macros_mixomics.xml Tue Sep 07 10:40:08 2021 +0000 @@ -1,7 +1,7 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">6.12</token> + <token name="@TOOL_VERSION@">6.14</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">bioconductor-mixomics</requirement> @@ -38,4 +38,4 @@ <citation type="doi">10.18129/B9.bioc.mixOmics</citation> </citations> </xml> -</macros> \ No newline at end of file +</macros>
--- a/macros_viscorvar.xml Tue Nov 17 13:01:44 2020 +0000 +++ b/macros_viscorvar.xml Tue Sep 07 10:40:08 2021 +0000 @@ -1,7 +1,7 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">0.7</token> + <token name="@TOOL_VERSION@">0.9</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">r-viscorvar</requirement> @@ -37,4 +37,4 @@ <citation type="doi">10.18129/B9.bioc.mixOmics</citation> --> </citations> </xml> -</macros> \ No newline at end of file +</macros>
--- a/mixomics_blocksplsda.R Tue Nov 17 13:01:44 2020 +0000 +++ b/mixomics_blocksplsda.R Tue Sep 07 10:40:08 2021 +0000 @@ -22,7 +22,6 @@ parser$add_argument('--correlation', dest='correlation', action="store_true", help="Add correlation between all blocks") parser$add_argument('--scheme', dest='scheme', default="horst", help="Scheme") -parser$add_argument('--mode', dest='mode', default="regression", help="Mode") parser$add_argument('--maxiter', dest='maxiter', type='integer', default=100, help="Maximum number of iterations") parser$add_argument('--scale', dest='scale', action="store_true", @@ -54,8 +53,6 @@ print(args$correlation) print("Scheme:") print(args$scheme) -print("Mode:") -print(args$mode) print("Max nb of iterations:") print(args$maxiter) print("Scale:") @@ -165,7 +162,6 @@ keepX = keepX, design = design, scheme = args$scheme, - mode = args$mode, scale = args$scale, init = args$init, tol = args$tol,
--- a/mixomics_blocksplsda.xml Tue Nov 17 13:01:44 2020 +0000 +++ b/mixomics_blocksplsda.xml Tue Sep 07 10:40:08 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="mixomics_blocksplsda" name="mixOmics block.splsda" version="@TOOL_VERSION@+galaxy2" profile="16.04" workflow_compatible="true"> +<tool id="mixomics_blocksplsda" name="mixOmics block.splsda" version="@TOOL_VERSION@+galaxy0" profile="16.04" workflow_compatible="true"> <description>performs N-integration and feature selection with Projection to Latent Structures models (PLS) with sparse Discriminant Analysis</description> @@ -33,7 +33,6 @@ --ncomp ${adv.ncomp} ${correlation} ##--scheme ${adv.scheme} - ##--mode ${adv.mode} --maxiter ${adv.maxiter} ##${adv.scale} --scale ## always activated hidden param @@ -79,12 +78,6 @@ <option value="horst" selected="true">horst</option> <option value="factorial" >factorial</option> <option value="centroid" >centroid</option> - </param> - <param name="mode" type="select" label="Mode"> - <option value="regression" selected="true">regression</option> - <option value="canonical" >canonical</option> - <option value="invariant" >invariant</option> - <option value="classic" >classic</option> </param> --> <param name="maxiter" type="integer" value="100" min="1" label="Maximum number of iterations" @@ -148,8 +141,8 @@ The blocks.splsda function is part of the mixOmics package for exploration and integration of omics datasets. This data integration takes as input parameters different omics datasets -(transcriptomic, metabolomic, metagenomic, ...) and a response variable (e.g. for a sample, the value of the response -variable is equal to « Treated » or « Control »). This data integration returns, for each omics dataset, variables +(transcriptomics, metabolomics, metagenomics, ...) and a response variable (e.g. for a sample, the value of the response +variable is equal to « Treated » or « Control »). This data integration is performed fo the scheme "horst" and the mode "regression". This data integration returns, for each omics dataset, variables which are correlated with the variables of the other omic datasets and the response variable. The other functions of this pipeline allow visualizing this correlated variables thanks to correlation circles and networks. @@ -198,9 +191,6 @@ The first row contains the metadata column names. The number of rows in the metadata file must be the same than the number of rows in the block data file, and the variables need to be in the same order. If a metadata file is provided, block.splsda output will be appended as new columns, otherwise a new file will be created. -Variables metadata files are optional. -If a file is provided, output metadata will be appended to the input file, otherwise a new output file will be created. - Global input files: ------------------- @@ -215,47 +205,14 @@ Samples metadata is in tabular format (.tsv). The first column contains the sample names. The first row contains the metadata column names. -Samples names must be in the same order in samples metadata (transposed) and all the blocks. One of the column (the last by default) must contain the samples groups for integration. +Samples names must be in the same order in samples metadata (transposed) and all the blocks. One of the column (the last by default) must contain the samples groups for data integration. ---------- Parameters ---------- -For each block (min 2 blocks): ------------------------------- - -Block name - Name of the block. If not provided, this will default to the input filename - Number of variables to select for each component - If set to 0 (default), all variables will be considered in the model - -Global parameters: ------------------- - -Sample description column number - -Number of components to include in the model - -Correlation between all blocks - -Advanced options: ------------------ - -Scheme - -Mode - -Maximum number of iterations - -Scale - -Init - -Convergence stopping value (tol) - -Near zero var - + tune.block.splsda can be used to set the number of variables to select on each component @HELP_MANUAL@
--- a/mixomics_plotindiv.xml Tue Nov 17 13:01:44 2020 +0000 +++ b/mixomics_plotindiv.xml Tue Sep 07 10:40:08 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="mixomics_plotindiv" name="mixOmics plotIndiv" version="@TOOL_VERSION@+galaxy2" profile="16.04" workflow_compatible="true"> +<tool id="mixomics_plotindiv" name="mixOmics plotIndiv" version="@TOOL_VERSION@+galaxy0" profile="16.04" workflow_compatible="true"> <description>provides scatter plots for individuals (experimental units) representation in (sparse)(I)PCA,(regularized)CCA, (sparse)PLS(DA) and (sparse)(R)GCCA(DA)</description> @@ -84,18 +84,11 @@ | 1 : Rdata block.splsda output | Rdata | +-------------------------------+------------+ + ---------- Parameters ---------- -Advanced options: -================= - -Plot legend - -Plot ellipse plots - - @HELP_MANUAL@ ------------ @@ -109,4 +102,4 @@ <expand macro="citations" /> -</tool> \ No newline at end of file +</tool>
--- a/mixomics_plotvar.xml Tue Nov 17 13:01:44 2020 +0000 +++ b/mixomics_plotvar.xml Tue Sep 07 10:40:08 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="mixomics_plotvar" name="mixOmics plotVar" version="@TOOL_VERSION@+galaxy2" profile="16.04" workflow_compatible="true"> +<tool id="mixomics_plotvar" name="mixOmics plotVar" version="@TOOL_VERSION@+galaxy0" profile="16.04" workflow_compatible="true"> <description>provides variables representation for (regularized) CCA, (sparse) PLS regression, PCA and (sparse) Regularized generalised CCA</description> @@ -90,14 +90,6 @@ Parameters ---------- -Advanced options: -================= - -Plot legend - -Cut-off - - @HELP_MANUAL@ ------------ @@ -105,10 +97,10 @@ ------------ plotVar.pdf - A pdf file with scatter plots for variables + A pdf file with scatter plots for the variables ]]></help> <expand macro="citations" /> -</tool> \ No newline at end of file +</tool>
--- a/viscorvar_circlecor.xml Tue Nov 17 13:01:44 2020 +0000 +++ b/viscorvar_circlecor.xml Tue Sep 07 10:40:08 2021 +0000 @@ -26,8 +26,6 @@ --output_var ${output_var} --output_pdf ${output_pdf} - @COMMAND_LOG_EXIT@ - ]]></command> <inputs> <param name="input_rdata" type="data" format="rdata" @@ -35,7 +33,7 @@ help="this is the RData output file from the matCorAddVar function"/> <param name="blocks_vec_list" type="data" format="tabular" label="List of blocks vector." - help="output *_blocks_comb.tsv file from matCorAddVar."/> + help="output *_blocks_comb.tsv file from the matCorAddVar function."/> <param name="select_blocks" type="select" label="Blocks" help="each element of List of blocks vector contain blocks for which selected variables can @@ -48,7 +46,7 @@ </param> <param name="responses_var_list" type="data" format="tabular" label="List of response variables." - help="output *_response_var.tsv file from matCorAddVar"/> + help="output *_response_var.tsv file from the matCorAddVar function"/> <param name="select_responses_var" type="select" display="checkboxes" multiple="true" label="Response variables" help="choose the response variables which will be plotted in the correlation circle"> @@ -89,11 +87,10 @@ Description ----------- -This tool allows visualizing variables of omics datasets which are correlated with -the response variables thanks to correlation circles. The determination of the omics -datasets which can be visualized is made by the tool matCorAddVar. This tool performs +This tool allows visualizing variables of omics datasets which are correlated with response variables thanks to correlation circles. The determination of the omics +datasets which can be visualized is made by the matCorAddVar tool. This tool performs a zoom in a rectangle to retrieve omics datasets variables which are correlated with a -response variable. +response variable. ----------------- Workflow position @@ -126,9 +123,9 @@ +===========================================================+===========+ | 1 : Rdata visCorVar.matCorAddVar output | rdata | +-----------------------------------------------------------+-----------+ -| 2 : ``*``_blocks_comb.tsv visCorVar.matCorAddVar output | tabular | +| 2 : \*_blocks_comb.tsv visCorVar.matCorAddVar output | tabular | +-----------------------------------------------------------+-----------+ -| 3 : ``*``_response_var.tsv visCorVar.matCorAddVar output | tabular | +| 3 : \*_response_var.tsv visCorVar.matCorAddVar output | tabular | +-----------------------------------------------------------+-----------+ ---------- @@ -145,10 +142,10 @@ Correlation circle pdf file viscorvar_circlecor_selected_var.tsv - List of variables selected in the correlation circle + List of selected variables which are contained in a rectangle of the correlation circle ]]></help> <expand macro="citations" /> -</tool> \ No newline at end of file +</tool>
--- a/viscorvar_computematsimilarity.xml Tue Nov 17 13:01:44 2020 +0000 +++ b/viscorvar_computematsimilarity.xml Tue Sep 07 10:40:08 2021 +0000 @@ -15,11 +15,9 @@ @COMMAND_RSCRIPT@/viscorvar_computematsimilarity.R --input_rdata ${input_rdata} - + --output_rdata ${output_rdata} - @COMMAND_LOG_EXIT@ - ]]></command> <inputs> <param name="input_rdata" type="data" format="rdata" @@ -93,10 +91,12 @@ ------------ viscorvar_computematsimilarity_output.RData - RData output + | RData output + | Contains the `computeMatSimilarity_result` R object containing the result of the computeMatSimilarity function + ]]></help> <expand macro="citations" /> -</tool> \ No newline at end of file +</tool>
--- a/viscorvar_matcoraddvar.xml Tue Nov 17 13:01:44 2020 +0000 +++ b/viscorvar_matcoraddvar.xml Tue Sep 07 10:40:08 2021 +0000 @@ -27,8 +27,6 @@ --output_response_var ${output_response_var} --output_blocks_comb ${output_blocks_comb} - @COMMAND_LOG_EXIT@ - ]]></command> <inputs> @@ -37,7 +35,7 @@ help="this is the RData output file from the block.splsda function" /> <param name="block_Y" type="data" format="tabular" label="Block Y" - help="Block Y is a table. A column determines which sample is associated with a phenotype (value equals to 1) or not (value equals to 0). For the file structure, see below in the section Input files" /> + help="Block Y is a table. A column corresponds to a phenotype and determines which sample is associated with this phenotype or not (value equals to 1 or 0). For the file structure, see below in the section Input files" /> <!-- Fichier avec noms de gènes/variables, donné par l'utilisateur --> <param name="var_of_interest_file" type="data" format="txt" optional="true" label="Variables of interest (Optional)" @@ -119,7 +117,7 @@ Block Y is in tabular format (.tsv). This table contains the name of the samples in the first column. The other columns correspond to phenotypes. -For each of these other columns, a column determines which sample is associated with a phenotype (value equals to 1) or not (value equals to 0). The names of the samples in Block Y (transposed), in the sample metadata (transposed) and for all datasets have to be in the same order. +For each of these other columns, a column corresponds to a phenotype and determines which sample is associated with this phenotype or not (value equals to 1 or 0). The names of the samples in Block Y (transposed), in the sample metadata (transposed) and for all datasets have to be in the same order. 3. Variables of interest structure All the variables of interest are in the same column. @@ -135,16 +133,14 @@ ------------ viscorvar_matcoraddvar_output.RData - RData output - -viscorvar_matcoraddvar_response_var.tsv - + | RData output + | Contains the `matCorAddVar_result` R object containing the result of the matCorAddVar function viscorvar_matcoraddvar_blocks_comb.tsv - + | viscorvar_matcoraddvar_blocks_comb.tsv contains the block names whose correlation circles can be overlaid ]]></help> <expand macro="citations" /> -</tool> \ No newline at end of file +</tool>
--- a/viscorvar_networkvar.R Tue Nov 17 13:01:44 2020 +0000 +++ b/viscorvar_networkvar.R Tue Sep 07 10:40:08 2021 +0000 @@ -66,8 +66,9 @@ print("names_response_variables:") print(names_response_variables) -res_networkVar = networkVar(res_compute_mat_similarity = res_compute_mat_similarity, - names_block_variables = names_block_variables, +res_networkVar = networkVar(res_compute_mat = res_compute_mat_similarity, + type_cor = "similarity", + names_selected_variables = names_block_variables, names_response_variables = names_response_variables, cutoff = 0) @@ -75,4 +76,4 @@ print("res_networkVar:") print(res_networkVar) -write.graph(res_networkVar$gR, file = args$output_graph, format = "graphml") \ No newline at end of file +write.graph(res_networkVar$gR, file = args$output_graph, format = "graphml")
--- a/viscorvar_networkvar.xml Tue Nov 17 13:01:44 2020 +0000 +++ b/viscorvar_networkvar.xml Tue Sep 07 10:40:08 2021 +0000 @@ -20,17 +20,15 @@ --output_graph ${output_graph} - @COMMAND_LOG_EXIT@ + ]]></command> - ]]></command> - <inputs> <param name="mat_similarity_rdata" type="data" format="rdata" label="this is the RData output file from the computeMatSimilarity function" - help="output RData file from computeMatSimilarity"/> + help="output RData file from the computeMatSimilarity function"/> <param name="var_list_file" type="data" format="tabular" label="Variables list file" - help="selected variables output tabular file from circleCor"/> + help="selected variables output tabular file from the circleCor function"/> <!-- Fichier avec noms de gènes/variables, donné par l'utilisateur --> <!-- <param name="var_of_interest_file" type="data" format="txt" optional="true" @@ -39,7 +37,7 @@ <param name="response_var_list" type="data" format="tabular" label="List of response variables" - help="output *_response_var.tsv file from matCorAddVar"/> + help="output *_response_var.tsv file from the matCorAddVar function"/> <param name="select_response_var" type="select" display="checkboxes" multiple="true" label="Response variables" help="response variables that will be plotted in the network"> @@ -72,10 +70,10 @@ ----------- This tool creates a network of correlated variables for omics datasets. The determination of -the omics datasets which can be visualized is made by the tool matCorAddVar. This network can +the omics datasets which can be visualized is made by the matCorAddVar tool. This network can be exported to graphml format and visualized with Cytoscape. The link between two variables is associated with the correlation between two variables : a threshold can be used in -Cytoscape to get a network of variables whose correlation is greater than this threshold +Cytoscape to get a network of variables whose correlations are greater than this threshold in absolute value. ----------------- @@ -105,9 +103,9 @@ +===========================================================+===========+ | 1 : Rdata visCorVar.computeMatSimilarity output | rdata | +-----------------------------------------------------------+-----------+ -| 2 : ``*``_selected_var.tsv visCorVar.circleCor output | tabular | +| 2 : \*_selected_var.tsv visCorVar.circleCor output | tabular | +-----------------------------------------------------------+-----------+ -| 3 : ``*``_response_var.tsv visCorVar.matCorAddVar output | tabular | +| 3 : \*_response_var.tsv visCorVar.matCorAddVar output | tabular | +-----------------------------------------------------------+-----------+ ---------- @@ -127,4 +125,4 @@ <expand macro="citations" /> -</tool> \ No newline at end of file +</tool>