# HG changeset patch
# User goeckslab
# Date 1764791203 0
# Node ID 152dc84840ca7f6395e3897968da30392482d346
planemo upload for repository https://github.com/goeckslab/tools-st/tree/main/tools/bayesTME commit 26edd05a863adac97cb54a9fb2ae5613ce95df50
diff -r 000000000000 -r 152dc84840ca macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Wed Dec 03 19:46:43 2025 +0000
@@ -0,0 +1,30 @@
+
+ 0.0.1
+ 0
+ 22.01
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+ jeffquinnmsk/bayestme:0a7cde6acac2ffc34e8ad00b7fab75f869d80de2
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+ 10.1016/j.cels.2023.06.003
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\ No newline at end of file
diff -r 000000000000 -r 152dc84840ca select_markers_and_plot.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/select_markers_and_plot.xml Wed Dec 03 19:46:43 2025 +0000
@@ -0,0 +1,241 @@
+
+ Plot Deconvolution Results (and Select Marker Genes) with BayesTME
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+ macros.xml
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\ No newline at end of file
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diff -r 000000000000 -r 152dc84840ca test-data/refBased_test_data/deconvolution_loss.pdf
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diff -r 000000000000 -r 152dc84840ca test-data/refBased_test_data/deconvolution_samples.h5
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diff -r 000000000000 -r 152dc84840ca test-data/refBased_test_data/marker_genes.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/refBased_test_data/marker_genes.csv Wed Dec 03 19:46:43 2025 +0000
@@ -0,0 +1,241 @@
+gene_name,rank_in_cell_type,cell_type
+BRI3,0,1
+SRSF3,1,1
+IFITM3,2,1
+LSM3,3,1
+MYL6,4,1
+AGR2,5,1
+CPNE3,6,1
+TOMM5,7,1
+SNRPG,8,1
+MORF4L2,9,1
+APOE,10,1
+TOMM7,11,1
+RAD21,12,1
+GFRA1,13,1
+WBP1,14,1
+CCT2,15,1
+NAA20,16,1
+NOP10,17,1
+DHX30,18,1
+HLA-DRA,19,1
+KRT10,20,1
+RARRES2,21,1
+SRSF5,22,1
+HMGA1,23,1
+MT2A,24,1
+POMP,25,1
+TKT,26,1
+TMED10,27,1
+TSTD1,28,1
+CNIH4,29,1
+PSMD2,30,1
+RABEP1,31,1
+APEX1,32,1
+TYROBP,33,1
+BANF1,34,1
+SNRPE,35,1
+ACADSB,36,1
+HSP90AB1,37,1
+PRDX3,38,1
+CSTB,39,1
+CNIH4,0,2
+ACADSB,1,2
+TKT,2,2
+HSP90AB1,3,2
+RAD21,4,2
+WBP1,5,2
+CCT2,6,2
+HMGA1,7,2
+BANF1,8,2
+HLA-DRA,9,2
+TSTD1,10,2
+PSMD2,11,2
+POMP,12,2
+BRI3,13,2
+MT2A,14,2
+MORF4L2,15,2
+TOMM7,16,2
+RARRES2,17,2
+SNRPG,18,2
+APEX1,19,2
+AGR2,20,2
+NAA20,21,2
+NOP10,22,2
+TMED10,23,2
+TOMM5,24,2
+KRT10,25,2
+DHX30,26,2
+TYROBP,27,2
+PRDX3,28,2
+SRSF3,29,2
+SNRPE,30,2
+IFITM3,31,2
+RABEP1,32,2
+GFRA1,33,2
+LSM3,34,2
+CPNE3,35,2
+APOE,36,2
+SRSF5,37,2
+MYL6,38,2
+CSTB,39,2
+MT2A,0,3
+WBP1,1,3
+CSTB,2,3
+SRSF5,3,3
+NOP10,4,3
+TMED10,5,3
+SRSF3,6,3
+DHX30,7,3
+MYL6,8,3
+TYROBP,9,3
+TSTD1,10,3
+APOE,11,3
+CCT2,12,3
+RAD21,13,3
+CPNE3,14,3
+NAA20,15,3
+LSM3,16,3
+ACADSB,17,3
+RARRES2,18,3
+RABEP1,19,3
+TOMM5,20,3
+SNRPE,21,3
+TKT,22,3
+IFITM3,23,3
+PRDX3,24,3
+HMGA1,25,3
+HLA-DRA,26,3
+POMP,27,3
+HSP90AB1,28,3
+KRT10,29,3
+TOMM7,30,3
+MORF4L2,31,3
+BANF1,32,3
+APEX1,33,3
+AGR2,34,3
+SNRPG,35,3
+GFRA1,36,3
+PSMD2,37,3
+CNIH4,38,3
+BRI3,39,3
+RABEP1,0,4
+PRDX3,1,4
+HSP90AB1,2,4
+SNRPE,3,4
+TYROBP,4,4
+SRSF5,5,4
+RAD21,6,4
+RARRES2,7,4
+POMP,8,4
+NAA20,9,4
+TKT,10,4
+MYL6,11,4
+CCT2,12,4
+GFRA1,13,4
+SRSF3,14,4
+ACADSB,15,4
+NOP10,16,4
+TOMM7,17,4
+BANF1,18,4
+HMGA1,19,4
+APEX1,20,4
+CSTB,21,4
+TMED10,22,4
+AGR2,23,4
+TSTD1,24,4
+HLA-DRA,25,4
+CNIH4,26,4
+TOMM5,27,4
+MORF4L2,28,4
+PSMD2,29,4
+KRT10,30,4
+IFITM3,31,4
+LSM3,32,4
+DHX30,33,4
+MT2A,34,4
+WBP1,35,4
+CPNE3,36,4
+SNRPG,37,4
+APOE,38,4
+BRI3,39,4
+APEX1,0,5
+CPNE3,1,5
+CNIH4,2,5
+CSTB,3,5
+BANF1,4,5
+HLA-DRA,5,5
+TOMM5,6,5
+MT2A,7,5
+MYL6,8,5
+KRT10,9,5
+SNRPE,10,5
+TMED10,11,5
+POMP,12,5
+AGR2,13,5
+MORF4L2,14,5
+LSM3,15,5
+PRDX3,16,5
+APOE,17,5
+HSP90AB1,18,5
+TYROBP,19,5
+HMGA1,20,5
+NOP10,21,5
+DHX30,22,5
+CCT2,23,5
+SRSF3,24,5
+SNRPG,25,5
+PSMD2,26,5
+TSTD1,27,5
+GFRA1,28,5
+RABEP1,29,5
+WBP1,30,5
+TOMM7,31,5
+IFITM3,32,5
+TKT,33,5
+NAA20,34,5
+ACADSB,35,5
+RAD21,36,5
+RARRES2,37,5
+BRI3,38,5
+SRSF5,39,5
+PSMD2,0,6
+GFRA1,1,6
+DHX30,2,6
+SNRPG,3,6
+KRT10,4,6
+IFITM3,5,6
+APOE,6,6
+SNRPE,7,6
+LSM3,8,6
+SRSF5,9,6
+AGR2,10,6
+ACADSB,11,6
+TKT,12,6
+RARRES2,13,6
+HLA-DRA,14,6
+HMGA1,15,6
+TYROBP,16,6
+PRDX3,17,6
+NAA20,18,6
+BRI3,19,6
+TOMM7,20,6
+TSTD1,21,6
+BANF1,22,6
+RABEP1,23,6
+POMP,24,6
+MORF4L2,25,6
+CPNE3,26,6
+APEX1,27,6
+TOMM5,28,6
+CSTB,29,6
+TMED10,30,6
+NOP10,31,6
+RAD21,32,6
+WBP1,33,6
+MYL6,34,6
+CCT2,35,6
+HSP90AB1,36,6
+SRSF3,37,6
+CNIH4,38,6
+MT2A,39,6
diff -r 000000000000 -r 152dc84840ca test-data/refBased_test_data/marker_genes.pdf
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diff -r 000000000000 -r 152dc84840ca test-data/refBased_test_data/omega.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/refBased_test_data/omega.csv Wed Dec 03 19:46:43 2025 +0000
@@ -0,0 +1,41 @@
+,0,1,2,3,4,5
+AGR2,0.3,0.2,0.0,0.1,0.2,0.2
+MORF4L2,0.3,0.2,0.1,0.1,0.2,0.1
+SNRPE,0.0,0.1,0.1,0.3,0.2,0.3
+HSP90AB1,0.0,0.4,0.1,0.3,0.2,0.0
+GFRA1,0.2,0.1,0.0,0.2,0.1,0.4
+ACADSB,0.0,0.4,0.2,0.2,0.0,0.2
+APOE,0.2,0.0,0.2,0.0,0.2,0.4
+MT2A,0.1,0.3,0.4,0.0,0.2,0.0
+IFITM3,0.3,0.1,0.1,0.1,0.0,0.4
+KRT10,0.1,0.1,0.1,0.1,0.2,0.4
+HLA-DRA,0.1,0.3,0.1,0.1,0.2,0.2
+TSTD1,0.1,0.3,0.2,0.1,0.1,0.2
+CCT2,0.2,0.3,0.2,0.2,0.1,0.0
+WBP1,0.2,0.3,0.4,0.0,0.1,0.0
+TOMM5,0.3,0.2,0.1,0.1,0.2,0.1
+RAD21,0.2,0.3,0.2,0.3,0.0,0.0
+CNIH4,0.1,0.4,0.0,0.1,0.4,0.0
+TMED10,0.1,0.2,0.3,0.1,0.2,0.1
+TOMM7,0.2,0.2,0.1,0.2,0.1,0.2
+PRDX3,0.0,0.1,0.1,0.4,0.2,0.2
+LSM3,0.3,0.0,0.2,0.0,0.2,0.3
+NOP10,0.1,0.2,0.3,0.2,0.1,0.1
+HMGA1,0.1,0.3,0.1,0.2,0.1,0.2
+TYROBP,0.0,0.1,0.2,0.3,0.2,0.2
+RARRES2,0.1,0.2,0.2,0.3,0.0,0.2
+CSTB,0.0,0.0,0.4,0.2,0.3,0.1
+CPNE3,0.3,0.0,0.2,0.0,0.4,0.1
+BRI3,0.5,0.3,0.0,0.0,0.0,0.2
+SNRPG,0.3,0.2,0.0,0.0,0.1,0.4
+MYL6,0.3,0.0,0.3,0.2,0.2,0.0
+SRSF5,0.1,0.0,0.3,0.3,0.0,0.3
+POMP,0.1,0.3,0.1,0.2,0.2,0.1
+APEX1,0.1,0.2,0.0,0.2,0.4,0.1
+BANF1,0.0,0.3,0.1,0.2,0.3,0.1
+DHX30,0.1,0.1,0.3,0.0,0.1,0.4
+RABEP1,0.1,0.1,0.2,0.4,0.1,0.1
+SRSF3,0.3,0.1,0.3,0.2,0.1,0.0
+PSMD2,0.1,0.3,0.0,0.1,0.1,0.4
+NAA20,0.2,0.2,0.2,0.2,0.0,0.2
+TKT,0.1,0.4,0.1,0.2,0.0,0.2
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diff -r 000000000000 -r 152dc84840ca test-data/refBased_test_data/relative_expression.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/refBased_test_data/relative_expression.csv Wed Dec 03 19:46:43 2025 +0000
@@ -0,0 +1,41 @@
+,0,1,2,3,4,5
+AGR2,-0.08380652219057083,-0.24061469733715057,-0.2815214991569519,-0.22048918902873993,-0.25506848096847534,0.08380652219057083
+MORF4L2,-0.23045410215854645,0.23045410215854645,-0.4615306854248047,-0.4566039443016052,-0.29516807198524475,-0.316114217042923
+SNRPE,-0.3119671046733856,-0.4708918631076813,-0.20415183901786804,-0.018912073224782944,-0.18750175833702087,0.018912073224782944
+HSP90AB1,-0.43157273530960083,-0.2963055372238159,-0.4264748990535736,0.2963055372238159,-0.4036998450756073,-0.5289340615272522
+GFRA1,-0.2077164351940155,-0.5465796589851379,-0.51600581407547,-0.11956971883773804,-0.42499789595603943,0.11956971883773804
+ACADSB,-0.4230344593524933,0.004193827509880066,-0.24471037089824677,-0.15493634343147278,-0.5466628074645996,-0.004193827509880066
+APOE,0.008595213294029236,-0.5154699683189392,-0.008595213294029236,-0.6065546870231628,-0.3440464437007904,-0.2128976732492447
+MT2A,-0.36652669310569763,-0.48939812183380127,0.04131711274385452,-0.5067987442016602,-0.04131711274385452,-0.684245228767395
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+HLA-DRA,-0.12335347384214401,-0.1282292604446411,-0.3626733720302582,-0.27917322516441345,0.12335347384214401,-0.19331201910972595
+TSTD1,-0.504315972328186,-0.1835874766111374,0.1835874766111374,-0.23516401648521423,-0.4245743453502655,-0.46142706274986267
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+RAD21,-0.19478176534175873,0.10942893475294113,-0.10942893475294113,-0.26478302478790283,-0.5624359846115112,-0.36201223731040955
+CNIH4,-0.5233721733093262,0.017981452867388725,-0.6497180461883545,-0.3417080044746399,-0.017981452867388725,-0.6313515901565552
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