re-run the modules for 7316-4463

d3b-center · Jul 6, 2023 · 035cc91 · 035cc91
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diff --git a/analyses/molecular-subtyping-HGG/01-HGG-molecular-subtyping-defining-lesions.nb.html b/analyses/molecular-subtyping-HGG/01-HGG-molecular-subtyping-defining-lesions.nb.html
diff --git a/analyses/molecular-subtyping-HGG/03-HGG-molecular-subtyping-cnv.nb.html b/analyses/molecular-subtyping-HGG/03-HGG-molecular-subtyping-cnv.nb.html
diff --git a/analyses/molecular-subtyping-HGG/04-HGG-molecular-subtyping-mutation.nb.html b/analyses/molecular-subtyping-HGG/04-HGG-molecular-subtyping-mutation.nb.html
diff --git a/analyses/molecular-subtyping-HGG/05-HGG-molecular-subtyping-fusion.nb.html b/analyses/molecular-subtyping-HGG/05-HGG-molecular-subtyping-fusion.nb.html
diff --git a/analyses/molecular-subtyping-HGG/06-HGG-molecular-subtyping-gene-expression.nb.html b/analyses/molecular-subtyping-HGG/06-HGG-molecular-subtyping-gene-expression.nb.html
diff --git a/analyses/molecular-subtyping-HGG/07-HGG-molecular-subtyping-combine-table.nb.html b/analyses/molecular-subtyping-HGG/07-HGG-molecular-subtyping-combine-table.nb.html
diff --git a/analyses/molecular-subtyping-HGG/08-1p19q-codeleted-oligodendrogliomas.nb.html b/analyses/molecular-subtyping-HGG/08-1p19q-codeleted-oligodendrogliomas.nb.html
diff --git a/analyses/molecular-subtyping-HGG/09-HGG-with-braf-clustering.nb.html b/analyses/molecular-subtyping-HGG/09-HGG-with-braf-clustering.nb.html
diff --git a/analyses/molecular-subtyping-HGG/10-HGG-TP53-annotation.nb.html b/analyses/molecular-subtyping-HGG/10-HGG-TP53-annotation.nb.html
diff --git a/analyses/molecular-subtyping-HGG/hgg-subset/hgg_metadata.tsv b/analyses/molecular-subtyping-HGG/hgg-subset/hgg_metadata.tsv
@@ -1539,7 +1539,6 @@ BS_8JEJCH4Z 7316-8826 1074976_DNA_N PT_G395P98S WXS Normal Peripheral Whole Bloo
 BS_8X2PEXCW 7316-4997 A15151 PT_NWYSD53S WGS Normal Peripheral Whole Blood NA Peripheral Whole Blood Female White Not Hispanic or Latino 1544 NA NA NA 854 DECEASED NA PBTA 2398 Novogene None documented NA NA C3080412 NA NA NA NA NA NA NA NA Female NA NA NA 1544 NA NA NA NA NA NA NA NA NA NA NA NA NA NA
 BS_8ZB4VFM0 7316-9014 1272896 PT_6H8X6RZ1 WGS Normal Peripheral Whole Blood NA Peripheral Whole Blood Female Not Reported Not Hispanic or Latino NA NA NA NA NA NA NA PBTA NA NA None documented NA NA C3506115 NA NA NA NA NA NA NA NA Female NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
 BS_922HG7C2 7316-3158 1213680 PT_Z0JKP1GY WGS Normal Peripheral Whole Blood NA Peripheral Whole Blood Male Reported Unknown Not Hispanic or Latino 4739 NA NA NA 690 DECEASED 690 PBTA 5429 NA None documented NA NA C1163211 NA NA NA NA NA NA NA NA Female NA NA NA 4739 Alive NA NA NA NA NA NA NA NA NA NA NA NA NA
-BS_9B41DFBH 7316-4463 1253625 PT_45E5JA1P Methylation Tumor Solid Tissue Initial CNS Tumor Cerebellum/Posterior Fossa Male White Not Hispanic or Latino 4914 Glial-neuronal tumor NOS NA NA 189 LIVING 189 PBTA 5103 NA None documented NA high grade glial neoplasm C2316951 Partial resection Posterior fossa Neuronal and mixed neuronal-glial tumor GNT NA NA NA NA Male NA NA NA 4914 Alive 5040 4752 NA NA 0.552061833333334 0.858775436666667 0.723054389287137 DMG_K27 0.447 HGG_F 0.423477799006052 unmethylated 0.0110234749098809
 BS_9BBWSCD6 7316-116 549889 PT_PR4YBBH3 WGS Normal Peripheral Whole Blood NA Peripheral Whole Blood Female White Unavailable 3739 NA NA NA 39 DECEASED 39 PBTA 3778 NantOmics None documented NA NA C29274 NA NA NA NA NA NA NA NA Female NA NA NA 3739 Alive NA NA NA NA NA NA NA NA NA NA NA NA NA
 BS_9ERAJGN5 7316-8045 1249818 PT_EW44V0NM WGS Normal Solid Tissue NA Brain Male Reported Unknown Unavailable 1537 NA NA NA 358 DECEASED 358 PBTA 1895 NA None documented NA NA C3487911 NA NA NA NA NA NA NA NA Male NA NA NA 1895 Deceased-due to disease NA NA NA NA NA NA NA NA NA NA NA NA NA
 BS_9G82HJFA 7316-1937 564265 PT_59D00MBQ WGS Normal Peripheral Whole Blood NA Peripheral Whole Blood Male Asian Not Hispanic or Latino 3283 NA NA NA 419 DECEASED 419 PBTA 3702 NantOmics None documented NA NA C384990 NA NA NA NA NA NA NA NA Male NA NA NA 3291 Alive NA NA NA NA NA NA NA NA NA NA NA NA NA
@@ -1602,7 +1601,6 @@ BS_KFFMZDJ0 7316-5814 A19667 PT_G16VK7FR WGS Normal Peripheral Whole Blood NA Pe
 BS_KWMFKN38 7316-8101 999797_DNA_N PT_3QFBAXAN WXS Normal Peripheral Whole Blood NA Peripheral Whole Blood Female Other Hispanic or Latino NA NA NA NA NA NA NA PBTA NA CHOP DGD None documented NA NA C3172416 NA NA NA NA NA NA NA NA Female NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
 BS_MB7WN0ZB 7316-1102 470031 PT_5BWZA0NT RNA-Seq Tumor Solid Tissue Initial CNS Tumor Ventricles Female White Not Hispanic or Latino 4456 Supratentorial or Spinal Cord PNET NA stranded 61 DECEASED 61 PBTA 4517 BGI@CHOP Genome Center None documented NA spnet C292125 Gross/Near total resection Ventricles Embryonal tumor Embryonal tumor NA NA NA NA Female NA NA NA 4456 Alive NA NA NA NA NA NA NA NA NA NA NA NA NA
 BS_MCFJEQJ9 7316-5003 A16936 PT_W5GP3F6B WGS Normal Peripheral Whole Blood NA Peripheral Whole Blood Male Asian Hispanic or Latino 2459 NA NA NA 258 DECEASED NA PBTA 2717 Novogene None documented NA NA C3092712 NA NA NA NA NA NA NA NA Unknown NA NA NA 2459 NA NA NA NA NA NA NA NA NA NA NA NA NA NA
-BS_MFWDM961 7316-4463 1182243 PT_45E5JA1P WGS Tumor Solid Tissue Initial CNS Tumor Cerebellum/Posterior Fossa Male White Not Hispanic or Latino 4914 Glial-neuronal tumor NOS NA NA 189 LIVING 189 PBTA 5103 NA None documented NA high grade glial neoplasm C2316951 Partial resection Posterior fossa Neuronal and mixed neuronal-glial tumor GNT NA NA NA NA Male 0.54038543435 0.45961456565 4 4914 Alive 5040 4752 NA NA NA NA NA NA NA NA NA NA NA
 BS_MNZ55TWJ 7316-9623 1273266 PT_NKETJQ7Q WGS Normal Solid Tissue NA Brain Male Reported Unknown Unavailable 1628 NA NA NA 287 DECEASED 287 PBTA 1915 NA None documented NA NA C4186920 NA NA NA NA NA NA NA NA Male NA NA NA 1915 Deceased-due to disease NA NA NA NA NA NA NA NA NA NA NA NA NA
 BS_MVYA262V 7316-3213 A05265 PT_9GKVQ9QS WGS Normal Peripheral Whole Blood NA Peripheral Whole Blood Female Reported Unknown Hispanic or Latino 2097 NA NA NA 171 DECEASED NA PBTA 2268 NantOmics None documented NA NA C3078690 NA NA NA NA NA NA NA NA Female NA NA NA 2097 NA NA NA NA NA NA NA NA NA NA NA NA NA NA
 BS_N1WCEX2B 7316-461 612646 PT_RA6AGBA7 WGS Normal Peripheral Whole Blood NA Peripheral Whole Blood Female Black or African American Not Hispanic or Latino 3209 NA NA NA 524 DECEASED 382 PBTA 3733 NantOmics None documented NA NA C96432 NA NA NA NA NA NA NA NA Female NA NA NA 3591 Alive NA NA NA NA NA NA NA NA NA NA NA NA NA
@@ -1647,7 +1645,6 @@ BS_TVXSXJFY 7316-8100 999323_DNA_N PT_8SF8D0M9 WXS Normal Peripheral Whole Blood
 BS_V1GT2FRQ 7316-10002 1260238 PT_TNJPSPW3 WXS Normal Peripheral Whole Blood NA Peripheral Whole Blood Female Reported Unknown Hispanic or Latino NA NA NA NA NA NA NA PBTA NA Ashion None documented NA NA C3508329 NA NA NA NA NA NA NA NA Female NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
 BS_V4QGT56S 7316-8851 1224665 PT_P571HTNK WGS Normal Peripheral Whole Blood NA Peripheral Whole Blood Female White Not Hispanic or Latino 2251 NA NA NA 190 LIVING 190 PBTA 2441 NA None documented NA NA C3684465 NA NA NA NA NA NA NA NA Female NA NA NA 2251 Alive NA NA NA NA NA NA NA NA NA NA NA NA NA
 BS_VC5PKT9Q 7316-5001 A16408 PT_KAQMYFYB WGS Normal Peripheral Whole Blood NA Peripheral Whole Blood Male Black or African American Not Hispanic or Latino 2219 NA NA NA 335 DECEASED NA PBTA 2554 Novogene None documented NA NA C3081396 NA NA NA NA NA NA NA NA Male NA NA NA 2219 NA NA NA NA NA NA NA NA NA NA NA NA NA NA
-BS_VGEX4C10 7316-4463 1214268 PT_45E5JA1P WGS Normal Peripheral Whole Blood NA Peripheral Whole Blood Male White Not Hispanic or Latino 4914 NA NA NA 189 LIVING 189 PBTA 5103 NA None documented NA NA C2316951 NA NA NA NA NA NA NA NA Male NA NA NA 4914 Alive NA NA NA NA NA NA NA NA NA NA NA NA NA
 BS_VKGSMV3F 7316-5000 A15737 PT_C9YDTZPA WGS Normal Peripheral Whole Blood NA Peripheral Whole Blood Male White Not Hispanic or Latino 1978 NA NA NA 399 DECEASED NA PBTA 2377 Novogene None documented NA NA C3081273 NA NA NA NA NA NA NA NA Male NA NA NA 1978 NA NA NA NA NA NA NA NA NA NA NA NA NA NA
 BS_VP3FYM4W 7316-5006 A18559 PT_DMAF1J4A WGS Normal Peripheral Whole Blood NA Peripheral Whole Blood Male White Not Hispanic or Latino 2233 NA NA NA 421 DECEASED NA PBTA 2654 Novogene None documented NA NA C3093204 NA NA NA NA NA NA NA NA Female NA NA NA 2233 NA NA NA NA NA NA NA NA NA NA NA NA NA NA
 BS_W0P2BF8X 7316-9838 1251063 PT_5Y0CE4WK Methylation Normal Solid Tissue NA Brain Unknown Reported Unknown Unavailable 2012 NA NA NA NA DECEASED NA PBTA 2012 NA Not Reported NA NA C3985938 NA NA NA NA NA NA NA NA Female NA NA NA 2012 Deceased-due to disease NA NA NA NA NA NA NA NA NA NA NA NA NA

diff --git a/analyses/molecular-subtyping-HGG/plots/HGG_stranded.pdf b/analyses/molecular-subtyping-HGG/plots/HGG_stranded.pdf
diff --git a/analyses/molecular-subtyping-HGG/plots/HGG_stranded.png b/analyses/molecular-subtyping-HGG/plots/HGG_stranded.png