Update nfosi jhu dataset

public/nst_nfosi_ntap/README.md

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+## Notes
+
+The patient cohort is from [The Johns Hopkins NF1 Biospecimen Repository](https://www.synapse.org/Synapse:syn53140231), which is an active biobanking project with rolling releases. It is funded by the [Neurofibromatosis Therapeutic Acceleration Program (NTAP)](https://www.n-tap.org/), led by Christine Pratilas, M.D., and David Loeb, M.D., Ph.D., with contributions from Angela Hirbe, PhD., and additional collaboration, data processing and data management by [NF-OSI / Sage Bionetworks](https://help.nf.synapse.org/NFdocs/about). 
+
+Patient raw sequencing data are generated by the institutional cores and shared on the secure Synapse platform with access restrictions. Sage Bionetworks does additional processing through the funded initiative described here: https://help.nf.synapse.org/NFdocs/data-processing. The [nf-core/rnaseq](https://nf-co.re/rnaseq/) workflow is used for gene expression from bulk RNA-seq and [nf-co.re/sarek](https://nf-co.re/sarek/) is used for somatic variant calling from whole exome sequencing (also for germline variant calling, but this is not shared on cBioPortal and only available on Synapse with access restrictons). After variant calling, variant annotation is done with [vcf2maf](https://github.com/Sage-Bionetworks-Workflows/nf-vcf2maf).
+
+Sage Bionetworks then appropriately packages the processed gene expression and mutations data with approved clinical data for contribution to cBioPortal, also funded by NTAP. Full clinical data are not contributed due to IRB restrictions. Released patient samples are confirmed with Christine Pratilas through an internal process. Updates may be occasionally made. For questions about clinical data and collaboration, please use the most up-to-date PI contact instructions on the [project space](https://www.synapse.org/Synapse:syn53133024/).

public/nst_nfosi_ntap/case_lists/cases_all.txt

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 cancer_study_identifier: nst_nfosi_ntap
 stable_id: nst_nfosi_ntap_all
 case_list_name: All samples
-case_list_description: All samples (19 samples)
+case_list_description: All samples (134 samples)
 case_list_category: all_cases_in_study
-case_list_ids: 2-010_Neurofibroma 2-026_Neurofibroma 2-013_Plexiform_Neurofibroma 2-004_Plexiform_Neurofibroma 2-012_Neurofibroma 2-031_Cell_Line 2-017_Neurofibroma 2-021_Neurofibroma 2-019_Neurofibroma 2-029_Neurofibroma 2-023_Plexiform_Neurofibroma 2-014_Neurofibroma 2-001_Plexiform_Neurofibroma 2-006_Plexiform_Neurofibroma 2-032_Plexiform_Neurofibroma 2-015_Plexiform_Neurofibroma 2-031_Malignant_Peripheral_Nerve_Sheath_Tumor 2-016_Neurofibroma 2-015_Neurofibroma
+case_list_ids: JH-2-075-3HE68-A JH-2-082-G8357-A JH-2-007-B14BB-AG2A6 JH-2-054-241HF-A JH-2-002-GAF53-A1011 JH-2-085-F2983-F783D JH-2-068-2BHHG-5F9FC JH-2-111-G645D-6C5FF JH-2-009-518B9-A JH-2-016-6H516-A JH-2-010-H915D-A JH-2-017-9FH8F-A JH-2-077-4H749-8GCFH JH-2-014-AH466-96B78 JH-2-055-9F5F3-6G883 JH-2-068-A733G-A JH-2-023-91HBD-A JH-2-001-8A1B1-7B15A JH-2-093-518GA-A JH-2-100-19H33-94G2C JH-2-003-H3G1H-HC8GG JH-2-091-CAA8H-A JH-2-021-6GFE7-A JH-2-068-FH52C-A JH-2-009-2578C-A JH-2-079-CB92G-A JH-2-021-6GFE7-7HBG6 JH-2-002-94FAA-A JH-2-001-8A1B1-A JH-2-095-4H3FE-A JH-2-060-4CE8D-A JH-2-076-41G1H-A JH-2-079-9D31F-A JH-2-006-D6BA4-BAEBD JH-2-092-B52E5-A JH-2-045-GH3AA-A JH-2-045-F7H3C-A JH-2-032-AE88A-A JH-2-031-9GEA9-A JH-2-055-1419H-9GG15 JH-2-002-GAF53-FB9H7 JH-2-029-7AE7F-GC2A3 JH-2-002-GAF53-A71AA JH-2-012-HE58H-A JH-2-013-7886G-A JH-2-017-9FH8F-93DE8 JH-2-029-7AE7F-A JH-2-032-AE88A-G36A1 JH-2-094-5HA24-A JH-2-016-4H597-A JH-2-045-GH3AA-D2C35 JH-2-103-H731E-A JH-2-094-151G9-A JH-2-044-83F15-A JH-2-060-9G31E-HD38A JH-2-002-94FAA-19DGB JH-2-015-55B8D-2B9EB JH-2-096-5E593-A JH-2-091-CAA8H-GDFG1 JH-2-075-4F211-A JH-2-055-FC9GH-A JH-2-090-19D3F-A JH-2-068-A7488-A JH-2-089-H8EBA-HH51C JH-2-002-FF824-A JH-2-092-B4F11-A JH-2-074-HE12C-A JH-2-072-3DD4G-A JH-2-009-518B9-77BH3 JH-2-100-19H33-A JH-2-082-B5148-A92CA JH-2-002-GAF53-2E57B JH-2-023-1G2BC-A JH-2-015-C436G-A JH-2-016-4H597-15C1D JH-2-019-DB5EH-A JH-2-057-37D5D-A JH-2-060-19EC4-A JH-2-004-9D9D7-7EC36 JH-2-023-91HBD-2G2E2 JH-2-104-51E2H-A JH-2-093-214AE-A JH-2-019-DB5EH-C461C JH-2-023-876HC-A JH-2-085-F2983-A JH-2-092-B4F11-2H1C1 JH-2-031-9GEA9-78GAB JH-2-086-5EA11-A JH-2-055-E1381-A JH-2-002-FF824-C5E25 JH-2-054-9255F-A JH-2-089-H8EBA-A JH-2-099-26HCE-A JH-2-002-354A1-A JH-2-023-876HC-622H1 JH-2-104-51E2H-1G93A JH-2-013-7886G-AA816 JH-2-094-5HA24-CC3H4 JH-2-060-99B2D-GG71G JH-2-044-83F15-GA258 JH-2-015-G41AC-A JH-2-086-5EA11-494GE JH-2-023-89E1F-A JH-2-016-6H516-818HB JH-2-111-G645D-A JH-2-010-H915D-BB99B JH-2-076-41G1H-7FGE5 JH-2-026-9FD64-A JH-2-093-214AE-H5A8H JH-2-002-GAF53-3BAGC JH-2-082-G8357-EG55A JH-2-015-6AD96-A JH-2-031-BFF3F-DG6C8 JH-2-014-AH466-A JH-2-076-811H2-A JH-2-015-55B8D-A JH-2-068-2BHHG-A JH-2-061-1H66H-AB35D JH-2-090-19D3F-G36F6 JH-2-012-HE58H-37B26 JH-2-026-9FD64-HF616 JH-2-082-B5148-A JH-2-006-D6BA4-A JH-2-107-AGD39-1CH62 JH-2-075-3HE68-C61FE JH-2-023-9DA42-A JH-2-092-B52E5-BFCBA JH-2-004-9D9D7-A JH-2-090-59DE8-A JH-2-077-88G11-A JH-2-113-7857D-A JH-2-102-3B72A-A JH-2-023-1G2BC-82G48 JH-2-061-1H66H-A

public/nst_nfosi_ntap/case_lists/cases_sequenced.txt

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 cancer_study_identifier: nst_nfosi_ntap
 stable_id: nst_nfosi_ntap_sequenced
 case_list_name: Samples with mutation data
-case_list_description: Samples with mutation data (19 samples)
+case_list_description: Samples with mutation data (80 samples)
 case_list_category: all_cases_with_mutation_data
-case_list_ids: 2-010_Neurofibroma 2-026_Neurofibroma 2-013_Plexiform_Neurofibroma 2-014_Neurofibroma 2-001_Plexiform_Neurofibroma 2-006_Plexiform_Neurofibroma 2-004_Plexiform_Neurofibroma 2-032_Plexiform_Neurofibroma 2-015_Plexiform_Neurofibroma 2-016_Neurofibroma 2-012_Neurofibroma 2-031_Malignant_Peripheral_Nerve_Sheath_Tumor 2-031_Cell_Line 2-017_Neurofibroma 2-015_Neurofibroma 2-021_Neurofibroma 2-019_Neurofibroma 2-029_Neurofibroma 2-023_Plexiform_Neurofibroma
+case_list_ids: JH-2-100-19H33-A JH-2-075-3HE68-A JH-2-082-G8357-A JH-2-113-7857D-A JH-2-015-C436G-A JH-2-054-241HF-A JH-2-002-GAF53-A1011 JH-2-001-8A1B1-A JH-2-009-2578C-A JH-2-057-37D5D-A JH-2-060-19EC4-A JH-2-016-6H516-A JH-2-023-1G2BC-A JH-2-017-9FH8F-A JH-2-068-A733G-A JH-2-023-91HBD-A JH-2-093-214AE-A JH-2-103-H731E-A JH-2-023-876HC-A JH-2-085-F2983-A JH-2-093-518GA-A JH-2-086-5EA11-A JH-2-055-E1381-A JH-2-054-9255F-A JH-2-089-H8EBA-A JH-2-021-6GFE7-A JH-2-068-FH52C-A JH-2-002-354A1-A JH-2-079-CB92G-A JH-2-009-518B9-A JH-2-002-94FAA-A JH-2-045-F7H3C-A JH-2-095-4H3FE-A JH-2-060-4CE8D-A JH-2-076-41G1H-A JH-2-079-9D31F-A JH-2-092-B52E5-A JH-2-045-GH3AA-A JH-2-074-HE12C-A JH-2-032-AE88A-A JH-2-031-9GEA9-A JH-2-023-89E1F-A JH-2-055-1419H-9GG15 JH-2-099-26HCE-A JH-2-002-GAF53-FB9H7 JH-2-111-G645D-A JH-2-012-HE58H-A JH-2-013-7886G-A JH-2-026-9FD64-A JH-2-029-7AE7F-A JH-2-015-6AD96-A JH-2-094-5HA24-A JH-2-016-4H597-A JH-2-014-AH466-A JH-2-076-811H2-A JH-2-015-55B8D-A JH-2-010-H915D-A JH-2-094-151G9-A JH-2-044-83F15-A JH-2-096-5E593-A JH-2-006-D6BA4-A JH-2-104-51E2H-A JH-2-019-DB5EH-A JH-2-023-9DA42-A JH-2-075-4F211-A JH-2-082-B5148-A JH-2-055-FC9GH-A JH-2-090-19D3F-A JH-2-004-9D9D7-A JH-2-090-59DE8-A JH-2-077-88G11-A JH-2-015-G41AC-A JH-2-102-3B72A-A JH-2-002-FF824-A JH-2-092-B4F11-A JH-2-068-A7488-A JH-2-068-2BHHG-A JH-2-091-CAA8H-A JH-2-072-3DD4G-A JH-2-061-1H66H-A

public/nst_nfosi_ntap/meta_mrnaseq_tpm.txt

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+cancer_study_identifier: nst_nfosi_ntap
+genetic_alteration_type: MRNA_EXPRESSION
+datatype: CONTINUOUS
+stable_id: mrna_seq_tpm
+show_profile_in_analysis_tab: true
+profile_name: Normalized gene expression
+profile_description: Normalized gene expression levels (TPM)
+data_filename: data_mrnaseq_tpm.txt