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Updated Docs Site with new Active Release Manifest #288

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3c95d61
Updating link
clsackett Jan 30, 2025
2cc1b4c
Fixing URL again
clsackett Jan 30, 2025
2450749
Merge pull request #452 from NCI-GDC/quick_fixes
wwysoc2 Jan 30, 2025
1aed838
Update Data_Release_Notes.md
clsackett Jan 30, 2025
a92ab40
Merge pull request #453 from NCI-GDC/quick_fixes
wwysoc2 Jan 30, 2025
be8fec1
Merge pull request #454 from NCI-GDC/develop
wwysoc2 Jan 30, 2025
6790fcb
Remove AWG portal documentation
clsackett Feb 4, 2025
19225b7
Merge pull request #455 from NCI-GDC/remove_AWG_portal_doc
clsackett Feb 4, 2025
5646a01
Changed markdown to HTML - will not render in table
wwysoc2 Feb 5, 2025
0206579
Merge pull request #456 from NCI-GDC/fix_video
wwysoc2 Feb 5, 2025
42327f0
Merge pull request #457 from NCI-GDC/develop
wwysoc2 Feb 5, 2025
a13750c
Update MAF_Format doc
clsackett Feb 6, 2025
3965759
Updating API User's Guide
clsackett Feb 6, 2025
f2eacd9
Updating API Appendix A
clsackett Feb 6, 2025
97ce9c6
Add cnv_change_5_category to API documentation
clsackett Feb 12, 2025
0d9cd3b
PEAR-2284 - Add the GDC Apps menu to the documentation site (#439)
amlehman Feb 13, 2025
13c389e
Merge branch 'develop' into update_API_doc
wwysoc2 Feb 14, 2025
c140bb0
Merge pull request #460 from NCI-GDC/update_API_doc
wwysoc2 Feb 14, 2025
2381a02
Fix typo
clsackett Feb 14, 2025
44752bd
Merge pull request #462 from NCI-GDC/cnv_5_cat_api_doc
clsackett Feb 14, 2025
353f366
Merge pull request #461 from NCI-GDC/update_API_AppendixA
clsackett Feb 14, 2025
f166cee
scRNA-Seq Gene Expression Endpoints - Data Analysis API doc
ebusygina Feb 17, 2025
e9eac9a
Added info that scRNA-Seq API supports up to 10 genes
ebusygina Feb 19, 2025
4a2176b
Deleted info about HDF5 files and changed examples values to float
ebusygina Feb 20, 2025
bac843e
first draft of roentgen release notes
wteouchicago Feb 26, 2025
d510342
fixes date
wteouchicago Feb 26, 2025
aa0b232
updates known issues, adjust wording
wteouchicago Feb 26, 2025
14eeb07
removes extra space
wteouchicago Feb 26, 2025
345708b
addresses PR comments, fixes
wteouchicago Feb 26, 2025
d2984bf
Merge pull request #465 from NCI-GDC/roentgen_release_notes_draft
wteouchicago Feb 26, 2025
2ed3f7e
Updated data format for values
ebusygina Feb 27, 2025
b7649ec
Adding info about the source of the data
ebusygina Feb 27, 2025
4157047
Removed info about X-Auth
ebusygina Feb 27, 2025
b10c778
add scrna tutorial to develop
karishma-gangwani Feb 27, 2025
ba007f9
images added to develop for scrna
karishma-gangwani Feb 27, 2025
955f638
changed paths in scrna tutorial
karishma-gangwani Feb 27, 2025
4492e56
Merge pull request #467 from NCI-GDC/scrna-guide
wwysoc2 Feb 27, 2025
e02df7b
Changed description about the matrix layer
ebusygina Feb 27, 2025
4bb27d1
screenshot updates plus minor text changes for roentgen
wteouchicago Feb 27, 2025
9cc86b4
Merge pull request #463 from NCI-GDC/evgeniia-DOC-473-scrna-seq
wwysoc2 Feb 28, 2025
86c89dc
Pear 2352 mvs search (#469)
philtom-ctds Feb 28, 2025
0ddb6e4
Removed ascii characters and added to mkdocs yaml
wwysoc2 Mar 3, 2025
ff38eb4
Merge pull request #470 from NCI-GDC/scrna-fix
wwysoc2 Mar 3, 2025
a0dcd52
Removed ascii characters - 2
wwysoc2 Mar 3, 2025
7e32b88
Merge pull request #471 from NCI-GDC/scrna-fix
wwysoc2 Mar 3, 2025
1542fa2
added scrna to mkdocs and PDF
wwysoc2 Mar 4, 2025
ef921d5
Update Data_Portal_UG.yml
wwysoc2 Mar 4, 2025
7b17771
Merge pull request #472 from NCI-GDC/mkdocs-change
wwysoc2 Mar 4, 2025
5e97a23
updates OCA description
wteouchicago Mar 5, 2025
95402c8
Merge pull request #468 from NCI-GDC/roentgen-portal-docs-updates
wteouchicago Mar 5, 2025
621897c
updates known issues and link
wteouchicago Mar 10, 2025
376898b
updated scRNA user guide
karishma-gangwani Mar 10, 2025
eb78f7e
formatting changes and image update
karishma-gangwani Mar 11, 2025
3cd7cf3
Merge pull request #474 from NCI-GDC/known_issues_update
wteouchicago Mar 12, 2025
e83ac62
DOC-425: Added 8 Workflow Types to mkdocs.yml
ebusygina Mar 12, 2025
b3ad1d1
Merge pull request #476 from NCI-GDC/evgeniia_DOC-425_v9
ebusygina Mar 12, 2025
6f5717e
More defined sections in WGS documentation
wwysoc2 Mar 12, 2025
bd66761
Revert "More defined sections in WGS documentation"
wwysoc2 Mar 12, 2025
cecfdcf
Revert "Revert "More defined sections in WGS documentation""
wwysoc2 Mar 12, 2025
ca21a71
Merge pull request #477 from NCI-GDC/wgs_impr
wwysoc2 Mar 13, 2025
953f996
DOC-478 - survival release notes
wwysoc2 Mar 17, 2025
1454b14
moved JIRA ticket
wwysoc2 Mar 17, 2025
0b375a1
Merge pull request #478 from NCI-GDC/survival-rns
wwysoc2 Mar 17, 2025
826d3d3
Merge pull request #475 from NCI-GDC/scrna-app-tutorial-updates
wwysoc2 Mar 19, 2025
d5d7288
Add SJ release notes for 2.4
siosonel Mar 19, 2025
31def35
Add cohort MAF fixes; highlight more scRNAseq features; remove duplic…
siosonel Mar 19, 2025
35ab453
Address Bill's comments
siosonel Mar 19, 2025
6fa5b74
Add a line between new features heading and the first entry under it
siosonel Mar 19, 2025
a5dd701
Merge pull request #479 from NCI-GDC/sj-release-notes-2.4
wwysoc2 Mar 19, 2025
dce3401
removed curly quotes
wwysoc2 Mar 19, 2025
5c99075
Added release notes for banner
wwysoc2 Mar 19, 2025
6c6bd1d
Changed wording
wwysoc2 Mar 19, 2025
4274853
Merge pull request #480 from NCI-GDC/dr42-data-notes
wwysoc2 Mar 19, 2025
b61e170
updates release date, minor fixes
wteouchicago Mar 20, 2025
d3cd47a
Merge pull request #481 from NCI-GDC/final_roentgen_release_notes
wwysoc2 Mar 20, 2025
cf36050
Merge pull request #482 from NCI-GDC/develop
wwysoc2 Mar 20, 2025
688047c
updated user guides, proteinpaint and sequence reads
karishma-gangwani Apr 22, 2025
c1e87df
update analysis center image
karishma-gangwani Apr 22, 2025
20570b1
update based on 508 compliance and removed repetition
karishma-gangwani Apr 22, 2025
b8645a3
DR43 Release Notes
wwysoc2 Apr 25, 2025
c4d64b1
Added details about VarScan
wwysoc2 Apr 28, 2025
b04d20e
PEAR-2385 - remove special sort case for biospecimen (#487)
amlehman May 2, 2025
597be8c
PEAR-2394 - fixes tsv/json button not working, twice the bootstrap is…
amlehman May 2, 2025
116395f
add utm codes (#466)
paribartandhakal May 2, 2025
bc0d362
Changed date, fixed typo
wwysoc2 May 6, 2025
4a792c6
Merge pull request #488 from NCI-GDC/dr43-release-notes
wwysoc2 May 6, 2025
66d7892
DOC-487 changes to update outdated UUIDs
ebusygina May 7, 2025
7fb430b
deleted space after the colon
ebusygina May 7, 2025
fc98089
DOC-489: Updating outdated info: scripts, shells, filters, etc
ebusygina May 7, 2025
1f64065
Merge pull request #490 from NCI-GDC/develop
wwysoc2 May 7, 2025
a13a488
Added manifests
wwysoc2 May 7, 2025
8ab4142
Merge pull request #492 from NCI-GDC/manifests-dr43
wwysoc2 May 7, 2025
6b3ee0e
Updated filters and curl for Simple Somatic Mutation Endpoint Example…
ebusygina May 7, 2025
e667dd2
Merge pull request #493 from NCI-GDC/develop
wwysoc2 May 8, 2025
8dcf6cd
Merge pull request #491 from NCI-GDC/evgeniia_DOC-489
ebusygina May 12, 2025
0024aa3
Updated an error message in BAM_Slicing.md
ebusygina May 12, 2025
77267c9
Merge pull request #489 from NCI-GDC/evgeniia_DOC-487
ebusygina May 13, 2025
e4013d0
Merge pull request #458 from NCI-GDC/update_MAF_format
clsackett May 14, 2025
c8b2b00
DOC-483: Documenting CNV segment API
ebusygina May 14, 2025
cc5b422
Minor fixes and changed one of the examples to tsv format
ebusygina May 15, 2025
51a1180
DOC-490: part 1. Fixing reference in-docs links
ebusygina May 15, 2025
324baaa
Merge pull request #494 from NCI-GDC/evgeniia_DOC-483
ebusygina May 15, 2025
cec4389
DOC-490, part 2: Removed broken links from the TCGA_VCF_1.1v2 documen…
ebusygina May 15, 2025
848b0ea
Addressing comments
ebusygina May 19, 2025
5ae291c
DOC-490, part 3: Fixing the hierarchy of the headers/subheaders
ebusygina May 19, 2025
a6efe4d
remove outlinks
karishma-gangwani May 19, 2025
b35c8fb
remove links, fix text
karishma-gangwani May 19, 2025
2d32158
Fixing hierarchy of Data Submission Walkthrough and TCGA_VCF_1.1v2
ebusygina May 19, 2025
30560bd
Slight change of hierarchy for the Data_Submission_Walkthrough file
ebusygina May 20, 2025
c4948c9
Sanger minus API release notes
wwysoc2 May 20, 2025
fe2a51e
Removed DTT-UI docs as it was removed for download from gdc.cancer.gov
wwysoc2 May 20, 2025
72a8ee2
Merge pull request #495 from NCI-GDC/evgeniia_DOC-490
ebusygina May 20, 2025
9f642b2
fixed version link
wwysoc2 May 20, 2025
9da6cb2
Merge pull request #497 from NCI-GDC/sanger-minus-release
wwysoc2 May 20, 2025
19fa561
Merge pull request #498 from NCI-GDC/develop
wwysoc2 May 20, 2025
0972c17
template for sanger release notes
wteouchicago May 29, 2025
f7d6959
Merge pull request #499 from NCI-GDC/sanger_release_notes_template
wteouchicago May 30, 2025
e270948
user guide updates for sanger
wteouchicago May 30, 2025
661a2db
removed dtt ui related pages from search
wteouchicago May 30, 2025
dfecb3f
fix broken image links
karishma-gangwani May 31, 2025
f9796d5
updates cnv tool link
wteouchicago Jun 2, 2025
c290f27
Merge pull request #500 from NCI-GDC/sanger-user-guide-updates
wteouchicago Jun 2, 2025
eb49575
moves v1 and dtt ui pages to Archive folder
wteouchicago Jun 2, 2025
872d52e
added user guide for cnv tool
karishma-gangwani May 31, 2025
67fa0d0
sanger release notes draft for UC.
wteouchicago Jun 3, 2025
19e81b6
typo fixes per PR comments
wteouchicago Jun 3, 2025
f273b3f
tweaks based on PR comments
wteouchicago Jun 3, 2025
5a95d48
DOC-495: Updated /segment_cnvs description
ebusygina Jun 3, 2025
970ef25
removes curly quotes
wteouchicago Jun 4, 2025
691e37a
Merge pull request #503 from NCI-GDC/sanger_release_notes_draft1
wteouchicago Jun 4, 2025
af11d96
moved the Segment CNV description from the table to the examples sect…
ebusygina Jun 4, 2025
91e4d0a
Merge pull request #504 from NCI-GDC/evgeniia_DOC-495
ebusygina Jun 4, 2025
68a79e3
rename CNV Tool to Copy Number Segment Tool
siosonel Jun 5, 2025
f4926fc
Merge pull request #502 from NCI-GDC/cnv-user-guide
siosonel Jun 5, 2025
ce29e13
Add release notes for the ProteinPaint-based tool updates and fixes
siosonel Jun 5, 2025
ef7f0ce
Added CVNtools to yml files
zhangm-02 Jun 5, 2025
76496ef
Fixed tool name and removed extra i
zhangm-02 Jun 5, 2025
e92870b
removes files already copied to Archive
wteouchicago Jun 5, 2025
38ba8d7
Add missing period to Copy Number Segment release note
siosonel Jun 5, 2025
ffe415f
Merge pull request #507 from zhangm-02/CNVtool_addition_496
zhangm-02 Jun 6, 2025
7b9c83f
remove reference to a removed screen recording
siosonel Jun 8, 2025
2cbd529
Merge pull request #485 from NCI-GDC/user_guide_sanger_release2
siosonel Jun 8, 2025
b363d24
Merge pull request #505 from NCI-GDC/sanger-pp-release-notes
siosonel Jun 11, 2025
61d5450
updates broken links
wteouchicago Jun 13, 2025
96a37f3
Added updated release notes
wwysoc2 Jun 17, 2025
d59a89a
Changed submission portal version
wwysoc2 Jun 17, 2025
f09e4cb
updates sanger release date
wteouchicago Jun 18, 2025
759df0b
changed release date
wwysoc2 Jun 26, 2025
905ebfc
updates release date
wteouchicago Jun 26, 2025
235f57f
Merge pull request #509 from NCI-GDC/DOC-297_fix_links
wteouchicago Jun 26, 2025
cd79be6
GEC branch re-do
wwysoc2 Jun 26, 2025
78a18f8
remove hash links
karishma-gangwani Jun 26, 2025
f9a557f
update link for image
karishma-gangwani Jun 27, 2025
50a6798
update all links
karishma-gangwani Jun 27, 2025
8f7327a
Merge pull request #501 from NCI-GDC/remove_dtt_ui_refs
wwysoc2 Jun 27, 2025
98a8c33
updates release date again
wteouchicago Jun 27, 2025
a67319a
Merge pull request #510 from NCI-GDC/DOC-498-SUBP-Version
wwysoc2 Jun 27, 2025
142fd79
Merge pull request #511 from NCI-GDC/sanger_release_notes_final
wteouchicago Jun 30, 2025
5c6a377
minor corrections
wwysoc2 Jun 30, 2025
b30c4d9
removed quote
wwysoc2 Jun 30, 2025
30ce5a6
Merge pull request #513 from NCI-GDC/new-gec-branch
wwysoc2 Jun 30, 2025
5a1dfd0
date change
wwysoc2 Jun 30, 2025
35ff7df
date change 2
wwysoc2 Jun 30, 2025
90920c5
Merge pull request #515 from NCI-GDC/submission-sanger-date
clsackett Jun 30, 2025
76230da
add known issues for ProteinPaint-based tools in Sanger release notes
siosonel Jun 30, 2025
bd23ab0
adjusts wording
wteouchicago Jun 30, 2025
4ab7c44
Fixing encoding issues
clsackett Jun 30, 2025
9a21e18
Merge pull request #517 from NCI-GDC/fix-encoding-errors
clsackett Jun 30, 2025
bca1600
Merge pull request #516 from NCI-GDC/pp-sanger-known-issues
siosonel Jun 30, 2025
ca18cff
adds precommit hooks for detecting curly quotes and non-ascii chars
wteouchicago Jul 1, 2025
4fe1c86
Update Data_Dictionary_Release_Notes.md
zhangm-02 Jul 21, 2025
b5e1b73
Merge pull request #519 from NCI-GDC/DOC-499_add_precommit_hooks
wwysoc2 Jul 21, 2025
2734e2c
Update Data_Dictionary_Release_Notes.md
zhangm-02 Jul 22, 2025
b192fd6
Update Data_Dictionary_Release_Notes.md
zhangm-02 Jul 22, 2025
fef72ad
Update Data_Dictionary_Release_Notes.md
zhangm-02 Jul 22, 2025
a5bfaee
Update Data_Dictionary_Release_Notes.md
zhangm-02 Jul 22, 2025
d7d2cd5
Update Data_Dictionary_Release_Notes.md
zhangm-02 Jul 23, 2025
0d969c9
Update Data_Dictionary_Release_Notes.md
zhangm-02 Jul 23, 2025
a215cdf
Update Data_Dictionary_Release_Notes.md
zhangm-02 Jul 23, 2025
17e652b
Changes to dictionary release notes
wwysoc2 Jul 23, 2025
5eed0f1
PEAR-2395 - remove deprecated properties for array type fields
amlehman Jul 29, 2025
2fa8566
PEAR-2415 - fix d3 error
amlehman Jul 30, 2025
914f1af
PEAR-2481 - fix style not accepting object in recent d3 version
amlehman Jul 30, 2025
8552469
Update Data_Dictionary_Release_Notes.md
clsackett Jul 31, 2025
f242381
Merge pull request #520 from NCI-GDC/zhangm02-dict-notes-v3.4-update
clsackett Jul 31, 2025
464d323
Update Data_Dictionary_Release_Notes.md
zhangm-02 Aug 4, 2025
75439bb
Update Data_Dictionary_Release_Notes.md
zhangm-02 Aug 4, 2025
ca73e08
Update Data_Dictionary_Release_Notes.md
zhangm-02 Aug 4, 2025
ecd884b
Merge pull request #526 from NCI-GDC/zhangm-02-patch-1
zhangm-02 Aug 4, 2025
8123bd6
Merge pull request #521 from NCI-GDC/PEAR-2395-deprecated-enums
wteouchicago Aug 8, 2025
460eda7
Merge pull request #522 from NCI-GDC/PEAR-2415-node-not-loading
wteouchicago Aug 8, 2025
8dfb7f9
Merge pull request #523 from NCI-GDC/PEAR-2481-return-of-the-breadcrumbs
wteouchicago Aug 8, 2025
d08679c
Added release notes and file list
wwysoc2 Aug 18, 2025
15f3748
Merge pull request #530 from NCI-GDC/mut2_info
wwysoc2 Aug 19, 2025
3eb01e5
changed file suffix to correct one
wwysoc2 Aug 19, 2025
17fb393
Merge pull request #531 from NCI-GDC/mut2_info
clsackett Aug 19, 2025
f201b7c
Added scRNA Tool
wwysoc2 Sep 11, 2025
25df686
Removed extra line
wwysoc2 Sep 11, 2025
adac1a1
Merge pull request #533 from NCI-GDC/new_yt
wwysoc2 Sep 11, 2025
cbf4dc9
Embed link
wwysoc2 Sep 11, 2025
731c18e
Merge pull request #534 from NCI-GDC/new_yt
wwysoc2 Sep 11, 2025
7f18212
removed old files from search, skips false positives for detect secrets
wteouchicago Sep 15, 2025
64231e5
DOC-488: Updating outdated links
ebusygina Sep 20, 2025
1456567
DOC-488 fixes
ebusygina Sep 23, 2025
81bbb7f
fixed typo
ebusygina Oct 9, 2025
bc0bf90
changed the link for the CDE Browser
ebusygina Oct 10, 2025
0116e13
Merge pull request #537 from NCI-GDC/evgeniia_DOC-488_update_outdated…
ebusygina Oct 10, 2025
c71a550
DR 44 release notes commit
wwysoc2 Oct 28, 2025
fd0c53d
Added GATK4 manifest
wwysoc2 Oct 28, 2025
f4371e1
Added data changes
wwysoc2 Oct 28, 2025
8aeaf24
Added manifest files to page.
wwysoc2 Oct 28, 2025
ecc8fa3
Added header to TSV file
wwysoc2 Oct 28, 2025
cd7cd00
updates copyright year
wteouchicago Oct 28, 2025
6e44096
Merge pull request #539 from NCI-GDC/update_copyright_year
wwysoc2 Oct 29, 2025
5a005fc
Merge pull request #538 from NCI-GDC/dr44-rns
wwysoc2 Oct 29, 2025
97306b7
Merge pull request #535 from NCI-GDC/DOC-503_move_page_to_archive
wwysoc2 Oct 29, 2025
a6dc1c2
Mistake with experimental strategy
wwysoc2 Oct 29, 2025
3925b98
Merge pull request #541 from NCI-GDC/dr44-rns
wwysoc2 Oct 29, 2025
a42beee
Added correct IDs
wwysoc2 Nov 3, 2025
8052549
Merge pull request #543 from NCI-GDC/dr44_manifest_fix
wwysoc2 Nov 3, 2025
8e91172
Slide Image correction
wwysoc2 Nov 5, 2025
d199856
Merge pull request #545 from NCI-GDC/dr44-rn-correction
wwysoc2 Nov 5, 2025
faad982
DOC-507 properly hide old docs from view
wteouchicago Nov 6, 2025
598bae8
DOC-494 adds section on Annotations Browser to Quick Start
wteouchicago Nov 6, 2025
eb9595b
adds link to encyclopedia entry on annotations
wteouchicago Nov 6, 2025
73b0ebf
updates encyclopedia page
wteouchicago Nov 6, 2025
1aad209
Merge pull request #548 from NCI-GDC/DOC-494_add_annotations_browser_…
wwysoc2 Nov 7, 2025
e90ca47
DOC-281: Encyclopedia TCGA_Barcode table fix
ebusygina Nov 11, 2025
9fe93ed
DOC-119: added excludeifany desc to API docs
ebusygina Nov 12, 2025
7dcb1ec
Updated excludeifany API operator description
ebusygina Nov 12, 2025
3259e23
updated exclude and excludeifany API operators description and added …
ebusygina Nov 13, 2025
84162f3
Added links to Code Tables Report
ebusygina Nov 13, 2025
f7b4fc2
Fixed typo in the Barcode Types table header
ebusygina Nov 13, 2025
8d4ac55
Merge pull request #549 from NCI-GDC/evgeniia_DOC-281_Encyclopedia_TC…
ebusygina Nov 13, 2025
bfbf807
Changed the example description according to Wendy's comment
ebusygina Nov 13, 2025
8eb06d3
Merge pull request #550 from NCI-GDC/evgeniia_DOC-119_excludeifany_ap…
ebusygina Nov 14, 2025
0280b66
DOC-480: Update the One_Consequence definition in the MAF Format docu…
ebusygina Nov 24, 2025
2cca657
Merge pull request #551 from NCI-GDC/evgeniia_DOC-480_One_Consequence…
ebusygina Nov 25, 2025
ac1bfcc
First draft release notes
wwysoc2 Nov 25, 2025
6c90761
Added ALCHEMIST treatment arm lists
wwysoc2 Nov 25, 2025
f670b32
Merge pull request #547 from NCI-GDC/DOC-507_properly_remove_old_pages
wteouchicago Dec 2, 2025
8a51584
Removed extra info and case lists
wwysoc2 Dec 3, 2025
72e91c4
Added manifest links
wwysoc2 Dec 4, 2025
b0fe3fa
Added line about added HCMI case
wwysoc2 Dec 4, 2025
ea661a7
Merge pull request #552 from NCI-GDC/DR45-notes
wwysoc2 Dec 4, 2025
c18bca2
Copyright year
wwysoc2 Jan 5, 2026
a79b7e2
Merge pull request #555 from NCI-GDC/2026-CR
wwysoc2 Jan 5, 2026
025010e
template for uhlenbeck release notes
wteouchicago Jan 7, 2026
7944ce9
removes some extra spaces and empty lines
wteouchicago Jan 7, 2026
b50e861
Merge pull request #557 from NCI-GDC/Uhlenbeck_portal_release_notes_t…
wteouchicago Jan 7, 2026

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