PCGR v.2.0rc - 2024 #223

sigven · 2024-04-29T08:16:33Z

Functionality to support new reference data management
Functionality to support RNA-seq (bulk) expression input - correlation against reference samples (TCGA/DepMap/Treehouse), preliminary outlier detection (TCGA only)
Functionality to support VEP cache as a separate entity from the PCGR reference data
New copy number input format - absolute, allele-specific (nMajor + nMinor)
Copy number annotation moved from pcgrr to Python workflow
Variant oncogenicity assessment (SNVs/InDels, based on VICC/ClinGen guidelines) implemented in Python workflow
More robust biomarker matching implemented in Python workflow - considering genomic coordinates, HGVSp entries (considering principal and non-principal matches)
New HTML templates - quarto-based
New Excel workbook output

…ures - new refbundle

Remove: - BiocGenerics - caret - ggpubr - IRanges - randomForest - usethis (this is only for dev + data-raw) Add: - cpsr - CNAqc - readr - stringi

Changes from devtools::check

…le_update_2023

conda: install openxlsx2 + CNAqc during build stage

Merge branch 'bundle_update_2023' of github.com:sigven/pcgr into bundle_update_2023 # Conflicts: # pcgrr/DESCRIPTION

sigven and others added 30 commits July 12, 2023 15:19

IN PROGRESS - new bundle structure

b1880c6

annoutils as part of pcgr, biomarker matching

a768577

conda recipe: bump R -> 4.2, Py -> 3.10

56c2ef7

refactor GH Actions

7b4ee9a

temp use umccr channel

77599eb

Bump version: 1.4.1 → 1.4.2

006db76

Unpin pcgr deps

c3281f7

Bump version: 1.4.2 → 1.4.3

ef8d740

pcgr: build with py 3.9 and 3.10

edb66ce

Bump version: 1.4.3 → 1.4.4

2d86e92

GHA: use noarch for pure python version-agnostic

6758c54

Bump version: 1.4.4 → 1.4.5

54ed801

fixes to code restructure and biomarker matching

99e32c6

biomarker match code - hgvsc and aa region

e541420

VEP csq prioritization

5d00cae

code re-structuring (vep)

6cf103a

check GENE_TRANSCRIPT_XREF in rec.INFO

9cc5817

re-structuring of pre-report data

692bbea

updates to pre-reporting (Python) part

30ce35c

removed non-used funcs

eaed040

revised refdata loading

a2398b9

fix ACMG and clean temp files

58c69fd

bump vep to 110; grab vcf2maf-umccr from bioconda

e37c9cb

gha: use micromamba

0b4b010

Bump version: 1.4.5 → 1.4.6

a9be3fb

dependency cleanup

e339cce

actions cleanup

df3ec57

Bump version: 1.4.6 → 1.4.1

fa8c2aa

add quarto dependency - see quarto-dev/quarto-cli#61

f1723f0

new pipe operator and input handling

83a995c

sigven and others added 13 commits April 22, 2024 13:38

quarto + excel 2024

8d291a6

fix bugs and add biomarkers to Excel output

e75e8fa

fix excel output error

197eb2a

fix bug when SNVs = 0

c831770

improve signature analysis for primary sites with no reference signat…

43277f4

…ures - new refbundle

DESCRIPTION dependency changes - see below:

3c27ca5

Remove: - BiocGenerics - caret - ggpubr - IRanges - randomForest - usethis (this is only for dev + data-raw) Add: - cpsr - CNAqc - readr - stringi

copy strip_html verbatim from xfun

9934b5f

copy MutationalPatterns:::.resample_mut_mat verbatim

a3be7b5

get_clin_assocs_snv_indel removed

65a7ab4

devtools::check warnings

8fe0718

has_name comes straight from rlang

6a19680

update man/

e33f103

Merge pull request #225 from umccr/bundle_update_2023_PD

6d6039e

Changes from devtools::check

sigven changed the title ~~PCGR v.1.5rc - 2024~~ PCGR v.2.0rc - 2024 Apr 30, 2024

sigven and others added 16 commits May 10, 2024 03:03

banner margin and doc updates

26c9078

Merge branch 'bundle_update_2023' of github.com:sigven/pcgr into bund…

5190a4a

…le_update_2023

docs update

2745c8c

conda: install openxlsx2 during build stage since no conda pkg

731aa08

conda: cleanup recipe dependencies

04837a6

conda: probably include cpsr dependency

df4409b

GHA: update actions

0ada9e6

remove cpsr dependency else cyclic madness ensues

08fef37

Bump version: 1.4.1.9001 → 1.4.1.9002

0a7773c

DESCRIPTION: add cpsr to Suggests

c317e62

crancheck: add amazing docs for dt_display, tsv_cols

70d6a0b

Merge pull request #226 from umccr/conda_deps

bd9caf8

conda: install openxlsx2 + CNAqc during build stage

removing cpsr dependency

ce78855

remove CPSR dependency

cba6e9e

Merge branch 'bundle_update_2023' of github.com:sigven/pcgr into bundle_update_2023 # Conflicts: # pcgrr/DESCRIPTION

remove CPSR dep

b578cd6

simplify dependencies

b649e71

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PCGR v.2.0rc - 2024 #223

PCGR v.2.0rc - 2024 #223

sigven commented Apr 29, 2024

PCGR v.2.0rc - 2024 #223

Are you sure you want to change the base?

PCGR v.2.0rc - 2024 #223

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sigven commented Apr 29, 2024