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nf-osi
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nfportalutils
Utilities for NF Portal project and data management
https://nf-osi.github.io/nfportalutils/
MIT License
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Update annotations.R
#139
jaybee84
closed
7 months ago
0
Update annotate-nf-processed-data.Rmd
#138
jaybee84
closed
10 months ago
1
Could add OR logic for fastq.gz
#137
allaway
opened
11 months ago
0
metadata is a resourceType
#136
allaway
opened
11 months ago
0
fq.gz is not always geneExpression
#135
allaway
opened
11 months ago
1
Feat/view fix
#134
anngvu
closed
11 months ago
2
Update the cBioPortal vignette
#133
anngvu
closed
7 months ago
0
Util to help with fixing schema issues for broken views
#132
anngvu
closed
11 months ago
0
Precheck for supplemental context/coverage for schematic revalidation
#131
anngvu
closed
7 months ago
0
Handle potential study schema update for `annotationStatus`
#130
anngvu
opened
11 months ago
0
Patch/fix ref
#129
anngvu
closed
11 months ago
0
Patch/issue 124
#128
anngvu
closed
12 months ago
0
Update schematic API utils due to changes
#127
anngvu
closed
9 months ago
1
Follow-up meta-qc enhancements
#126
anngvu
opened
1 year ago
0
Util to create normalized clinical data
#125
anngvu
opened
1 year ago
0
Small fixes in nextflow utils
#124
anngvu
closed
12 months ago
0
Add meta-qc utils per # 87
#123
anngvu
closed
1 year ago
1
Add script for more sophisticated scoring of annotations
#122
anngvu
opened
1 year ago
0
Feat/pathfinder
#121
anngvu
closed
1 year ago
0
Util to help get the id of something nested within a folder hierarchy
#120
anngvu
closed
11 months ago
0
Patch/cbioportal utils
#119
anngvu
closed
1 year ago
0
Annotation and organization utils for nf-output CNV
#118
anngvu
closed
1 year ago
0
Add iterative submission to handle Synapse platform API limits when using `annotate_with_manifest` with large manifests
#117
anngvu
opened
1 year ago
0
Add cBioportal packaging for submission of CNV and RNA-seq data
#116
anngvu
closed
1 year ago
0
Handle version semantics for collections
#115
anngvu
closed
1 year ago
0
Add annotation and organization utils for CNVkit outputs
#114
anngvu
closed
1 year ago
0
Patch/figures other export params
#113
anngvu
closed
1 year ago
0
Handle different versioning logic for items in a dataset vs items in a dataset collection
#112
anngvu
closed
1 year ago
1
nfportalutils not utilizing .synapseConfig
#111
allaway
opened
1 year ago
0
Updates in samplesheet util and vignette
#110
anngvu
closed
1 year ago
0
Remove entityId in schema test
#109
anngvu
closed
1 year ago
0
Update nf-related vignette
#108
anngvu
closed
1 year ago
0
Add handling for yet another samplesheet version
#107
anngvu
closed
1 year ago
0
Update annotation scripts for NF processed datasets to automatically add license
#106
anngvu
closed
1 month ago
5
Add utils for dataset collection manipulation
#105
anngvu
closed
1 year ago
0
Add script for generating dataset citations
#104
anngvu
closed
1 year ago
0
Patch/utils
#103
anngvu
closed
1 year ago
0
Handle case in `as_table_schema` when table has no rows yet
#102
anngvu
closed
1 year ago
0
Pin pandas to 1.5.3 bc of breaking changes
#101
anngvu
closed
1 year ago
0
Enforce string user ids
#100
anngvu
closed
1 year ago
0
Feature request in #98
#99
anngvu
closed
1 year ago
0
Update `new_project` functionality to handle new `initPublicView` configuration
#98
anngvu
closed
1 year ago
0
Patch/deprecations fixes docs
#97
anngvu
closed
1 year ago
0
Be more paranoid (test given id) when assigning admin user in new project
#96
anngvu
closed
1 year ago
0
Remove dead code and dependencies for old GSheets stuff
#95
anngvu
closed
1 year ago
0
Refactor synapse-adjacent functions to use new reticulate-based synapser
#94
allaway
opened
1 year ago
3
Remove username and password authentication
#93
anngvu
closed
1 year ago
0
Fix outdated test expectations
#92
anngvu
closed
1 year ago
0
Update Dockerfile due to recent debian changes
#91
anngvu
closed
1 year ago
0
Update make_folder to handle annotations
#90
anngvu
closed
1 year ago
0
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