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Bioconductor
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GenomicDataCommons
Provide R access to the NCI Genomic Data Commons portal.
http://bioconductor.github.io/GenomicDataCommons/
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remove legacy arguments, function, methods and endpoints
#116
LiNk-NY
closed
2 months ago
0
defunct legacy inputs and endpoint
#115
LiNk-NY
closed
5 months ago
0
slicing HTTP410 error
#114
lmckinno
closed
6 months ago
1
Timeout was reached: [api.gdc.cancer.gov]
#113
mansi-aggarwal-2504
closed
9 months ago
3
about filter Metastatic sample
#112
yinchaoyi
closed
10 months ago
1
legacy error while running slicing
#111
SinhaI
closed
1 year ago
6
legacy endpoint is defunct
#110
LiNk-NY
closed
1 year ago
1
Error in bind_rows, when the diagnosis dataframe is NULL
#109
zx8754
closed
1 year ago
1
remove all magrittr pipes and dependency, use native |>
#108
LiNk-NY
closed
2 months ago
0
token not recognized for slicing
#107
ajggit
closed
1 year ago
1
Slicing function does not work
#106
JulianRozenberg
closed
1 year ago
4
size parameter in `manifest` not working
#105
LiNk-NY
closed
1 year ago
4
Is there any way to use the package with data release v12?
#104
shadihames
closed
2 years ago
1
update manifest chunk in overview.Rmd, closes #100
#103
LiNk-NY
closed
2 years ago
0
update example to new field values in files()
#102
LiNk-NY
closed
2 years ago
1
OncoPrint section not working in somatic_mutations.Rmd
#101
LiNk-NY
closed
1 year ago
0
HTSeq - Counts removed from the data release
#100
LiNk-NY
closed
2 years ago
6
validate the version of the gdc-client
#99
LiNk-NY
closed
2 years ago
1
HTTP 403 forbidden error when calling gdcdata to download open access files from new GDC Data Release v32
#98
hermidalc
closed
2 years ago
2
gdcdata should not depend on internet connection when cache=TRUE and you have all the files in your local cache
#97
hermidalc
opened
2 years ago
1
implement is / NOT MISSING in filter
#96
LiNk-NY
closed
2 years ago
0
Slide file query shows file incorrectly associated with multiple slides when GDC portal shows it's associated with only one
#95
hermidalc
closed
2 years ago
8
Making GenomicDataCommons less daunting to use for the average user
#94
hermidalc
opened
2 years ago
0
filter syntax for GDC query API "IS MISSING" and "NOT MISSING" operators
#93
hermidalc
closed
1 year ago
7
gdcdata prints extraneous manifest console output
#92
hermidalc
closed
2 years ago
0
BAM slicing bug requires token be missing
#91
seandavi
closed
2 years ago
1
Error in gdc_token() : file.exists(token_file) is not TRUE
#90
SisiChen16
closed
2 years ago
4
field_picker function does not exist
#89
wt12318
closed
2 years ago
3
use auto readr::type_convert to resolve issues between type in return…
#88
LiNk-NY
closed
2 years ago
0
gdc_clinical unable to pull patient data from case_ids
#87
Deepam84
closed
2 years ago
3
TCGA data ids not matching in cases() and files()
#86
cpguy101
closed
2 years ago
1
`readr` 2.0.0 causes console flooding
#85
KaiAragaki
closed
3 years ago
2
make legacy data downloadable, closes #82
#84
LiNk-NY
closed
2 years ago
0
Unable to Install package in most recent version of R.
#83
andrewsris
closed
3 years ago
0
bug in gdcdata?
#82
LiNk-NY
closed
2 years ago
1
Querying a previous GDC data release version
#81
hermidalc
opened
3 years ago
0
BAM slicing from legacy archive
#80
pbousquets
closed
1 year ago
2
Add default s3 methods for tidy functions to avoid harmful masking
#79
alanocallaghan
closed
3 years ago
0
GenomicDataCommons masks dplyr functions
#78
alanocallaghan
closed
1 year ago
10
How to get the type of file normal or tumor in the manifest file
#77
ranijames
closed
2 years ago
5
TCGA-OV: Normal controls visible on portal but not through bioconductor query
#76
chartl
closed
4 years ago
1
Add TSV return format support
#75
seandavi
opened
4 years ago
0
Add support for GraphQL endpoint
#74
seandavi
opened
4 years ago
0
Progress Bar Should Display Download Speed
#73
DarioS
opened
5 years ago
0
Download Fails if File In Legacy Archive
#72
DarioS
closed
2 years ago
1
Strange results on merging clinical id
#71
bioinfo-dirty-jobs
closed
5 years ago
2
Clinical data are empty
#70
bioinfo-dirty-jobs
opened
5 years ago
3
problem download some data from one project
#69
bioinfo-dirty-jobs
closed
5 years ago
2
Problems on Download some Methylation Beta Value from server
#68
bioinfo-dirty-jobs
opened
5 years ago
0
Error 503
#67
bioinfo-dirty-jobs
closed
5 years ago
1
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