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morinlab
/
GAMBLR
Set of standardized functions to operate with genomic data
https://morinlab.github.io/GAMBLR/
MIT License
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get_ssm_by_regions() is duplicating variants, and assigning them to the incorrect regions
#106
ckrushton
closed
2 years ago
3
Removed allow_clusted flag, which is not supported by downstream functions
#105
ckrushton
closed
1 year ago
3
Add additional blacklist to annotate_ssm_blacklist()
#104
hayashaalan
closed
1 year ago
2
new feature: right annotations in prettyOncoplot
#103
Kdreval
closed
2 years ago
0
Tidyverse isn't really "importable"
#102
lkhilton
closed
1 year ago
2
Kdreval dev
#101
Kdreval
closed
2 years ago
0
estimate_purity is broken when only sample_id is provided
#100
rdmorin
closed
8 months ago
2
Remote GAMBLR (outside GSC) is now a thing. Testers wanted!
#99
rdmorin
closed
2 years ago
1
hg38 support for collate_nfkbiz_results
#98
mattssca
closed
8 months ago
1
get_ssm_by_region incorrectly subsets on five columns, regardless if basic_column is TRUE
#97
mattssca
closed
1 year ago
1
update collate functions to work for genome and capture data
#96
rdmorin
closed
2 years ago
1
Possible error in read_tsv
#95
mattssca
closed
1 year ago
2
Functions for QC data
#94
rdmorin
closed
1 year ago
1
add cohort colours and fix MZL
#93
rdmorin
closed
2 years ago
2
init prettyCoOncoplot
#92
Kdreval
closed
2 years ago
2
Cmattsson dev
#91
mattssca
closed
2 years ago
4
Fix duplicated argument
#90
rdmorin
closed
2 years ago
0
get_gene_cn_and_expression does not return CN states
#89
Kdreval
closed
2 years ago
1
Bug fixes, new plotting functions, vignette examples, etc.
#88
mattssca
closed
2 years ago
1
get_coding_ssm for capture data does not return variants
#87
Kdreval
closed
2 years ago
10
Implement flatfile functionality for CNV and introduce cnvKompare
#86
Kdreval
closed
2 years ago
2
plot updates, vignette & bug fixes, etc.
#85
mattssca
closed
2 years ago
2
Bug fix: positional arguments in get_ssm_by_samples call to get_ssm_b…
#84
lkhilton
closed
2 years ago
0
Reduce duplicated code relate to get_coding_ssm_status
#83
mattssca
closed
2 years ago
1
fix flatfile reading in get_manta_sv
#82
rdmorin
closed
2 years ago
0
get_mutation_frequency_bin_matrix example in vignette causes R session to hang
#81
rdmorin
closed
1 year ago
1
ashm_multi_rainbow_plot broken?
#80
rdmorin
closed
2 years ago
3
pretty_lollipop_plot example in vignette not working
#79
rdmorin
closed
2 years ago
1
PrettyOncoplot example in vignette throws an error
#78
rdmorin
closed
2 years ago
2
Vignette refers to some functionality that is deprecated or gone
#77
rdmorin
closed
2 years ago
2
ashm_multi_rainbow_plot colour issue
#76
rdmorin
closed
2 years ago
1
ashm_rainbow_plot example in vignette is broken
#75
rdmorin
closed
2 years ago
3
Broken functionality (from_flatfile) in get_manta_sv
#74
rdmorin
closed
2 years ago
1
New functions: calculate PGA and adjust ploidy
#73
Kdreval
closed
2 years ago
0
fix broken get_gambl_metadata function
#72
rdmorin
closed
2 years ago
4
updating ssm functions to read from latest deblacklsited maf
#71
mattssca
closed
2 years ago
2
Updates to the prettyRainfallPlot
#70
Kdreval
closed
2 years ago
1
add rainfall plot basic functionality
#69
rdmorin
closed
2 years ago
0
Functionality to prepare matrix for NMF clustering + bug fixes
#68
Kdreval
closed
2 years ago
1
splendidHeatmap mismatches the features between clusters if metadata is not sorted
#67
Kdreval
closed
2 years ago
1
Synchronise bed files of lymphoma genes with lymphoma genes list
#66
Kdreval
closed
2 years ago
1
fixing typo that broke GAMBLR install
#65
mattssca
closed
2 years ago
0
Update get_coding_ssm to load variants from latest results
#64
rdmorin
closed
2 years ago
3
Add a function to tidy LymphGen Subtype.Prediction columns
#63
lkhilton
closed
2 years ago
1
ensure Morinlab fork of g3viz is installed as a dependency
#62
rdmorin
closed
2 years ago
2
changed final purity above 1 to equal 1 and fix some bugs in purity e…
#61
kristenadaley
closed
2 years ago
0
Update to handle capture data
#60
rdmorin
closed
2 years ago
1
Kdreval dev
#59
Kdreval
closed
2 years ago
1
Issue with rtracklayer specific to R4
#58
Kdreval
closed
2 years ago
2
Separate annotation of lymphoma drivers that aren't exactly hot spots
#57
rdmorin
closed
2 years ago
1
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