morinlab / GAMBLR.results

A collection of functions to access results of the Genomic Analysis of Mature B-cell Lymphomas

morinlab/GAMBLR.results Issues

SV support is broken
Updated 5 months ago1
Add paramters to `get_ssm_by_region(s)` while keeping backwards compatibility
Closed 5 months ago1
GAMBLR.results can't find `liftover_bedpe` function
Updated 6 months ago
Add projection to get_cn_states
Updated 6 months ago
Break stuff
Closed 6 months ago1
Allow `get_gambl_metadata` to return a table with both `tissue_status` values
Updated 6 months ago
`cbio_create()` does not support a mix of seq types
Closed 6 months ago1
`cbio_create()` generates metadata with pathology mislabelled as Subtype
Closed 6 months ago1
`cbio_study_check()` does not respect the seq_type argument
Closed 6 months ago1
`cbio_create()` has a typo in argument
Closed 6 months ago1
cbio_create improvements
Closed 6 months ago1
`get_ssm_by_sample` returns non informative error when using non-existent sample ID.
Updated 7 months ago
Remove hardcoding in `collate_csr_results`
Updated 7 months ago1
Issues with the `collate_sbs_results` part of `collate_results`
Updated 7 months ago1
hg38 support for collate_nfkbiz_results
Updated 7 months ago1
estimate_purity is broken when only sample_id is provided
Updated 7 months ago2
The get_cnv_and_ssm_status is outdated
Updated 7 months ago
annotate_ssm_motif_context needs improvements
Closed 5 months ago1
Error in `get_gene_cn_and_expression`
Updated 7 months ago1
Discrepant parameter names in GAMBLR.results::get_ssm_by_sample and GAMBLR.data::get_ssm_by_sample
Closed 8 months ago1
`get_ssm_by_regions()` fails on regions with 0 mutations
Updated 8 months ago
Function import tags vs. in-code package prefixing
Updated 8 months ago
Missing documentation for the following GAMBLR.results functions
Updated 8 months ago
`get_manta_sv()` fails
Closed 9 months ago1
`get_ssm_by_regions` can't output 116 columns
Closed 9 months ago1
Harmonize naming of the parameters in `get_sample_cn_segments`
Closed 8 months ago