morinlab GAMBLR.results issues

morinlab / GAMBLR.results

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

MIT License

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Rewrite of get_gambl_metadata and new helper functions

#62 rdmorin closed 2 months ago
1
Transferring some functions here

#61 rdmorin closed 2 months ago
1
Harmonise `get_cnv_and_ssm_status` with the .data version

#60 vladimirsouza opened 2 months ago
0
Change how `get_gene_expression` handle duplications

#59 vladimirsouza opened 3 months ago
0
Fix get_ssm_by_regions when maf_data is provided

#58 vladimirsouza closed 3 months ago
0
Fix link_seq_types

#57 vladimirsouza closed 3 months ago
0
Dont export funcs

#56 vladimirsouza closed 4 months ago
0
Fix id_ease when metadata and seq_type are provided

#55 vladimirsouza closed 4 months ago
0
SV support is broken

#54 Kdreval opened 4 months ago
1
Add parameters to get_ssm_by_region(s)

#53 vladimirsouza closed 5 months ago
0
Add paramters to `get_ssm_by_region(s)` while keeping backwards compatibility

#52 vladimirsouza closed 5 months ago
1
Add link seq types

#51 vladimirsouza closed 5 months ago
0
Add bedToBigBed to config

#50 vladimirsouza closed 5 months ago
0
GAMBLR.results can't find `liftover_bedpe` function

#49 vladimirsouza opened 5 months ago
0
Add projection to get_cn_states

#48 kmcoyle opened 5 months ago
0
add missing files for previous bug fix

#47 rdmorin closed 5 months ago
0
restore original functionality to this repository

#46 rdmorin closed 5 months ago
0
bug fix: fix outdated id_ease return style

#45 Kdreval closed 5 months ago
0
Break stuff

#44 Kdreval closed 5 months ago
1
Allow `get_gambl_metadata` to return a table with both `tissue_status` values

#43 lkhilton opened 5 months ago
0
update to `get_coding_ssm_status` to support gene-specific handling of silent variants

#42 Kdreval closed 5 months ago
0
Transfer remote functionality and update readme

#41 Kdreval closed 5 months ago
0
moving the review_hotspots to helpers child

#40 Kdreval closed 6 months ago
0
Fixing cBioPortal functionality

#39 Kdreval closed 6 months ago
2
`cbio_create()` does not support a mix of seq types

#38 Kdreval closed 6 months ago
1
`cbio_create()` generates metadata with pathology mislabelled as Subtype

#37 Kdreval closed 6 months ago
1
`cbio_study_check()` does not respect the seq_type argument

#36 Kdreval closed 6 months ago
1
`cbio_create()` has a typo in argument

#35 Kdreval closed 6 months ago
1
cbio_create improvements

#34 Kdreval closed 6 months ago
1
Fix get_gene_expression

#33 vladimirsouza closed 3 months ago
17
`get_ssm_by_sample` returns non informative error when using non-existent sample ID.

#32 mattssca opened 7 months ago
0
Remove hardcoding in `collate_csr_results`

#31 Kdreval opened 7 months ago
1
Issues with the `collate_sbs_results` part of `collate_results`

#30 Kdreval opened 7 months ago
1
hg38 support for collate_nfkbiz_results

#29 Kdreval opened 7 months ago
1
New annotate_ssm_motif

#28 HoumanLM closed 6 months ago
0
estimate_purity is broken when only sample_id is provided

#27 Kdreval opened 7 months ago
2
The get_cnv_and_ssm_status is outdated

#26 Kdreval opened 7 months ago
0
Migrating liftover_bedpe to GAMBLR.utils

#25 mattssca closed 7 months ago
0
annotate_ssm_motif_context needs improvements

#24 Kdreval closed 5 months ago
1
Error in `get_gene_cn_and_expression`

#23 vladimirsouza opened 7 months ago
1
PR transfer: transferring the updates from parent GAMBLR

#22 Kdreval closed 6 months ago
2
PR transfer: different engines in get_gene_expression

#21 Kdreval closed 7 months ago
0
Discrepant parameter names in GAMBLR.results::get_ssm_by_sample and GAMBLR.data::get_ssm_by_sample

#20 mattssca closed 7 months ago
1
`get_ssm_by_regions()` fails on regions with 0 mutations

#19 lkhilton opened 8 months ago
0
Fix get_cnv_and_ssm_status documentation

#18 vladimirsouza closed 8 months ago
0
Fixing internal calls of get_sample_cn_segments

#17 mattssca closed 8 months ago
1
Function import tags vs. in-code package prefixing

#16 mattssca opened 8 months ago
0
Harmonize naming of the parameters in get_sample_cn_segments issue #4

#15 mattssca closed 8 months ago
7
Migrate functions

#14 vladimirsouza closed 8 months ago
0
Vsouza hotfixes

#13 vladimirsouza closed 8 months ago
2