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MSKCC-Epi-Bio
/
gnomeR
Package to wrangle and visualize genomic data in R
https://mskcc-epi-bio.github.io/gnomeR/
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`purrr::when()` will be depreciated
#203
michaelcurry1123
closed
1 year ago
3
Internal gen bin tidy
#202
michaelcurry1123
closed
1 year ago
0
Check other functions that may be affected by sample ID column
#201
karissawhiting
closed
1 year ago
3
Review remaining arguments in `create_gene_binary()` and move `specify_panel` explanation to details in docs
#200
karissawhiting
closed
1 year ago
0
add older impact (pre 348) genes to alias table
#199
karissawhiting
closed
2 years ago
0
Review package checks and iClusterPlus errors in github actions
#198
karissawhiting
closed
2 years ago
2
Consider adding an additional merged version where fusions/cna/mutations are all separate side by side merged tables. Maybe we can come up with a prototype of this at the hackathon
#197
karissawhiting
opened
2 years ago
2
Review `rm_empty` argument in `create_gene_binary()`
#196
karissawhiting
closed
1 year ago
1
CNA Processing Functions
#195
karissawhiting
closed
2 years ago
0
separate genbin_matrix from rest of changes
#194
hfuchs5
closed
2 years ago
0
internal recode cna alt func
#193
hfuchs5
closed
2 years ago
1
split out sanitize functions from utils
#192
karissawhiting
closed
2 years ago
0
create which_panel func
#191
hfuchs5
closed
2 years ago
0
Data processing vignette
#190
akriti21
closed
1 year ago
1
Add an example of wide CNA data to package
#189
karissawhiting
closed
2 years ago
1
Hf hackathon
#188
hfuchs5
closed
1 year ago
4
added default freq_cutoff with check
#187
michaelcurry1123
closed
2 years ago
0
Tbl genomic
#186
michaelcurry1123
closed
2 years ago
0
Update README
#185
karissawhiting
closed
2 years ago
1
Update col names
#184
karissawhiting
closed
2 years ago
0
Troubleshoot ggheatmap function
#183
karissawhiting
closed
1 year ago
0
Review fusions processing
#181
karissawhiting
closed
1 year ago
3
Review `pivot_cna_longer()` and `reformat_cna()` functions
#180
karissawhiting
closed
2 years ago
1
Review `cna_binary` and `cna_relax` arguments in binary matrix function
#179
karissawhiting
closed
1 year ago
1
Create internal function to check/recode alteration column in CNA long data
#178
karissawhiting
closed
2 years ago
0
Create common internal function for use in .mutations_gene_binary(), .cna_gene_binary(), and .fusions_gene_binary()
#177
karissawhiting
closed
1 year ago
2
IMPACT Checklist Vignette
#176
karissawhiting
opened
2 years ago
3
Review and Replace Main Example Data Sets
#175
karissawhiting
closed
2 years ago
0
make `tbl_genomic` an official 'gtsummary' table
#174
michaelcurry1123
closed
2 years ago
4
Error returned for binmat oncokb = TRUE when cbioportalR updated
#173
slb2240
closed
2 years ago
1
Add function to pass gene to see which IMPACT panels it is on
#172
karissawhiting
closed
2 years ago
2
Check column names of input df and allow create_binary_matrix() to accept maf, api or snakecase version of maf names
#171
karissawhiting
closed
2 years ago
6
Combine alias warning messages in create_gene_binary()
#170
karissawhiting
closed
1 year ago
0
updates to reformat cna and alias annotation
#169
karissawhiting
closed
2 years ago
0
Edit pathway annotation using gene-level data in `add_pathways()` function
#167
carokos
closed
1 year ago
2
Update to Readme
#166
karissawhiting
closed
2 years ago
0
update pathways
#163
karissawhiting
closed
2 years ago
0
Update readme
#162
karissawhiting
closed
2 years ago
0
Add unit tests
#161
karissawhiting
closed
2 years ago
0
Add more unit test to binary_matrix()
#160
ChristineZ-msk
closed
2 years ago
1
Changed mut_type default in binary_matrix
#159
jflynn264
closed
2 years ago
0
Started a vignette to import data from cbioportal
#158
akriti21
closed
2 years ago
0
Genomic tbl summary
#157
michaelcurry1123
closed
2 years ago
3
Adding some unit tests to sample, mut/fusion/cna and snp_only args
#156
ChristineZ-msk
closed
2 years ago
1
add `add_pathway()` function
#155
carokos
closed
2 years ago
1
Add pathways function
#154
karissawhiting
closed
2 years ago
5
update branch to test checks
#153
karissawhiting
closed
2 years ago
0
Update binary matrix
#152
karissawhiting
closed
2 years ago
0
Review `gen_summary()` and `gen_uni_cox()` and consider switching to use {gtsummary} functions
#151
karissawhiting
closed
2 years ago
4
Change mut_type argument default to keep NAs and only eliminate GERMLINE as default
#150
karissawhiting
closed
2 years ago
0
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