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#790 Part3: adding CNV based subtyping for LGAT #845

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d37abea
adding new SNV subtypes for LGAT
kgaonkar6 Nov 16, 2020
3fbf314
adding LGAT updated rna fusion based subtyping
kgaonkar6 Nov 16, 2020
dc6e743
adding additional subtypes
kgaonkar6 Nov 16, 2020
eb65034
re-doing subtyping so removing the last step for now
kgaonkar6 Nov 16, 2020
271958a
updating run_subtyping.sh
kgaonkar6 Nov 16, 2020
599c044
updating run_subtyping.sh
kgaonkar6 Nov 16, 2020
e7abf5c
removing subtyping list
kgaonkar6 Nov 16, 2020
25c3961
removing subtyping list
kgaonkar6 Nov 16, 2020
4da2449
run Fus subtyping
kgaonkar6 Nov 16, 2020
2281e95
removing subtyping list
kgaonkar6 Nov 16, 2020
8357872
adding fusion and fused genes per subtype
kgaonkar6 Nov 16, 2020
cd1e4d2
update README
kgaonkar6 Nov 17, 2020
2f30d89
Merge branch 'master' into lgat_add_subtyping_SNV
kgaonkar6 Nov 17, 2020
0a1a2a5
Merge branch 'master' into lgat_add_subtyping_Fus
kgaonkar6 Nov 17, 2020
ea1a86c
adding changes from 842
kgaonkar6 Nov 17, 2020
2f99022
Merge branch 'lgat_add_subtyping_Fus' of https://github.com/kgaonkar6…
kgaonkar6 Nov 17, 2020
9289932
update README
kgaonkar6 Nov 17, 2020
128e2ab
edit to comment
kgaonkar6 Nov 17, 2020
dbf3304
inital commit
kgaonkar6 Nov 17, 2020
0e1ecae
rename variable to mention rna
kgaonkar6 Nov 17, 2020
f792c78
cnv subtypes
kgaonkar6 Nov 17, 2020
d51fbf5
cnv subtype
kgaonkar6 Nov 18, 2020
49c1cb5
cnv subtype with exon overlap check
kgaonkar6 Nov 18, 2020
32e05f7
changed to nb
kgaonkar6 Nov 19, 2020
93a2e44
Merge branch 'lgat_add_subtyping_SNV' of https://github.com/kgaonkar6…
kgaonkar6 Nov 19, 2020
05bf366
remove Rscript
kgaonkar6 Nov 19, 2020
408166d
Update README.md
kgaonkar6 Nov 19, 2020
4b972e4
Update analyses/molecular-subtyping-LGAT/01-subset-files-for-LGAT.Rmd
kgaonkar6 Nov 19, 2020
906bfb8
Update analyses/molecular-subtyping-LGAT/01-subset-files-for-LGAT.Rmd
kgaonkar6 Nov 19, 2020
5fca7ad
Update analyses/molecular-subtyping-LGAT/01-subset-files-for-LGAT.Rmd
kgaonkar6 Nov 19, 2020
38bab2f
adding comments remove silent snv
kgaonkar6 Nov 19, 2020
e12a603
adding sample_id
kgaonkar6 Nov 19, 2020
dee0179
adding H3F3B
kgaonkar6 Nov 19, 2020
27f270c
updates to files
kgaonkar6 Nov 19, 2020
dfad4ab
Merge branch 'master' into lgat_add_subtyping_SNV
kgaonkar6 Nov 19, 2020
a176102
Merge branch 'master' into lgat_add_subtyping_Fus
kgaonkar6 Nov 20, 2020
17ea9e0
changes from part1
kgaonkar6 Nov 20, 2020
a1653e1
Merge branch 'lgat_add_subtyping_Fus' of https://github.com/kgaonkar6…
kgaonkar6 Nov 20, 2020
4ff6d63
R to nb
kgaonkar6 Nov 20, 2020
5814664
Merge branch 'master' into lgat_add_subtyping_CNV
kgaonkar6 Nov 20, 2020
3310171
merging from part2
kgaonkar6 Nov 20, 2020
594cd49
Merge branch 'lgat_add_subtyping_CNV' of https://github.com/kgaonkar6…
kgaonkar6 Nov 20, 2020
62f256f
pushed part1
kgaonkar6 Nov 20, 2020
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Original file line number Diff line number Diff line change
Expand Up @@ -153,4 +153,4 @@ writeLines(jsonlite::prettify(jsonlite::toJSON(terms_list)), output_file)

```{r}
sessionInfo()
```
```
81 changes: 0 additions & 81 deletions analyses/molecular-subtyping-LGAT/01-subset-files-for-LGAT.R

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141 changes: 0 additions & 141 deletions analyses/molecular-subtyping-LGAT/02-make-lgat-final-table.Rmd

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2,025 changes: 0 additions & 2,025 deletions analyses/molecular-subtyping-LGAT/02-make-lgat-final-table.nb.html

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