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Fix mapping #37

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wants to merge 142 commits into from
Closed

Fix mapping #37

wants to merge 142 commits into from

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iblacksand
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iblacksand and others added 30 commits September 18, 2023 13:26
@iblacksand
add ramp mapping
4731ba5
@iblacksand
add install script
bd50cb1
@iblacksand
changed mappped to mapped 💀
ecf08bb
@iblacksand
formatting
b65ce88
@iblacksand
adds working version of k-medoid
afbe812
@iblacksand
set default k to 5 to fit examples
5b6538f
@iblacksand
faster jaccard
a22c5f4
@iblacksand
Working KEGG link. need to remove redundant results
9d5a8cf
@iblacksand
Adds working wikidata links
0633bbb
@iblacksand
add CLARA
5eeee7c
@iblacksand
add ability to toggle redundancy methods
5256603
@iblacksand
fix GSEA for metabolites
6f519c2
@iblacksand
fix ORA
51a96ac
@iblacksand
add maxK for kMedoid and fix affinity prop labeling
2d33462
@iblacksand
add start of adding Rust to package
cf60e74
@iblacksand
add rewrite of fill_input_matrix
9105be2 
fix typo
@iblacksand
adds fill_input_data_frame, but returns list
f8f17cc
@iblacksand
add basic output for GSEA
644b3a9
@iblacksand
add GSEA config
77e1123
@iblacksand
add GSEA vector creation
cf0ec6e
@iblacksand
convert list to dataframe using as.data.frame
3f88cec
@iblacksand
first version of Rust GSEA
7eddc1f 
R package runs, but the names of rows/columns are not correct in the final dataframe
@iblacksand
working version of GSEA
2e3e2da
@iblacksand
Add working ORA
1179275
@iblacksand
add better readme
ec742ee
@iblacksand
attempt to fix running sum with no luck
f510980
@iblacksand
Update README.md
1406f92
@iblacksand
Fix running_sum and finalize first working version of R package
2ba2540
@iblacksand
Fix repo in install instructions
fef4641
@iblacksand
add requirements
144a82a
iblacksand and others added 29 commits January 4, 2024 14:54
@iblacksand
update documentation
479306e
@iblacksand
Use gene symbols for wikipathways to avoid xreferencing
b68ca52
@iblacksand
update to use dev version
ec01203
@iblacksand
update package used
9139c5f
@iblacksand
update to latest dev
ec318db
@iblacksand
Merge branch 'master' into update
bcab3e5
@iblacksand
Merge pull request #10 from bzhanglab/update
2f9c848 
Update JS/CSS path to relative in report when host name is localhost
@iblacksand
Update lib to use git version and rename function calls
f4de204
@iblacksand
remove multiomic:: calls
9414952
@iblacksand
Update webgestalt_lib to v0.2.0 (#12)
f911344 
* Update lib to use git version and rename function calls

* remove multiomic:: calls
@iblacksand
Fix issue #11 by reducing font size (#13)
0fdbd54
@iblacksand
Update lib to use crate.io version and rename function calls (#14)
5a35dda 
* Update lib to use git version and rename function calls

* remove multiomic:: calls
@iblacksand
work on transitioning kegg gsea
f05d4c1
@iblacksand
fix multicoloring for kegg in gsea
50f8936
@iblacksand
kegg ora fix
6c22445
@iblacksand
use white kegg maps
9e4f935
@iblacksand
Fix des breakage and wikipathway coloring
75958d6
@iblacksand
fix FDR calculations for multi-list gsea
2fa8b73
@iblacksand
add description and move github page link
8990aa3
@iblacksand
use github action instead of gh-pages for pages
569b2d7
@iblacksand
Merge pull request #15 from iblacksand/gsea-coloring
9bac130 
Add GSEA coloring for KEGG and WikiPathways and fix FDR
@iblacksand
updates permissions
56fdbd0
@iblacksand
use get_gmt for metabolite resolution. needs testing
4048aff
@iblacksand
add metabolite resolution with extra checks
ac7fc19
@iblacksand
update checkout action
2c6c52e
@iblacksand
better id mapping error
395f567
@iblacksand
Start work on moving rust to vendor and better cran checks
ec68aa2
@iblacksand
add windows config
acb8974
@iblacksand
Merge pull request #16 from iblacksand/metabolite-resolution
f6d0d7f 
Add metabolite detection and better ID mapping errors
@iblacksand iblacksand closed this Mar 3, 2024
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@iblacksand