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Enhancements and Bug Fixes #55

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merged 57 commits into from
Sep 18, 2024
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fb401d6
adding exceptions
Cristianetaniguti Aug 15, 2024
7c885ec
fixed issues #37 and #38
Cristianetaniguti Aug 16, 2024
0e287cd
Fixed PCA image download bug
alex-sandercock Aug 16, 2024
e31bf35
Merge pull request #12 from Breeding-Insight/development
Cristianetaniguti Aug 28, 2024
fd8255f
Add empty tab + fix tests
Cristianetaniguti Aug 28, 2024
2fd6a1c
Merge branch 'main' of https://github.com/Cristianetaniguti/Genomics_…
Cristianetaniguti Aug 28, 2024
8f7e599
Merge pull request #39 from Cristianetaniguti/main
alex-sandercock Aug 28, 2024
56ddbba
Merge pull request #45 from Breeding-Insight/development
alex-sandercock Aug 28, 2024
3c4b1a0
Removed AF plots and values from table
alex-sandercock Aug 28, 2024
91ca93c
Removed diversity tab input
alex-sandercock Aug 28, 2024
5b39803
Updated reference to Predictive Ability
alex-sandercock Aug 28, 2024
f58e43d
fixed chrom order bug
alex-sandercock Aug 28, 2024
a9daa92
allows links between modules
Cristianetaniguti Aug 28, 2024
e1c559f
issues #43 and #44
Cristianetaniguti Aug 29, 2024
27ac86a
Merge pull request #46 from Breeding-Insight/gs-updates
Cristianetaniguti Aug 29, 2024
683f342
Merge branch 'main' into development
Cristianetaniguti Aug 29, 2024
ac4f05f
Merge pull request #13 from Breeding-Insight/development
Cristianetaniguti Aug 29, 2024
26aa2d2
Added GBLUP Support
alex-sandercock Aug 29, 2024
bd5ec81
added package
alex-sandercock Aug 29, 2024
a987d1d
add help files
Cristianetaniguti Aug 29, 2024
00abaf6
Added A,G, and H mat for GBLUP
alex-sandercock Aug 30, 2024
a5e94ef
Updated AO label
alex-sandercock Aug 30, 2024
da72577
Merge pull request #14 from Breeding-Insight/gs-updates
Cristianetaniguti Sep 3, 2024
5b503c1
GS review (in progress)
Cristianetaniguti Sep 3, 2024
593633c
Updated PCA Window and summary
alex-sandercock Sep 6, 2024
a59511b
Fixed Bug for genotype conversion
alex-sandercock Sep 11, 2024
915c02b
tests for GCAcc
Cristianetaniguti Sep 12, 2024
56c0d9a
check fix
Cristianetaniguti Sep 12, 2024
418eb73
fix
Cristianetaniguti Sep 12, 2024
8161a2d
MADC Matrix Checks
alex-sandercock Sep 12, 2024
f514099
Merge pull request #48 from Cristianetaniguti/main
alex-sandercock Sep 12, 2024
4be310e
Revert GS_Acc to previous version
alex-sandercock Sep 12, 2024
32bbe69
Updated NavBar and added SessionInfo
alex-sandercock Sep 13, 2024
9863724
Updated Footer Version
alex-sandercock Sep 13, 2024
661e311
Updated Package Version
alex-sandercock Sep 13, 2024
fde1cce
Added PCA Summary
alex-sandercock Sep 13, 2024
a5eb9ad
adapting input controls
Cristianetaniguti Sep 13, 2024
0dec351
add back folds progress bar
Cristianetaniguti Sep 13, 2024
20859fe
fix test
Cristianetaniguti Sep 13, 2024
c2c2597
Merge branch 'main' into gs-updates
Cristianetaniguti Sep 13, 2024
c888115
Merge pull request #15 from Breeding-Insight/gs-updates
Cristianetaniguti Sep 13, 2024
eb1730d
Reverted file
alex-sandercock Sep 16, 2024
7037ea1
adapt
Cristianetaniguti Sep 16, 2024
036ddf1
bugfix
Cristianetaniguti Sep 16, 2024
a436c29
rm GEBV from CV
Cristianetaniguti Sep 16, 2024
414e3b2
Merge branch 'gs-updates' into main
Cristianetaniguti Sep 16, 2024
0da389d
add message back
Cristianetaniguti Sep 16, 2024
3885c20
Added option to subset dosage calling samples
Sep 16, 2024
4750636
Added MADC data check
Sep 17, 2024
6066fc9
Merge pull request #52 from Cristianetaniguti/main
alex-sandercock Sep 17, 2024
3a19f5c
Merge branch 'development' into gs-updates
alex-sandercock Sep 17, 2024
05c13ca
Merge pull request #16 from Breeding-Insight/gs-updates
Cristianetaniguti Sep 17, 2024
994f385
Merge pull request #47 from Breeding-Insight/gs-updates
Cristianetaniguti Sep 17, 2024
963186e
fix #53
Cristianetaniguti Sep 17, 2024
2d44388
add help material updog #43
Cristianetaniguti Sep 17, 2024
d186a56
fix test
Cristianetaniguti Sep 17, 2024
2514aad
Merge pull request #54 from Cristianetaniguti/main
alex-sandercock Sep 18, 2024
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1 change: 1 addition & 0 deletions .Rbuildignore
Original file line number Diff line number Diff line change
Expand Up @@ -9,3 +9,4 @@ $run_dev.*
^\www$
^LICENSE$
^\.github$
^Dockerfile$
2 changes: 1 addition & 1 deletion DESCRIPTION
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
Package: BIGapp
Title: Breeding Insight Genomics Shiny Application
Version: 0.5.1
Version: 0.6.0
Authors@R:
c(
person(c("Alexander", "M."), "Sandercock",
Expand Down
7 changes: 7 additions & 0 deletions NAMESPACE
Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,9 @@ import(updog)
import(utils)
import(vcfR)
importClassesFrom(adegenet,genlight)
importFrom(AGHmatrix,Amatrix)
importFrom(AGHmatrix,Gmatrix)
importFrom(AGHmatrix,Hmatrix)
importFrom(BIGr,updog2vcf)
importFrom(DT,DTOutput)
importFrom(DT,datatable)
Expand Down Expand Up @@ -43,6 +45,8 @@ importFrom(bs4Dash,sidebarMenu)
importFrom(bs4Dash,tabBox)
importFrom(bs4Dash,tabItem)
importFrom(bs4Dash,tabItems)
importFrom(bs4Dash,updateBox)
importFrom(bs4Dash,updatebs4TabItems)
importFrom(bs4Dash,valueBox)
importFrom(bs4Dash,valueBoxOutput)
importFrom(config,get)
Expand Down Expand Up @@ -77,11 +81,14 @@ importFrom(plotly,renderPlotly)
importFrom(purrr,map)
importFrom(purrr,set_names)
importFrom(rrBLUP,A.mat)
importFrom(rrBLUP,kin.blup)
importFrom(rrBLUP,mixed.solve)
importFrom(scales,comma_format)
importFrom(shiny,NS)
importFrom(shiny,includeMarkdown)
importFrom(shiny,shinyApp)
importFrom(shiny,tagList)
importFrom(shiny,updateTabsetPanel)
importFrom(shinyWidgets,materialSwitch)
importFrom(shinyWidgets,progressBar)
importFrom(shinyWidgets,updateVirtualSelect)
Expand Down
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