facilebio FacileAnalysis issues

facilebio / FacileAnalysis

Modular & interactive analysis components for bioinformatics

https://facilebio.github.io/FacileAnalysis

Other

17 stars 4 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

Update voom workflow to use voomLmFit

#55 lianos opened 1 year ago
0
Extracts the shiny bits from this package and pushed them to new iFacileAnalysis packages

#54 lianos closed 1 year ago
0
Gracefully handle situations when there are subsets of "active samples" that do not have data from the given assay_name under test

#53 lianos opened 1 year ago
0
Update the fpca$percent_var result to a tibble

#52 lianos opened 1 year ago
0
Updates to native pipe

#51 lianos closed 1 year ago
0
Bugfixes and cleanup

#50 jonocarroll closed 2 years ago
0
req() an input to prevent crashing when used in a shiny app

#49 jonocarroll closed 2 years ago
0
generate badges at documentation build time instead of package build time

#48 edavidaja closed 2 years ago
0
Add DEqMS support in fdge for proteomics differential abundance analysis

#47 lianos opened 3 years ago
0
multiGSEA -> sparrow change passes all tests

#46 lianos closed 3 years ago
0
Lots of little tweaks

#45 lianos closed 3 years ago
0
Add option to run shine() gadgets as RStudio jobs in the backround

#44 lianos opened 3 years ago
1
Add support for timecourse analysis via the moanin package

#43 lianos opened 3 years ago
0
Minimum logFC value not honored from shiny input of ffsea ORA config UI

#42 lianos opened 4 years ago
1
Quadrant analysis

#41 lianos closed 4 years ago
0
Add unit test to exercise duplicateCorrelation/block support in compare(ttest1, ttest2)

#40 lianos opened 4 years ago
0
Enable group-level weight specification in flm_def constrast construction

#39 lianos opened 4 years ago
0
Explore using {callr} to launch shine gadgets in background

#38 lianos opened 4 years ago
1
Enable feature filtering (fdge, fpca) to restrict feature types used in analysis

#37 lianos opened 4 years ago
1
Turn unfds/refds into internal (unexported) S3 generics

#36 lianos opened 4 years ago
0
Provide shiny front end to feature filter in fdgeRunOptions module

#35 lianos opened 4 years ago
0
Refactors reactivity in rdgeRunOptions.

#34 lianos closed 4 years ago
0
Supports ReactiveGeneSetDb

#33 lianos closed 4 years ago
0
Add group-level average expression columns to fdge output

#32 lianos opened 4 years ago
0
Update ffseaView to show ANOVA result

#31 lianos opened 4 years ago
0
Improve coloring by feature(s) in fpcaView

#30 lianos opened 4 years ago
0
fpcaView resets feature colorings when any aesthetic map is changed

#29 lianos opened 4 years ago
0
Enable viz.FacilePcaAnalysisResult to support coloring by feature/geneset expression

#28 lianos opened 4 years ago
0
Enable pathway analysis over PC loadings in fpcaAnalysis shiny module

#27 lianos opened 4 years ago
0
Biocbox: API and implementation cleanup to better support diversity of FacileBiocDataStores

#26 lianos closed 4 years ago
0
Error trying to install FacileAnalysis 0.2.16

#25 FleckDaniel opened 4 years ago
1
Create filter_by_feature_abundance

#24 lianos opened 4 years ago
2
biocbox/fdge refactor

#23 lianos opened 4 years ago
0
fpca shiny bits does not present extra sample covariates in samples() in UI

#22 lianos opened 4 years ago
0
f*Gadget() functions are hosed

#21 lianos closed 4 years ago
1
Unify feature filtering approaches (fdge, fpca)

#20 lianos opened 4 years ago
0
Implement more robust compare.FacileTtestAnalysisResult (interaction test)

#19 lianos opened 4 years ago
0
Wrap PCAtools functionality

#18 lianos opened 5 years ago
0
Implement a "shiny configuration view" over GeneSetDb

#17 lianos opened 5 years ago
0
Support "dream" method for fdge analysis of RNA-seq data with random effects

#16 lianos opened 5 years ago
0
Fix corner cases for compare.FacileTtestAnalysisResult

#15 lianos closed 4 years ago
1
Disable Run button while running fdge or ffsea analysis in shiny modules

#14 lianos opened 5 years ago
0
Allow "single-covariate" selections to support multi-covariate selection, which generates levels on the fly

#13 lianos opened 5 years ago
0
Implement report.FacilePcaAnalysisResult

#12 lianos opened 5 years ago
0
Implement shine.FacilePcaAnalysisResult

#11 lianos closed 5 years ago
0
Assert that dims >= 3 first?

#10 tomsing1 closed 5 years ago
3
Fixed a few typos in FacileAnalysis-RNAseq.Rmd

#9 tomsing1 closed 5 years ago
0
Implement ranks-based tests (like wilcoxon) for fdge

#8 lianos opened 5 years ago
0
fdgeModelDefRun: Protect user from selecting fixed covariates that result in a non-full-rank design

#7 lianos opened 5 years ago
1
Installation error

#6 tomsing1 closed 5 years ago
2