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waldronlab
/
lefser
R implementation of the LEfSe method
https://waldronlab.io/lefser/
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support multigroup
#52
LiNk-NY
opened
1 day ago
0
Revert "Revert "update code in fillPmatZmat""
#51
LiNk-NY
opened
1 day ago
0
Revert "update code in fillPmatZmat"
#50
shbrief
closed
1 day ago
4
Provide option of colorblind-friendly palette
#49
lwaldron
opened
1 day ago
0
Clarify what `blockCol` is
#48
lwaldron
opened
1 day ago
1
Error in svd(X, nu = 0L) : a dimension is zero
#47
jdaledge
opened
1 week ago
7
Order of preprocessing affects the warning: relativeAb and get_terminal_nodes
#46
shbrief
opened
1 week ago
0
Check whether this random number generation step is necessary
#45
shbrief
closed
1 week ago
1
Documentation on using terminal nodes
#44
shbrief
closed
1 week ago
1
update code in fillPmatZmat
#43
LiNk-NY
closed
1 day ago
0
outdated references to random subsets
#42
lwaldron
closed
1 week ago
3
variables are collinear
#41
lwaldron
opened
2 weeks ago
5
Implements MHT correction. Unit tests still need fixing. See #39.
#40
lwaldron
closed
1 week ago
1
add support for multiple hypothesis testing adjustment
#39
lwaldron
closed
1 week ago
0
Make this run faster
#38
shbrief
opened
2 months ago
1
Error in lda.default(x, grouping, ...)
#37
J5886
closed
2 weeks ago
4
Consistent behavior when no results
#36
lwaldron
closed
4 months ago
0
Add message when there are no results
#35
lwaldron
closed
4 months ago
5
Append and created a testthat unit test of the fix
#34
Peacesandy
closed
4 months ago
9
lefser producing empty results when given pathway data
#33
jmartin77777
closed
3 months ago
4
appear to be constant with groups
#32
celinechen1885
closed
4 months ago
8
Adding referenceGroup and treatmentGroup arguments, and updating plot
#31
asyakhl
closed
8 months ago
5
upgrade plot labels
#30
asyakhl
closed
10 months ago
1
Effect Size Update
#29
asyakhl
closed
10 months ago
1
Check data for relative abundances and provide helper function
#28
LiNk-NY
closed
10 months ago
0
droplevels in the blockCol, closes #19
#27
LiNk-NY
closed
8 months ago
0
add example to show how to convert phyloseq to SummarizedExperiment i…
#26
LiNk-NY
closed
8 months ago
0
Include group labels in lefserPlot, closes #15
#25
LiNk-NY
closed
8 months ago
0
Error in cols * 0.05 : non-numeric argument to binary operator
#24
chuynh96
closed
2 weeks ago
3
Informative error with no significant results by KW test
#23
lwaldron
closed
1 year ago
0
Svdfix
#22
lwaldron
closed
1 year ago
0
Conversion to relative abundance prior to lefser analysis
#21
agatadziegiel
closed
10 months ago
3
Update lefser.R
#20
cafferychen777
closed
1 year ago
1
Error in .local(.Object, ...) : ‘x’ and ‘y’ do not contain data
#19
dannynielsen0
closed
8 months ago
1
Different results in lefser and LEfSe?
#18
CarolineWasen
closed
2 weeks ago
1
Comparison of more than two groups
#17
anapopov
opened
3 years ago
1
If I have phyloseq file instead of example data how I show start
#16
Hesham999666
closed
8 months ago
5
Group in lefserPlot does not reflect levels in groupCol factor
#15
Jorisvansteenbrugge
closed
8 months ago
2
Test data to summarisedExperiment
#14
susheelbhanu
closed
10 months ago
5
Requires >= R 4.0, but not available for R version 4.0.0?
#13
morganx
closed
10 months ago
3
updated vignette and lefserAnalysis man file
#12
asyakhl
closed
3 years ago
0
LDA threshold score added to analysis function
#11
asyakhl
closed
3 years ago
0
Extract info from se
#10
asyakhl
closed
3 years ago
0
Document GROUP and BLOCK assignment
#9
lwaldron
closed
1 week ago
0
How to set LDA score cutoff and Kruskal-Wallis p-value cutoff?
#8
lwaldron
closed
2 months ago
3
vignette not building
#7
lwaldron
closed
10 months ago
2
use of unexported function from EnrichmentBrowser
#6
lwaldron
closed
3 years ago
5
add some background to vignette
#5
lwaldron
closed
1 week ago
1
unit tests
#4
lwaldron
closed
4 months ago
2
Specify the datataset you want to use
#3
lwaldron
closed
3 years ago
2
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