NEWS
lefser 1.15.3
- The column names of
lefser
output is changed to c("features", "scores")
from c("Names", "scores")
- [New feature] The
get_terminal_nodes
function to select only the terminal
nodes of the hierarchical features (e.g., taxonomic data).
- [Major algorithm update] Add an option for adjusting the first Kruskal-Wallis
Rank Sum Test and Wilcoxon-Rank Sum test for multiple hypothesis testing
through the new argument
method
in the lefser
function.
lefser 1.14.0
- [Error fix] The
lefserPlot
function merged the duplicated labels when the
truncated name of the feature is used. Now those are plotted separately.
- [New feature] The
lefserPlot
function accepts the title
argument that
adds the barplot title.
- [Update] The feature names of the
lefserPlot
outputs are re-positioned
for the improved readability.
- [Major algorithm update] Sub-sampling and bootstrap for LDA step in the
lefser
function is removed. Now the LDA score is calculated directly from
the whole samples.
lefser 1.12.0
Significant user-visible changes
- The
checkAbundances
argument in lefser()
checks that data are as relative
abundances and warns if otherwise (@LiNk-NY @sdgamboa, #28)
relativeAb
helper function available to convert data (@LiNk-NY)
- Deprecate the
expr
argument and use relab
(short for relative abundances)
- Add group labels to
lefserPlot
(@LiNk-NY #25, @asyakhl #31)
- 'Interoperating with
phyloseq
' section added to the vignette (#16)
lefser 1.0.0
lefser
is an R/Bioconductor implementation of the LEfSe
method for microbiome marker
discovery (https://doi.org/10.1186/gb-2011-12-6-r60)
- LEfSe uses the Kruskal-Wallis test, Wilcoxon-Rank Sum test, and Linear
Discriminant Analysis to find biomarkers in groups and sub-group blocks.
lefser
also implements the format of the LEfSe barplot of results