diff --git a/404.html b/404.html index c4b9674..9aa1ba5 100644 --- a/404.html +++ b/404.html @@ -38,7 +38,7 @@ lefser - 1.11.4 + 1.11.5 diff --git a/articles/index.html b/articles/index.html index c811a23..63a4657 100644 --- a/articles/index.html +++ b/articles/index.html @@ -23,7 +23,7 @@ lefser - 1.11.4 + 1.11.5 diff --git a/articles/lefser.html b/articles/lefser.html index 81f51e7..d6af94e 100644 --- a/articles/lefser.html +++ b/articles/lefser.html @@ -39,7 +39,7 @@ lefser - 1.11.4 + 1.11.5 @@ -174,12 +174,12 @@

Overview and example use of le ## 5 k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Ruminococcaceae|g__Ruminococcus|s__Ruminococcus_sp_5_1_39BFAA|t__GCF_000159975 ## 6 k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium_hallii ## scores -## 1 -6.216414 -## 2 -5.908016 -## 3 -5.895093 -## 4 -5.590072 -## 5 -5.590072 -## 6 -5.547374 +## 1 -6.229292 +## 2 -5.944323 +## 3 -5.933313 +## 4 -5.622914 +## 5 -5.622914 +## 6 -5.518944

Visualizing results with lefserPlot @@ -273,7 +273,7 @@

sessionInfo## [8] base ## ## other attached packages: -## [1] phyloseq_1.44.0 lefser_1.11.4 +## [1] phyloseq_1.44.0 lefser_1.11.5 ## [3] SummarizedExperiment_1.30.2 Biobase_2.60.0 ## [5] GenomicRanges_1.52.1 GenomeInfoDb_1.36.4 ## [7] IRanges_2.34.1 S4Vectors_0.38.2 diff --git a/articles/lefser_files/figure-html/unnamed-chunk-8-1.png b/articles/lefser_files/figure-html/unnamed-chunk-8-1.png index 4e9724b..229aecf 100644 Binary files a/articles/lefser_files/figure-html/unnamed-chunk-8-1.png and b/articles/lefser_files/figure-html/unnamed-chunk-8-1.png differ diff --git a/authors.html b/authors.html index 4acd7ac..be13102 100644 --- a/authors.html +++ b/authors.html @@ -23,7 +23,7 @@ lefser - 1.11.4 + 1.11.5

@@ -84,13 +84,13 @@

Citation

Khleborodova A (2023). lefser: R implementation of the LEfSE method for microbiome biomarker discovery. -R package version 1.11.4, https://github.com/waldronlab/lefser. +R package version 1.11.5, https://github.com/waldronlab/lefser. 

@Manual{,
   title = {lefser: R implementation of the LEfSE method for microbiome biomarker discovery},
   author = {Asya Khleborodova},
   year = {2023},
-  note = {R package version 1.11.4},
+  note = {R package version 1.11.5},
   url = {https://github.com/waldronlab/lefser},
 }
diff --git a/index.html b/index.html index 06a71b2..d584476 100644 --- a/index.html +++ b/index.html @@ -42,7 +42,7 @@ lefser - 1.11.4 + 1.11.5 diff --git a/news/index.html b/news/index.html index 5fe3b53..dc412bf 100644 --- a/news/index.html +++ b/news/index.html @@ -23,7 +23,7 @@ lefser - 1.11.4 + 1.11.5 diff --git a/pkgdown.yml b/pkgdown.yml index 419be29..0fadd9d 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -3,7 +3,7 @@ pkgdown: 2.0.7 pkgdown_sha: ~ articles: lefser: lefser.html -last_built: 2023-10-20T21:22Z +last_built: 2023-10-20T21:37Z urls: reference: https://waldronlab.io/lefser/reference article: https://waldronlab.io/lefser/articles diff --git a/reference/index.html b/reference/index.html index 978b4d3..68a5191 100644 --- a/reference/index.html +++ b/reference/index.html @@ -23,7 +23,7 @@ lefser - 1.11.4 + 1.11.5 diff --git a/reference/lefser.html b/reference/lefser.html index c29cfd7..97dc10a 100644 --- a/reference/lefser.html +++ b/reference/lefser.html @@ -27,7 +27,7 @@ lefser - 1.11.4 + 1.11.5 @@ -178,12 +178,12 @@

Examples

#> 5 k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus_eutactus #> 6 k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus_eutactus|t__GCF_000154425 #> scores -#> 1 -6.411232 -#> 2 -6.411232 -#> 3 -6.411205 -#> 4 -5.787917 -#> 5 -5.647113 -#> 6 -5.609561 +#> 1 -6.347444 +#> 2 -6.347444 +#> 3 -6.347413 +#> 4 -5.722422 +#> 5 -5.575588 +#> 6 -5.559177 # (2) Using classes and sublasses data(zeller14) @@ -200,16 +200,16 @@

Examples

#> 1 k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae #> 2 k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium #> 3 k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas -#> 4 k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas_asaccharolytica|t__Porphyromonas_asaccharolytica_unclassified -#> 5 k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas_asaccharolytica -#> 6 k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus_stomatis +#> 4 k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas_asaccharolytica +#> 5 k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas_asaccharolytica|t__Porphyromonas_asaccharolytica_unclassified +#> 6 k__Bacteria|p__Fusobacteria|c__Fusobacteriia #> scores -#> 1 -5.230725 -#> 2 -5.212278 -#> 3 -5.050998 -#> 4 -4.961072 -#> 5 -4.934663 -#> 6 -4.810627 +#> 1 -5.267833 +#> 2 -5.228945 +#> 3 -4.998489 +#> 4 -4.927101 +#> 5 -4.899673 +#> 6 -4.870512 diff --git a/reference/lefserPlot-1.png b/reference/lefserPlot-1.png index 0cb8742..86f6cc4 100644 Binary files a/reference/lefserPlot-1.png and b/reference/lefserPlot-1.png differ diff --git a/reference/lefserPlot.html b/reference/lefserPlot.html index b7fcfde..7b36941 100644 --- a/reference/lefserPlot.html +++ b/reference/lefserPlot.html @@ -24,7 +24,7 @@ lefser - 1.11.4 + 1.11.5 @@ -115,12 +115,12 @@

Examples

#> 5 k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus_eutactus #> 6 k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus_eutactus|t__GCF_000154425 #> scores -#> 1 -6.315413 -#> 2 -6.315413 -#> 3 -6.315381 -#> 4 -5.712236 -#> 5 -5.581008 -#> 6 -5.555817 +#> 1 -6.361900 +#> 2 -6.361900 +#> 3 -6.361867 +#> 4 -5.708269 +#> 5 -5.562677 +#> 6 -5.551201 #> #> lefser> # (2) Using classes and sublasses #> lefser> data(zeller14) @@ -137,19 +137,19 @@

Examples

#> #> lefser> head(res_block) #> Names -#> 1 k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium -#> 2 k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae +#> 1 k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae +#> 2 k__Bacteria|p__Fusobacteria|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium #> 3 k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas #> 4 k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas_asaccharolytica|t__Porphyromonas_asaccharolytica_unclassified #> 5 k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas_asaccharolytica -#> 6 k__Bacteria|p__Fusobacteria +#> 6 k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Peptostreptococcaceae|g__Peptostreptococcus|s__Peptostreptococcus_stomatis #> scores -#> 1 -5.319767 -#> 2 -5.216802 -#> 3 -5.010703 -#> 4 -4.950247 -#> 5 -4.933431 -#> 6 -4.830540 +#> 1 -5.226136 +#> 2 -5.224838 +#> 3 -4.987593 +#> 4 -4.928606 +#> 5 -4.920586 +#> 6 -4.802129 lefserPlot(res_group) diff --git a/reference/relativeAb.html b/reference/relativeAb.html index e72cca4..862f7be 100644 --- a/reference/relativeAb.html +++ b/reference/relativeAb.html @@ -24,7 +24,7 @@ lefser - 1.11.4 + 1.11.5 diff --git a/reference/zeller14.html b/reference/zeller14.html index 04519e8..70afced 100644 --- a/reference/zeller14.html +++ b/reference/zeller14.html @@ -25,7 +25,7 @@ lefser - 1.11.4 + 1.11.5