diff --git a/404.html b/404.html index cf621f72..9861f4ea 100644 --- a/404.html +++ b/404.html @@ -32,7 +32,7 @@ bugphyzz - 0.0.1.11 + 0.0.1.12 diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html index 783f0ed6..f7647860 100644 --- a/CODE_OF_CONDUCT.html +++ b/CODE_OF_CONDUCT.html @@ -17,7 +17,7 @@ bugphyzz - 0.0.1.11 + 0.0.1.12 diff --git a/CONTRIBUTING.html b/CONTRIBUTING.html index 9f83d0b6..98f5ae58 100644 --- a/CONTRIBUTING.html +++ b/CONTRIBUTING.html @@ -17,7 +17,7 @@ bugphyzz - 0.0.1.11 + 0.0.1.12 diff --git a/LICENSE-text.html b/LICENSE-text.html index a2afb665..a7e4402f 100644 --- a/LICENSE-text.html +++ b/LICENSE-text.html @@ -17,7 +17,7 @@ bugphyzz - 0.0.1.11 + 0.0.1.12 diff --git a/SUPPORT.html b/SUPPORT.html index 15716bb3..6e713393 100644 --- a/SUPPORT.html +++ b/SUPPORT.html @@ -17,7 +17,7 @@ bugphyzz - 0.0.1.11 + 0.0.1.12 diff --git a/articles/attributes.html b/articles/attributes.html index ba239d30..0077a7dd 100644 --- a/articles/attributes.html +++ b/articles/attributes.html @@ -33,7 +33,7 @@ bugphyzz - 0.0.1.11 + 0.0.1.12 @@ -96,22 +96,22 @@

Sources and Attributes

Sources

The 17 sources of annotations in bugphyzz:

-
- +
+

Attributes

Definition of attributes and attribute values. Ontology terms can be searched at OSLv3 and OSLv4.

-
- +
+

Sources x Attributes

-
- +
+

Session info @@ -136,7 +136,7 @@

Session info#> bit64 4.0.5 2020-08-30 [1] RSPM (R 4.3.0) #> blob 1.2.4 2023-03-17 [1] RSPM (R 4.3.0) #> bslib 0.6.1 2023-11-28 [1] RSPM (R 4.3.0) -#> bugphyzz * 0.0.1.11 2024-03-22 [1] Bioconductor +#> bugphyzz * 0.0.1.12 2024-03-22 [1] Bioconductor #> cachem 1.0.8 2023-05-01 [1] RSPM (R 4.3.0) #> cli 3.6.2 2023-12-11 [1] RSPM (R 4.3.0) #> crayon 1.5.2 2022-09-29 [1] RSPM (R 4.3.0) diff --git a/articles/bugphyzz.html b/articles/bugphyzz.html index 73a95473..b224aff6 100644 --- a/articles/bugphyzz.html +++ b/articles/bugphyzz.html @@ -33,7 +33,7 @@ bugphyzz - 0.0.1.11 + 0.0.1.12

@@ -472,20 +472,20 @@

Run a bug set enrichment analysistse_subset$GROUP <- ifelse( tse_subset$body_subsite == 'subgingival_plaque', 0, 1 ) -edger <- EnrichmentBrowser::deAna( - expr = tse_subset, de.method = 'edgeR', padj.method = 'fdr', +se <- EnrichmentBrowser::deAna( + expr = tse_subset, de.method = 'limma', padj.method = 'fdr', filter.by.expr = FALSE, ) -dat <- data.frame(colData(edger)) +dat <- data.frame(colData(se)) design <- stats::model.matrix(~ GROUP, data = dat) -assay(edger) <- limma::voom( - counts = assay(edger), design = design, plot = FALSE +assay(se) <- limma::voom( + counts = assay(se), design = design, plot = FALSE )$E

Perform GSEA and display the results:

 gsea <- EnrichmentBrowser::sbea(
-  method = 'gsea', se = edger, gs = aer_sigs_g, perm = 1000,
+  method = 'gsea', se = se, gs = aer_sigs_g, perm = 1000,
   alpha = 0.1 
 )
 gsea_tbl <- as.data.frame(gsea$res.tbl) |> 
@@ -619,7 +619,7 @@ 
Session information#>  bold                       1.3.0       2023-05-02 [1] RSPM (R 4.3.0)
 #>  bookdown                   0.38        2024-03-04 [1] RSPM (R 4.3.0)
 #>  bslib                      0.6.1       2023-11-28 [1] RSPM (R 4.3.0)
-#>  bugphyzz                 * 0.0.1.11    2024-03-22 [1] Bioconductor
+#>  bugphyzz                 * 0.0.1.12    2024-03-22 [1] Bioconductor
 #>  cachem                     1.0.8       2023-05-01 [1] RSPM (R 4.3.0)
 #>  cli                        3.6.2       2023-12-11 [1] RSPM (R 4.3.0)
 #>  cluster                    2.1.4       2022-08-22 [2] CRAN (R 4.3.2)
diff --git a/articles/index.html b/articles/index.html
index 00a664a2..4cd8551e 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -17,7 +17,7 @@
       
       
         bugphyzz
-        0.0.1.11
+        0.0.1.12
diff --git a/authors.html b/authors.html index 096520fd..537922e6 100644 --- a/authors.html +++ b/authors.html @@ -17,7 +17,7 @@ bugphyzz - 0.0.1.11 + 0.0.1.12 @@ -89,13 +89,13 @@

Citation

Gamboa S, Waldron L, Eckenrode K, Ye J, Wokaty J (2024). bugphyzz: A harmonized data resource and software for enrichment analysis of microbial physiologies. -R package version 0.0.1.11, https://github.com/waldronlab/bugphyzz. +R package version 0.0.1.12, https://github.com/waldronlab/bugphyzz. 

@Manual{,
   title = {bugphyzz: A harmonized data resource and software for enrichment analysis of microbial physiologies},
   author = {Samuel Gamboa and Levi Waldron and Kelly Eckenrode and Jonathan Ye and Jennifer Wokaty},
   year = {2024},
-  note = {R package version 0.0.1.11},
+  note = {R package version 0.0.1.12},
   url = {https://github.com/waldronlab/bugphyzz},
 }
diff --git a/index.html b/index.html index 4c7563cd..f5bd68e5 100644 --- a/index.html +++ b/index.html @@ -35,7 +35,7 @@ bugphyzz - 0.0.1.11 + 0.0.1.12 diff --git a/pkgdown.yml b/pkgdown.yml index 384c7616..8b1aaca6 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -4,7 +4,7 @@ pkgdown_sha: ~ articles: attributes: attributes.html bugphyzz: bugphyzz.html -last_built: 2024-03-22T14:30Z +last_built: 2024-03-22T17:41Z urls: reference: https://waldronlab.io/bugphyzz/reference article: https://waldronlab.io/bugphyzz/articles diff --git a/reference/getTaxonSignatures.html b/reference/getTaxonSignatures.html index 9f81e5fc..824b269f 100644 --- a/reference/getTaxonSignatures.html +++ b/reference/getTaxonSignatures.html @@ -19,7 +19,7 @@ bugphyzz - 0.0.1.11 + 0.0.1.12 @@ -99,13 +99,13 @@

Examples

bp <- importBugphyzz() #> Importing multistate data... #> Downloading, bugphyzz_multistate.tsv. -#> Using data downloaded on 2024-03-22 14:30:29. +#> Using data downloaded on 2024-03-22 17:41:54. #> Importing binary data... #> Downloading, bugphyzz_binary.tsv. -#> Using data downloaded on 2024-03-22 14:30:38. +#> Using data downloaded on 2024-03-22 17:42:24. #> Importing numeric data... #> Downloading, bugphyzz_numeric.tsv. -#> Using data downloaded on 2024-03-22 14:30:41. +#> Using data downloaded on 2024-03-22 17:42:28. sig_names_1 <- getTaxonSignatures(taxid, bp) sig_names_2 <- getTaxonSignatures(taxonName, bp, tax_id_type = "Taxon_name") diff --git a/reference/importBugphyzz.html b/reference/importBugphyzz.html index 4406b83a..ddb316bb 100644 --- a/reference/importBugphyzz.html +++ b/reference/importBugphyzz.html @@ -19,7 +19,7 @@ bugphyzz - 0.0.1.11 + 0.0.1.12 @@ -147,11 +147,11 @@

Examples


 bp <- importBugphyzz()
 #> Importing multistate data...
-#> Using data downloaded on 2024-03-22 14:30:29.
+#> Using data downloaded on 2024-03-22 17:41:54.
 #> Importing binary data...
-#> Using data downloaded on 2024-03-22 14:30:38.
+#> Using data downloaded on 2024-03-22 17:42:24.
 #> Importing numeric data...
-#> Using data downloaded on 2024-03-22 14:30:41.
+#> Using data downloaded on 2024-03-22 17:42:28.
 names(bp)
 #>  [1] "aerophilicity"                        
 #>  [2] "antimicrobial resistance"             
diff --git a/reference/index.html b/reference/index.html
index 63634f39..c830571f 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -17,7 +17,7 @@
       
       
         bugphyzz
-        0.0.1.11
+        0.0.1.12
diff --git a/reference/makeSignatures.html b/reference/makeSignatures.html index 6dd0dde0..c9d93f3b 100644 --- a/reference/makeSignatures.html +++ b/reference/makeSignatures.html @@ -19,7 +19,7 @@ bugphyzz - 0.0.1.11 + 0.0.1.12 @@ -132,11 +132,11 @@

Examples


 bp <- importBugphyzz()
 #> Importing multistate data...
-#> Using data downloaded on 2024-03-22 14:30:29.
+#> Using data downloaded on 2024-03-22 17:41:54.
 #> Importing binary data...
-#> Using data downloaded on 2024-03-22 14:30:38.
+#> Using data downloaded on 2024-03-22 17:42:24.
 #> Importing numeric data...
-#> Using data downloaded on 2024-03-22 14:30:41.
+#> Using data downloaded on 2024-03-22 17:42:28.
 sigs <- purrr::map(bp, makeSignatures)
 sigs <- purrr::list_flatten(sigs, name_spec = "{inner}")
 
diff --git a/reference/physiologies.html b/reference/physiologies.html
index f7e92f68..330b38e4 100644
--- a/reference/physiologies.html
+++ b/reference/physiologies.html
@@ -19,7 +19,7 @@
       
       
         bugphyzz
-        0.0.1.11
+        0.0.1.12
diff --git a/reference/showPhys.html b/reference/showPhys.html index be895d6d..76ff93ed 100644 --- a/reference/showPhys.html +++ b/reference/showPhys.html @@ -19,7 +19,7 @@ bugphyzz - 0.0.1.11 + 0.0.1.12 diff --git a/sitemap.xml b/sitemap.xml index d510d685..052db6ed 100644 --- a/sitemap.xml +++ b/sitemap.xml @@ -30,60 +30,6 @@ https://waldronlab.io/bugphyzz/index.html - - https://waldronlab.io/bugphyzz/reference/dot-appendLinks.html - - - https://waldronlab.io/bugphyzz/reference/dot-attributes.html - - - https://waldronlab.io/bugphyzz/reference/dot-checkColumnValues.html - - - https://waldronlab.io/bugphyzz/reference/dot-checkColumnValuesDF.html - - - https://waldronlab.io/bugphyzz/reference/dot-checkColumnValuesList.html - - - https://waldronlab.io/bugphyzz/reference/dot-checkRequiredColumns.html - - - https://waldronlab.io/bugphyzz/reference/dot-checkRequiredColumnsDF.html - - - https://waldronlab.io/bugphyzz/reference/dot-checkRequiredColumnsList.html - - - https://waldronlab.io/bugphyzz/reference/dot-errListToTable.html - - - https://waldronlab.io/bugphyzz/reference/dot-errorHandler.html - - - https://waldronlab.io/bugphyzz/reference/dot-requiredColumns.html - - - https://waldronlab.io/bugphyzz/reference/dot-stop_custom.html - - - https://waldronlab.io/bugphyzz/reference/dot-stop_invalid_column_values.html - - - https://waldronlab.io/bugphyzz/reference/dot-stop_required_columns_misplaced.html - - - https://waldronlab.io/bugphyzz/reference/dot-stop_required_columns_missing.html - - - https://waldronlab.io/bugphyzz/reference/dot-stop_required_missing_row_value.html - - - https://waldronlab.io/bugphyzz/reference/dot-stop_uncatalogued_column.html - - - https://waldronlab.io/bugphyzz/reference/dot-template.html - https://waldronlab.io/bugphyzz/reference/getTaxonSignatures.html