dependency hell

DESCRIPTION

@@ -24,23 +24,23 @@ Imports:
     chngpt,
     uwot,
     pscl,
-    Biostrings,
     dbscan,
     igraph,
-    ShortRead,
     ComplexUpset,
     plotly,
-    seqinr,
     Hmisc,
     ape,
-    compositions,
-    rBLAST
+    compositions
 Depends:
     R (>= 2.10)
 Suggests: 
     knitr,
     brms,
     NetCoMi,
+    ShortRead,
+    Biostrings,
+    rBLAST,
+    seqinr,
     rmarkdown
 Remotes:
     github::stefpeschel/NetCoMi

NAMESPACE

@@ -31,17 +31,10 @@ import(patchwork)
 import(stats)
 import(uwot)
 import(viridis)
-importFrom(Biostrings,DNAString)
-importFrom(Biostrings,DNAStringSet)
-importFrom(Biostrings,reverseComplement)
 importFrom(ComplexUpset,upset)
 importFrom(FactoMineR,PCA)
 importFrom(Hmisc,rcorr)
 importFrom(MASS,glm.nb)
-importFrom(ShortRead,countFastq)
-importFrom(ShortRead,readFastq)
-importFrom(ShortRead,sread)
-importFrom(ShortRead,writeFastq)
 importFrom(ape,pcoa)
 importFrom(compositions,clr)
 importFrom(dbscan,dbscan)
@@ -69,9 +62,6 @@ importFrom(plotly,plot_ly)
 importFrom(plotly,subplot)
 importFrom(plyr,rbind.fill)
 importFrom(pscl,zeroinfl)
-importFrom(rBLAST,blast)
-importFrom(rBLAST,makeblastdb)
-importFrom(seqinr,write.fasta)
 importFrom(stats,median)
 importFrom(stats,qnorm)
 importFrom(stats,quantile)

R/b_da.R

@@ -30,7 +30,7 @@
 #' @examples
 #' \donttest{
 #' if ("brms" %in% installed.packages()) {
-#'   ex <- b_da(asv, col = "ASV1", predictors = "tissue", intercept = FALSE)
+#'   ex <- b_da(asv, col = "ASV1", predictors = "tissue", intercept = FALSE, chains = 1, iter = 500)
 #' }
 #' }
 #' @export

R/blastASVs.R

@@ -12,10 +12,7 @@
 #' @param maxMatches An optional number of maximum matches to return per sequence in seqs1.
 #' Defaults to Inf, which will return all matches above the cutoff.
 #' @param cores Number of cores optionally to run in parallel. Defaults to 1 if "mc.cores" is not set.
-#' @keywords calibrate, ZINB, NB
-#' @importFrom rBLAST makeblastdb blast
-#' @importFrom Biostrings DNAStringSet
-#' @importFrom seqinr write.fasta
+#' @keywords BLAST
 #' @import parallel
 #' @return A dataframe of blast results
 #'

R/demultiplex.R

@@ -25,8 +25,6 @@
 #'
 #' @keywords demultiplex, dada2
 #'
-#' @importFrom ShortRead readFastq sread writeFastq countFastq
-#' @importFrom Biostrings reverseComplement DNAString
 #' @importFrom utils write.csv
 #' @importFrom methods is
 #' @import parallel