v0.7 for master

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: MiscMetabar
 Type: Package
 Title: Miscellaneous Functions for Metabarcoding Analysis
-Version: 0.6.0
+Version: 0.7.0
 Authors@R: person("Adrien", "Taudière", email = "[email protected]",
   role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0003-1088-1182"))
 Description: The MiscMetabar package aims to facilitate the description, transformation, exploration, and reproducibility of metabarcoding analysis. Mainly build on the top of phyloseq, dada2 R packages. MiscMetabar help to build reproducible and robust bioinformatic pipeline in R. MiscMetabar make ecological analysis of alpha and beta-diversity simple and powerfull by integrating a large number of analysis, some of them from other R packages.  
@@ -96,8 +96,7 @@ Imports:
 Remotes: 
     bioc::phyloseq,
     bioc::dada2,
-    bioc::ANCOMBC,
-    github::briatte/ggnetwork
+    bioc::ANCOMBC
 Config/testthat/edition: 3
 Config/testthat/parallel: true
 VignetteBuilder: knitr

NAMESPACE

@@ -69,6 +69,7 @@ export(perc)
 export(phyloseq_to_edgeR)
 export(physeq_graph_test)
 export(physeq_heat_tree)
+export(physeq_or_string_to_dna)
 export(plot_LCBD_pq)
 export(plot_SCBD_pq)
 export(plot_deseq2_phyloseq)
@@ -99,6 +100,7 @@ export(subset_taxa_pq)
 export(subset_taxa_tax_control)
 export(summary_plot_phyloseq)
 export(summary_plot_pq)
+export(swarm_clustering)
 export(tax_bar_pq)
 export(tax_datatable)
 export(tbl_sum_samdata)
@@ -113,6 +115,7 @@ export(venn_phyloseq)
 export(venn_pq)
 export(verify_pq)
 export(vs_search_global)
+export(vsearch_clustering)
 export(write_phyloseq)
 export(write_pq)
 import(dada2)

NEWS.md

@@ -3,6 +3,9 @@
 - Add functions `chimera_detection_vs()` and `chimera_removal_vs()` to process chimera detection and removal using [vsearch](https://github.com/torognes/vsearch) software 
 - Add functions `filter_trim()`, `sample_data_with_new_names()` and `rename_samples()` to facilitate the use of [targets](https://books.ropensci.org/targets/) for bioinformatic pipeline.
 - Add function `add_info_to_sam_data()` to expand sam_data slot using a data.frame and using nb_asv and nb_seq 
+- Add functions `swarm_clustering()` and `vsearch_clustering()` and add `swarm` method in the function `asv2otu()`
+- Add function `physeq_or_string_to_dna()` mostly for internal use
+- Add function `cutadapt_remove_primers()` to remove primers using [cutadapt](https://github.com/marcelm/cutadapt/)
 
 ## BREAKING CHANGES