Merge pull request #52 from adrientaudiere/dev

bugfix: retry to install mumu

.github/workflows/R-CMD-check.yaml

@@ -41,6 +41,12 @@ jobs:
         with:
           extra-packages: any::rcmdcheck
           needs: check
+
+      - name: Install vsearch
+        run: sudo apt-get install vsearch
+
+      - name: Install blastn
+        run: sudo apt-get install ncbi-blast+
 
       - uses: r-lib/actions/check-r-package@v2
         with:

.github/workflows/test-coverage.yaml

@@ -32,11 +32,11 @@ jobs:
         run: sudo apt-get install ncbi-blast+
 
       - name: Install mumu
-        run: >
+        run: |
          git clone https://github.com/frederic-mahe/mumu.git \
-         && cd ./mumu/\
-         && make\
-         && make check\
+         && cd ./mumu/ \
+         && make \
+         && make check \
          && sudo make install 
 
       - name: Test coverage

README.Rmd

@@ -45,7 +45,7 @@ BiocManager.
 You can install the stable version from [GitHub](https://github.com/)
 with:
 
-```{r}
+```{r, results = 'hide'}
 if (!require("BiocManager", quietly = TRUE)) {
   install.packages("BiocManager")
 }
@@ -61,7 +61,7 @@ devtools::install_github("adrientaudiere/MiscMetabar")
 You can install the development version from
 [GitHub](https://github.com/) with:
 
-```{r}
+```{r, results = 'hide'}
 if (!require("BiocManager", quietly = TRUE)) {
   install.packages("BiocManager")
 }
@@ -89,7 +89,7 @@ For developers, I also wrote a vignette describing som [rules of codes](https://
 
 ### Summarize a physeq object
 
-```{r example, message=FALSE}
+```{r example}
 library("MiscMetabar")
 library("phyloseq")
 library("magrittr")

_pkgdown.yml

@@ -38,6 +38,161 @@ navbar:
     - text: Rules of code
       href: articles/Rules.html
 
+reference:
+- title: Describe phyloseq object
+  contents:
+  - summary_plot_pq
+  - tbl_sum_samdata
+  - verify_pq
+
+
+- title: Transform phyloseq object
+- subtitle: Taxonomy
+  contents: 
+  - add_funguild_info
+  - add_new_taxonomy_pq
+  - add_blast_info
+  - blast_to_phyloseq
+  - blast_pq
+  - blast_to_derep
+  - filter_asv_blast
+
+- subtitle: OTU table
+  contents: 
+  - as_binary_otu_table
+  - asv2otu
+  - lulu_pq
+  - mumu_pq
+  - subset_taxa_pq
+  - subset_taxa_tax_control
+
+- subtitle: Sample datase
+  contents:
+  - subset_samples_pq 
+
+- subtitle: Phylogenetic tree
+  contents: 
+  - build_phytree_pq
+
+- subtitle: Others
+  contents: 
+  - add_dna_to_phyloseq
+  - clean_pq
+
+
+- title: Explore phyloseq object
+- subtitle: alpha-diversity
+  contents:
+  - accu_plot
+  - accu_samp_threshold
+  - hill_pq
+  - hill_tuckey_pq
+  - iNEXT_pq
+
+
+- subtitle: beta-diversity
+  contents:
+  - accu_samp_threshold
+  - adonis_pq
+  - biplot_pq
+  - circle_pq
+  - compare_pairs_pq
+  - ggvenn_pq
+  - graph_test_pq
+  - LCBD_pq
+  - multi_biplot_pq
+  - plot_LCBD_pq
+  - plot_tsne_pq
+  - ridges_pq
+  - sankey_pq
+  - SRS_curve_pq
+  - tsne_pq
+  - upset_pq
+  - upset_test_pq
+  - venn_pq
+
+- subtitle: Differencial abundance analysis
+  contents:
+  - multipatt_pq
+  - phyloseq_to_edgeR
+  - plot_edgeR_pq
+  - plot_deseq2_pq
+  - plot_mt
+
+- subtitle: Taxonomy
+  contents:
+  - heat_tree_pq
+  - krona
+  - merge_krona
+  - multitax_bar_pq
+  - plot_guild_pq
+  - plot_tax_pq
+  - rotl_pq
+  - search_exact_seq_pq
+  - tax_bar_pq
+  - tax_datatable
+  - treemap_pq
+  - vs_search_global
+
+- title: Improve reproducibility
+- subtitle: Import/export phyloseq object
+  contents:
+  - read_pq
+  - save_pq
+  - write_pq
+- subtitle: Track info along pipeline
+  contents:
+  - count_seq
+  - track_wkflow
+  - track_wkflow_samples
+- subtitle: Utilities for [targets](https://books.ropensci.org/targets/) pipeline
+  contents:
+  - list_fastq_files
+  - rename_samples_otu_table
+  - select_one_sample
+  - simplify_taxo
+  - subsample_fastq
+
+- title: Datasets
+  contents: 
+  - data_fungi
+  - data_fungi_sp_known
+  - Tengeler2020_pq
+
+- title: Others utilities
+  contents:
+  - all_object_size
+  - diff_fct_diff_class
+  - dist_bycol
+  - dist_pos_control
+  - funky_color
+  - get_file_extension
+  - install_pkg_needed
+  - multiplot
+  - perc
+
+
+
+- title: Deprecated
+  contents:
+  - adonis_phyloseq 
+  - biplot_physeq
+  - clean_physeq 
+  - ggVenn_phyloseq
+  - hill_phyloseq 
+  - hill_tuckey_phyloseq
+  - lulu_phyloseq
+  - otu_circle
+  - physeq_graph_test
+  - physeq_heat_tree
+  - plot_deseq2_phyloseq
+  - plot_edgeR_phyloseq
+  - read_phyloseq
+  - sankey_phyloseq
+  - summary_plot_phyloseq
+  - venn_phyloseq
+  - write_phyloseq
+
 
 development:
   mode: auto