From 4dca3db2ebb81af463bc1dbbdd677ad05d380fd3 Mon Sep 17 00:00:00 2001 From: cpauvert Date: Thu, 13 Jun 2024 15:22:21 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20ClavelLa?= =?UTF-8?q?b/maldipickr@bb242947a3520c4fe7a12c022ccc34330bfae0e9=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- dev/CODE_OF_CONDUCT.html | 17 +++++++++++++++-- dev/CONTRIBUTING.html | 17 +++++++++++++++-- dev/LICENSE.html | 17 +++++++++++++++-- ...replicate-bruker-maldi-biotyper-spectra.html | 17 +++++++++++++++-- .../import-data-from-bruker-maldi-biotyper.html | 17 +++++++++++++++-- dev/articles/index.html | 17 +++++++++++++++-- dev/authors.html | 17 +++++++++++++++-- dev/index.html | 17 +++++++++++++++-- dev/news/index.html | 17 +++++++++++++++-- dev/pkgdown.yml | 2 +- dev/reference/check_spectra.html | 17 +++++++++++++++-- .../delineate_with_identification.html | 17 +++++++++++++++-- dev/reference/delineate_with_similarity.html | 17 +++++++++++++++-- dev/reference/get_spectra_names.html | 17 +++++++++++++++-- dev/reference/import_biotyper_spectra.html | 17 +++++++++++++++-- dev/reference/import_spede_clusters.html | 17 +++++++++++++++-- dev/reference/index.html | 17 +++++++++++++++-- dev/reference/is_well_on_edge.html | 17 +++++++++++++++-- dev/reference/maldipickr-package.html | 17 +++++++++++++++-- dev/reference/merge_processed_spectra.html | 17 +++++++++++++++-- dev/reference/pick_spectra.html | 17 +++++++++++++++-- dev/reference/pipe.html | 17 +++++++++++++++-- dev/reference/process_spectra.html | 17 +++++++++++++++-- dev/reference/read_biotyper_report.html | 17 +++++++++++++++-- dev/reference/read_many_biotyper_reports.html | 17 +++++++++++++++-- dev/reference/remove_spectra.html | 17 +++++++++++++++-- dev/reference/set_reference_spectra.html | 17 +++++++++++++++-- 27 files changed, 391 insertions(+), 53 deletions(-) diff --git a/dev/CODE_OF_CONDUCT.html b/dev/CODE_OF_CONDUCT.html index 51198d9..e90b713 100644 --- a/dev/CODE_OF_CONDUCT.html +++ b/dev/CODE_OF_CONDUCT.html @@ -1,8 +1,21 @@ -Contributor Covenant Code of Conduct • maldipickrContributor Covenant Code of Conduct • maldipickr + Skip to contents diff --git a/dev/CONTRIBUTING.html b/dev/CONTRIBUTING.html index dbb5a9c..9809f29 100644 --- a/dev/CONTRIBUTING.html +++ b/dev/CONTRIBUTING.html @@ -1,8 +1,21 @@ -Contributing to {maldipickr} • maldipickrContributing to {maldipickr} • maldipickr + Skip to contents diff --git a/dev/LICENSE.html b/dev/LICENSE.html index 8149987..6ffcbef 100644 --- a/dev/LICENSE.html +++ b/dev/LICENSE.html @@ -1,8 +1,21 @@ -GNU General Public License • maldipickrGNU General Public License • maldipickr + Skip to contents diff --git a/dev/articles/dereplicate-bruker-maldi-biotyper-spectra.html b/dev/articles/dereplicate-bruker-maldi-biotyper-spectra.html index 1ccf4c3..352969d 100644 --- a/dev/articles/dereplicate-bruker-maldi-biotyper-spectra.html +++ b/dev/articles/dereplicate-bruker-maldi-biotyper-spectra.html @@ -18,7 +18,7 @@ - + @@ -26,7 +26,20 @@ + Skip to contents diff --git a/dev/articles/import-data-from-bruker-maldi-biotyper.html b/dev/articles/import-data-from-bruker-maldi-biotyper.html index 3fcfa6e..c3d47ea 100644 --- a/dev/articles/import-data-from-bruker-maldi-biotyper.html +++ b/dev/articles/import-data-from-bruker-maldi-biotyper.html @@ -18,7 +18,7 @@ - + @@ -26,7 +26,20 @@ + Skip to contents diff --git a/dev/articles/index.html b/dev/articles/index.html index 4666c17..2d3fcc3 100644 --- a/dev/articles/index.html +++ b/dev/articles/index.html @@ -1,8 +1,21 @@ -Articles • maldipickrArticles • maldipickr + Skip to contents diff --git a/dev/authors.html b/dev/authors.html index d3c3770..352d516 100644 --- a/dev/authors.html +++ b/dev/authors.html @@ -1,8 +1,21 @@ -Authors and Citation • maldipickrAuthors and Citation • maldipickr + Skip to contents diff --git a/dev/index.html b/dev/index.html index d98d9f6..ae94366 100644 --- a/dev/index.html +++ b/dev/index.html @@ -18,7 +18,7 @@ - + @@ -26,7 +26,20 @@ + Skip to contents diff --git a/dev/news/index.html b/dev/news/index.html index 02fe349..bc6db57 100644 --- a/dev/news/index.html +++ b/dev/news/index.html @@ -1,8 +1,21 @@ -Changelog • maldipickrChangelog • maldipickr + Skip to contents diff --git a/dev/pkgdown.yml b/dev/pkgdown.yml index 9b72fc0..db61388 100644 --- a/dev/pkgdown.yml +++ b/dev/pkgdown.yml @@ -4,7 +4,7 @@ pkgdown_sha: ~ articles: dereplicate-bruker-maldi-biotyper-spectra: dereplicate-bruker-maldi-biotyper-spectra.html import-data-from-bruker-maldi-biotyper: import-data-from-bruker-maldi-biotyper.html -last_built: 2024-06-12T08:16Z +last_built: 2024-06-13T15:22Z urls: reference: https://clavellab.github.io/maldipickr/reference article: https://clavellab.github.io/maldipickr/articles diff --git a/dev/reference/check_spectra.html b/dev/reference/check_spectra.html index 14bc02e..3ae8064 100644 --- a/dev/reference/check_spectra.html +++ b/dev/reference/check_spectra.html @@ -1,8 +1,21 @@ -Evaluate the spectra regularities — check_spectra • maldipickrEvaluate the spectra regularities — check_spectra • maldipickr + Skip to contents diff --git a/dev/reference/delineate_with_identification.html b/dev/reference/delineate_with_identification.html index df6f67a..b9b0a26 100644 --- a/dev/reference/delineate_with_identification.html +++ b/dev/reference/delineate_with_identification.html @@ -1,12 +1,25 @@ Delineate clusters from taxonomic identifications — delineate_with_identification • maldipickrDelineate clusters from taxonomic identifications — delineate_with_identification • maldipickr + Skip to contents diff --git a/dev/reference/delineate_with_similarity.html b/dev/reference/delineate_with_similarity.html index 9b8127b..65965df 100644 --- a/dev/reference/delineate_with_similarity.html +++ b/dev/reference/delineate_with_similarity.html @@ -1,12 +1,25 @@ Delineate clusters from a similarity matrix — delineate_with_similarity • maldipickrDelineate clusters from a similarity matrix — delineate_with_similarity • maldipickr + Skip to contents diff --git a/dev/reference/get_spectra_names.html b/dev/reference/get_spectra_names.html index 8a7ebb8..aff6eda 100644 --- a/dev/reference/get_spectra_names.html +++ b/dev/reference/get_spectra_names.html @@ -1,10 +1,23 @@ Extract spectra names and check for uniqueness — get_spectra_names • maldipickrExtract spectra names and check for uniqueness — get_spectra_names • maldipickr + Skip to contents diff --git a/dev/reference/import_biotyper_spectra.html b/dev/reference/import_biotyper_spectra.html index 13a54f1..3211a69 100644 --- a/dev/reference/import_biotyper_spectra.html +++ b/dev/reference/import_biotyper_spectra.html @@ -1,8 +1,21 @@ -Importing spectra from the Bruker MALDI Biotyper device — import_biotyper_spectra • maldipickrImporting spectra from the Bruker MALDI Biotyper device — import_biotyper_spectra • maldipickr + Skip to contents diff --git a/dev/reference/import_spede_clusters.html b/dev/reference/import_spede_clusters.html index 3542c0f..2475e3f 100644 --- a/dev/reference/import_spede_clusters.html +++ b/dev/reference/import_spede_clusters.html @@ -1,12 +1,25 @@ Import clusters results generated by SPeDE — import_spede_clusters • maldipickrImport clusters results generated by SPeDE — import_spede_clusters • maldipickr + Skip to contents diff --git a/dev/reference/index.html b/dev/reference/index.html index ca6ec00..4d2a485 100644 --- a/dev/reference/index.html +++ b/dev/reference/index.html @@ -1,8 +1,21 @@ -Function reference • maldipickrFunction reference • maldipickr + Skip to contents diff --git a/dev/reference/is_well_on_edge.html b/dev/reference/is_well_on_edge.html index 8cbd162..cf0bf74 100644 --- a/dev/reference/is_well_on_edge.html +++ b/dev/reference/is_well_on_edge.html @@ -1,8 +1,21 @@ -Identify the wells on the plate's edge — is_well_on_edge • maldipickrIdentify the wells on the plate's edge — is_well_on_edge • maldipickr + Skip to contents diff --git a/dev/reference/maldipickr-package.html b/dev/reference/maldipickr-package.html index dccb9d6..a648e93 100644 --- a/dev/reference/maldipickr-package.html +++ b/dev/reference/maldipickr-package.html @@ -1,10 +1,23 @@ maldipickr: Dereplicate and Cherry-Pick Mass Spectrometry Spectra — maldipickr-package • maldipickrmaldipickr: Dereplicate and Cherry-Pick Mass Spectrometry Spectra — maldipickr-package • maldipickr + Skip to contents diff --git a/dev/reference/merge_processed_spectra.html b/dev/reference/merge_processed_spectra.html index 353f844..f05e1eb 100644 --- a/dev/reference/merge_processed_spectra.html +++ b/dev/reference/merge_processed_spectra.html @@ -1,8 +1,21 @@ -Merge multiple processed spectra and peaks — merge_processed_spectra • maldipickrMerge multiple processed spectra and peaks — merge_processed_spectra • maldipickr + Skip to contents diff --git a/dev/reference/pick_spectra.html b/dev/reference/pick_spectra.html index e25aeb4..a257e24 100644 --- a/dev/reference/pick_spectra.html +++ b/dev/reference/pick_spectra.html @@ -4,7 +4,7 @@ spectra and therefore clusters can be explicitly removed (masked) from the picking decision if they have been previously picked or should be discarded, using logical columns in the metadata table. -If no metadata are provided, the reference spectra of each cluster will be picked.">Cherry-pick Bruker MALDI Biotyper spectra — pick_spectra • maldipickrCherry-pick Bruker MALDI Biotyper spectra — pick_spectra • maldipickr + Skip to contents diff --git a/dev/reference/pipe.html b/dev/reference/pipe.html index 68c99c0..c3ae064 100644 --- a/dev/reference/pipe.html +++ b/dev/reference/pipe.html @@ -1,8 +1,21 @@ -Pipe operator — %>% • maldipickrPipe operator — %>% • maldipickr + Skip to contents diff --git a/dev/reference/process_spectra.html b/dev/reference/process_spectra.html index 3888357..78b4308 100644 --- a/dev/reference/process_spectra.html +++ b/dev/reference/process_spectra.html @@ -1,8 +1,21 @@ -Process Bruker MALDI Biotyper spectra à la Strejcek et al. (2018) — process_spectra • maldipickrProcess Bruker MALDI Biotyper spectra à la Strejcek et al. (2018) — process_spectra • maldipickr + Skip to contents diff --git a/dev/reference/read_biotyper_report.html b/dev/reference/read_biotyper_report.html index 786fe31..413dafe 100644 --- a/dev/reference/read_biotyper_report.html +++ b/dev/reference/read_biotyper_report.html @@ -1,12 +1,25 @@ Importing Bruker MALDI Biotyper CSV report — read_biotyper_report • maldipickrImporting Bruker MALDI Biotyper CSV report — read_biotyper_report • maldipickr + Skip to contents diff --git a/dev/reference/read_many_biotyper_reports.html b/dev/reference/read_many_biotyper_reports.html index 97e0b04..7cc69b8 100644 --- a/dev/reference/read_many_biotyper_reports.html +++ b/dev/reference/read_many_biotyper_reports.html @@ -1,8 +1,21 @@ -Importing a list of Bruker MALDI Biotyper CSV reports — read_many_biotyper_reports • maldipickrImporting a list of Bruker MALDI Biotyper CSV reports — read_many_biotyper_reports • maldipickr + Skip to contents diff --git a/dev/reference/remove_spectra.html b/dev/reference/remove_spectra.html index b4bcdbe..35547f8 100644 --- a/dev/reference/remove_spectra.html +++ b/dev/reference/remove_spectra.html @@ -1,8 +1,21 @@ -Remove (raw or processed) spectra — remove_spectra • maldipickrRemove (raw or processed) spectra — remove_spectra • maldipickr + Skip to contents diff --git a/dev/reference/set_reference_spectra.html b/dev/reference/set_reference_spectra.html index 250f305..76b2ecb 100644 --- a/dev/reference/set_reference_spectra.html +++ b/dev/reference/set_reference_spectra.html @@ -1,12 +1,25 @@ Set a reference spectrum for each cluster — set_reference_spectra • maldipickrSet a reference spectrum for each cluster — set_reference_spectra • maldipickr + Skip to contents