diff --git a/pkgdown.yml b/pkgdown.yml
index 2178bd0..cc79cf5 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -3,7 +3,7 @@ pkgdown: 2.0.9
pkgdown_sha: ~
articles:
bcbioR_quick_start: bcbioR_quick_start.html
-last_built: 2024-06-25T13:09Z
+last_built: 2024-06-26T18:00Z
urls:
reference: http://bcb.io/bcbioR/reference
article: http://bcb.io/bcbioR/articles
diff --git a/search.json b/search.json
index ea312ed..2e53712 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
-[{"path":"http://bcb.io/bcbioR/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2024 bcbioR authors Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"http://bcb.io/bcbioR/articles/bcbioR_quick_start.html","id":"color-blind-friendly-palette","dir":"Articles","previous_headings":"","what":"Color blind friendly palette","title":"bcbioR quick start","text":"Compatible ggplot. get colors directly: full palette:","code":"set.seed(596) dsamp <- diamonds[sample(nrow(diamonds), 1000), ] ggplot(dsamp, aes(carat, price)) + geom_point(aes(colour = clarity)) + scale_color_cb_friendly() cb_friendly_cols(1:16) #> blue light_orange olive_green purple pink sky_blue #> \"#2759F6\" \"#FFD37D\" \"olivedrab3\" \"#9176C8\" \"#E93380\" \"#4FAEEB\" #> blue_grey forest_green yellow dark_purple dark_orange army_green #> \"#92A6BC\" \"#3C877B\" \"yellow\" \"#402999\" \"#D5392C\" \"#C3C380\" #> black dark_grey light_blue brown #> \"black\" \"darkgrey\" \"lightblue\" \"#661100\" library(hues) swatch(cb_friendly_cols(1:16))"},{"path":"http://bcb.io/bcbioR/articles/bcbioR_quick_start.html","id":"set-projects","dir":"Articles","previous_headings":"","what":"Set projects","title":"bcbioR quick start","text":"HCBC uses structured based directory organize projects. can set using: support multiple analyses type: RNAseq scRNAseq TEAseq COSMX get example code can use similar command: Use scrnaseq, teaseq cosmx get templates.","code":"tmp_dir=withr::local_tempdir() bcbio_templates(type=\"base\", outpath=tmp_dir) fs::dir_ls(tmp_dir, recurse=TRUE) #> /tmp/RtmpZ3vjwZ/file182d42b230a3/README.md #> /tmp/RtmpZ3vjwZ/file182d42b230a3/code #> /tmp/RtmpZ3vjwZ/file182d42b230a3/code/placeholder.R #> /tmp/RtmpZ3vjwZ/file182d42b230a3/data #> /tmp/RtmpZ3vjwZ/file182d42b230a3/data/readme #> /tmp/RtmpZ3vjwZ/file182d42b230a3/information.R #> /tmp/RtmpZ3vjwZ/file182d42b230a3/meta #> /tmp/RtmpZ3vjwZ/file182d42b230a3/meta/placeholder.R #> /tmp/RtmpZ3vjwZ/file182d42b230a3/scripts #> /tmp/RtmpZ3vjwZ/file182d42b230a3/scripts/placeholder #> /tmp/RtmpZ3vjwZ/file182d42b230a3/skeleton.Rmd analysis_tmp=fs::path_join(c(tmp_dir, \"reports\")) bcbio_templates(type=\"rnaseq\", outpath=analysis_tmp) fs::dir_ls(analysis_tmp, recurse=TRUE) #> /tmp/RtmpZ3vjwZ/file182d42b230a3/reports/DE #> /tmp/RtmpZ3vjwZ/file182d42b230a3/reports/DE/DEG.Rmd #> /tmp/RtmpZ3vjwZ/file182d42b230a3/reports/DE/PCA_variance_analysis.Rmd #> /tmp/RtmpZ3vjwZ/file182d42b230a3/reports/DE/load_data.R #> /tmp/RtmpZ3vjwZ/file182d42b230a3/reports/DE/params_de-example.R #> /tmp/RtmpZ3vjwZ/file182d42b230a3/reports/DE/params_de.R #> /tmp/RtmpZ3vjwZ/file182d42b230a3/reports/DE/run_markdown.R #> /tmp/RtmpZ3vjwZ/file182d42b230a3/reports/QC #> /tmp/RtmpZ3vjwZ/file182d42b230a3/reports/QC/QC.Rmd #> /tmp/RtmpZ3vjwZ/file182d42b230a3/reports/QC/QC_nf-core.Rmd #> /tmp/RtmpZ3vjwZ/file182d42b230a3/reports/QC/params_qc.R #> /tmp/RtmpZ3vjwZ/file182d42b230a3/reports/QC/params_qc_nf-core-example.R #> /tmp/RtmpZ3vjwZ/file182d42b230a3/reports/QC/params_qc_nf-core.R #> /tmp/RtmpZ3vjwZ/file182d42b230a3/reports/QC/placeholder #> /tmp/RtmpZ3vjwZ/file182d42b230a3/reports/QC/run_markdown.R #> /tmp/RtmpZ3vjwZ/file182d42b230a3/reports/README.md #> /tmp/RtmpZ3vjwZ/file182d42b230a3/reports/information.R #> /tmp/RtmpZ3vjwZ/file182d42b230a3/reports/skeleton.Rmd"},{"path":"http://bcb.io/bcbioR/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Pantano Lorena. Author, maintainer.","code":""},{"path":"http://bcb.io/bcbioR/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Lorena P (2024). bcbioR: Templates functions guide downstream analysis data interpretation. R package version 0.1.3, http://bcb.io/bcbioR/.","code":"@Manual{, title = {bcbioR: Templates and functions to guide downstream analysis and data interpretation}, author = {Pantano Lorena}, year = {2024}, note = {R package version 0.1.3}, url = {http://bcb.io/bcbioR/}, }"},{"path":"http://bcb.io/bcbioR/index.html","id":"bcbior","dir":"","previous_headings":"","what":"Templates and functions to guide downstream analysis and data interpretation","title":"Templates and functions to guide downstream analysis and data interpretation","text":"goal bcbioR create guidelines NGS data interpretation based experience Harvard Chan Bioinformatics Core everybody contributes package.","code":""},{"path":"http://bcb.io/bcbioR/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Templates and functions to guide downstream analysis and data interpretation","text":"can install development version bcbioR GitHub :","code":"# install.packages(\"devtools\") devtools::install_github(\"bcbio/bcbioR\") devtools::install_github(\"bcbio/bcbioR\",ref = \"devel\")"},{"path":"http://bcb.io/bcbioR/index.html","id":"quick-start","dir":"","previous_headings":"","what":"Quick start","title":"Templates and functions to guide downstream analysis and data interpretation","text":"Use code generate standard project name folders. code create folders files.","code":"library(bcbioR) ## basic example code # will help you to build a folder name following HCBC naming rules bcbio_set_project()"},{"path":"http://bcb.io/bcbioR/index.html","id":"set-base-project","dir":"","previous_headings":"Quick start","what":"Set base project","title":"Templates and functions to guide downstream analysis and data interpretation","text":"use setwd() set current directory place want work. bcbioR functions automatically write whatever directory set. following code pop Rmd template populate folder HCBC data structure guidelines","code":"setwd(\"/path/to/analysis/folder\") bcbio_templates(type=\"base\", outpath=\"/path/to/analysis/folder\")"},{"path":"http://bcb.io/bcbioR/index.html","id":"set-rnaseq-report-folder","dir":"","previous_headings":"Quick start","what":"Set RNAseq report folder","title":"Templates and functions to guide downstream analysis and data interpretation","text":"code populate folder HCBC data structure guidelines Rmd code: need create reports folder prior running code. create populate reports folder.","code":"bcbio_templates(type=\"rnaseq\", outpath=\"/path/to/analysis/folder/reports\")"},{"path":"http://bcb.io/bcbioR/index.html","id":"discover-more","dir":"","previous_headings":"Quick start","what":"Discover more…","title":"Templates and functions to guide downstream analysis and data interpretation","text":"Go vignette know vignette(\"bcbioR_quick_start\",package=\"bcbioR\")","code":""},{"path":[]},{"path":"http://bcb.io/bcbioR/index.html","id":"open-an-issue","dir":"","previous_headings":"How to Contribute","what":"Open an issue","title":"Templates and functions to guide downstream analysis and data interpretation","text":"find bug want new feature want add code templates","code":""},{"path":"http://bcb.io/bcbioR/index.html","id":"modify-the-code","dir":"","previous_headings":"How to Contribute","what":"Modify the code","title":"Templates and functions to guide downstream analysis and data interpretation","text":"Clone repository Make sure devel branch Create new branch git checkout -b feature1 Modify code, add commit Push GitHub new branch Create PR branch devel Assignt PR Alex best practices developing: install devtools Use usethis::use_import_from(\"stringr\",\"str_replace_all\") add new function using code.","code":""},{"path":"http://bcb.io/bcbioR/index.html","id":"contributors","dir":"","previous_headings":"How to Contribute","what":"Contributors","title":"Templates and functions to guide downstream analysis and data interpretation","text":"Lorena Pantano Alex Bartlett Emma Berdan Heather Wick James Billingsley Zhu Zhuo Elizabeth Partan","code":""},{"path":"http://bcb.io/bcbioR/reference/bcbioR-package.html","id":null,"dir":"Reference","previous_headings":"","what":"bcbioR: Templates and functions to guide downstream analysis and data interpretation — bcbioR-package","title":"bcbioR: Templates and functions to guide downstream analysis and data interpretation — bcbioR-package","text":"Collaborative code repository Harvard Chan Bioinformatics Core.","code":""},{"path":[]},{"path":"http://bcb.io/bcbioR/reference/bcbioR-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"bcbioR: Templates and functions to guide downstream analysis and data interpretation — bcbioR-package","text":"Maintainer: Pantano Lorena lorena.pantano@gmail.com","code":""},{"path":"http://bcb.io/bcbioR/reference/bcbio_nfcore_check.html","id":null,"dir":"Reference","previous_headings":"","what":"Function to check samplesheet for nf-core — bcbio_nfcore_check","title":"Function to check samplesheet for nf-core — bcbio_nfcore_check","text":"Function check samplesheet nf-core","code":""},{"path":"http://bcb.io/bcbioR/reference/bcbio_nfcore_check.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function to check samplesheet for nf-core — bcbio_nfcore_check","text":"","code":"bcbio_nfcore_check(file)"},{"path":"http://bcb.io/bcbioR/reference/bcbio_nfcore_check.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function to check samplesheet for nf-core — bcbio_nfcore_check","text":"file path CSV file nf-core","code":""},{"path":"http://bcb.io/bcbioR/reference/bcbio_nfcore_check.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Function to check samplesheet for nf-core — bcbio_nfcore_check","text":"","code":"bcbio_nfcore_check(system.file(\"extdata\", \"rnaseq_good.csv\", package = \"bcbioR\") ) #> Rows: 6 Columns: 8 #> ── Column specification ──────────────────────────────────────────────────────── #> Delimiter: \",\" #> chr (8): sample, fastq_1, fastq_2, strandedness, tissue, sex, 4_weeks, bone_... #> #> ℹ Use `spec()` to retrieve the full column specification for this data. #> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. #> All good."},{"path":"http://bcb.io/bcbioR/reference/bcbio_set_project.html","id":null,"dir":"Reference","previous_headings":"","what":"Function to help with project name used for parent folder — bcbio_set_project","title":"Function to help with project name used for parent folder — bcbio_set_project","text":"function ask user input : numeric code PI full name technology tissue organism project description","code":""},{"path":"http://bcb.io/bcbioR/reference/bcbio_set_project.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function to help with project name used for parent folder — bcbio_set_project","text":"","code":"bcbio_set_project()"},{"path":"http://bcb.io/bcbioR/reference/bcbio_set_project.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Function to help with project name used for parent folder — bcbio_set_project","text":"string list hbc_code, project folder name","code":""},{"path":"http://bcb.io/bcbioR/reference/bcbio_set_project.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Function to help with project name used for parent folder — bcbio_set_project","text":"removes special character _. output guideline folder used can .","code":""},{"path":"http://bcb.io/bcbioR/reference/bcbio_templates.html","id":null,"dir":"Reference","previous_headings":"","what":"Function to help deploy analysis folder inside a project folder — bcbio_templates","title":"Function to help deploy analysis folder inside a project folder — bcbio_templates","text":"function contains Rmd, R, md, files help structure analysis following HCBC best-practices. rnaseq, deploy: QC DE Rmd additional files help facilitate analysis needed.","code":""},{"path":"http://bcb.io/bcbioR/reference/bcbio_templates.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function to help deploy analysis folder inside a project folder — bcbio_templates","text":"","code":"bcbio_templates(type = \"rnaseq\", outpath)"},{"path":"http://bcb.io/bcbioR/reference/bcbio_templates.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function to help deploy analysis folder inside a project folder — bcbio_templates","text":"type string indicating type analysis, supported: base rnaseq, scrnaseq, teaseq cosmx outpath string path indicating copy files ","code":""},{"path":"http://bcb.io/bcbioR/reference/bcbio_templates.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Function to help deploy analysis folder inside a project folder — bcbio_templates","text":"Normally helper files inside report folder inside project folder.","code":""},{"path":"http://bcb.io/bcbioR/reference/bcbio_templates.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Function to help deploy analysis folder inside a project folder — bcbio_templates","text":"","code":"if (FALSE) { bcbio_templates(\"rnaseq\", \"path_to_projects/project1/reports\") }"},{"path":"http://bcb.io/bcbioR/reference/bcbio_vsd_data.html","id":null,"dir":"Reference","previous_headings":"","what":"varianceStabilizingTransformation Object from Test Data — bcbio_vsd_data","title":"varianceStabilizingTransformation Object from Test Data — bcbio_vsd_data","text":"example output varianceStabilizingTransformation show different visualization code","code":""},{"path":"http://bcb.io/bcbioR/reference/bcbio_vsd_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"varianceStabilizingTransformation Object from Test Data — bcbio_vsd_data","text":"","code":"bcbio_vsd_data"},{"path":[]},{"path":"http://bcb.io/bcbioR/reference/bcbio_vsd_data.html","id":"bcbio-vsd-data","dir":"Reference","previous_headings":"","what":"bcbio_vsd_data","title":"varianceStabilizingTransformation Object from Test Data — bcbio_vsd_data","text":"VSD object DESeq2 data","code":""},{"path":"http://bcb.io/bcbioR/reference/cb_friendly_colors.html","id":null,"dir":"Reference","previous_headings":"","what":"list of colorblind-friendly colors, developed by James and client — cb_friendly_colors","title":"list of colorblind-friendly colors, developed by James and client — cb_friendly_colors","text":"list colorblind-friendly colors, developed James client","code":""},{"path":"http://bcb.io/bcbioR/reference/cb_friendly_colors.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"list of colorblind-friendly colors, developed by James and client — cb_friendly_colors","text":"","code":"cb_friendly_colors"},{"path":"http://bcb.io/bcbioR/reference/cb_friendly_colors.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"list of colorblind-friendly colors, developed by James and client — cb_friendly_colors","text":"object class character length 17.","code":""},{"path":"http://bcb.io/bcbioR/reference/cb_friendly_cols.html","id":null,"dir":"Reference","previous_headings":"","what":"fetch color from list by name — cb_friendly_cols","title":"fetch color from list by name — cb_friendly_cols","text":"fetch color list name","code":""},{"path":"http://bcb.io/bcbioR/reference/cb_friendly_cols.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"fetch color from list by name — cb_friendly_cols","text":"","code":"cb_friendly_cols(...)"},{"path":"http://bcb.io/bcbioR/reference/cb_friendly_cols.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"fetch color from list by name — cb_friendly_cols","text":"... list color names","code":""},{"path":"http://bcb.io/bcbioR/reference/cb_friendly_pal.html","id":null,"dir":"Reference","previous_headings":"","what":"access cb friendly palette by name, reversing if necessary — cb_friendly_pal","title":"access cb friendly palette by name, reversing if necessary — cb_friendly_pal","text":"access cb friendly palette name, reversing necessary","code":""},{"path":"http://bcb.io/bcbioR/reference/cb_friendly_pal.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"access cb friendly palette by name, reversing if necessary — cb_friendly_pal","text":"","code":"cb_friendly_pal(palette = \"main\", reverse = F, ...)"},{"path":"http://bcb.io/bcbioR/reference/cb_friendly_pal.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"access cb friendly palette by name, reversing if necessary — cb_friendly_pal","text":"palette name palette returned reverse boolean, reverse order colors palette ... pass ggplot","code":""},{"path":"http://bcb.io/bcbioR/reference/cb_friendly_palettes.html","id":null,"dir":"Reference","previous_headings":"","what":"define main colorblind-friendly palette as well as sub-palettes — cb_friendly_palettes","title":"define main colorblind-friendly palette as well as sub-palettes — cb_friendly_palettes","text":"define main colorblind-friendly palette well sub-palettes","code":""},{"path":"http://bcb.io/bcbioR/reference/cb_friendly_palettes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"define main colorblind-friendly palette as well as sub-palettes — cb_friendly_palettes","text":"","code":"cb_friendly_palettes"},{"path":"http://bcb.io/bcbioR/reference/cb_friendly_palettes.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"define main colorblind-friendly palette as well as sub-palettes — cb_friendly_palettes","text":"object class list length 5.","code":""},{"path":"http://bcb.io/bcbioR/reference/list_cb_friendly_cols.html","id":null,"dir":"Reference","previous_headings":"","what":"list cb friendly colors — list_cb_friendly_cols","title":"list cb friendly colors — list_cb_friendly_cols","text":"list cb friendly colors","code":""},{"path":"http://bcb.io/bcbioR/reference/list_cb_friendly_cols.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"list cb friendly colors — list_cb_friendly_cols","text":"","code":"list_cb_friendly_cols()"},{"path":"http://bcb.io/bcbioR/reference/scale_color_cb_friendly.html","id":null,"dir":"Reference","previous_headings":"","what":"use cb friendly colors as color aesthetic with ggplot — scale_color_cb_friendly","title":"use cb friendly colors as color aesthetic with ggplot — scale_color_cb_friendly","text":"use cb friendly colors color aesthetic ggplot","code":""},{"path":"http://bcb.io/bcbioR/reference/scale_color_cb_friendly.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"use cb friendly colors as color aesthetic with ggplot — scale_color_cb_friendly","text":"","code":"scale_color_cb_friendly( palette = \"main\", discrete = TRUE, reverse = FALSE, ... )"},{"path":"http://bcb.io/bcbioR/reference/scale_color_cb_friendly.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"use cb friendly colors as color aesthetic with ggplot — scale_color_cb_friendly","text":"palette name palette returned discrete boolean, whether make palette discretely divided colors continuous reverse boolean, reverse order colors palette ... pass ggplot","code":""},{"path":"http://bcb.io/bcbioR/reference/scale_fill_cb_friendly.html","id":null,"dir":"Reference","previous_headings":"","what":"use cb friendly colors as fill aesthetic with ggplot — scale_fill_cb_friendly","title":"use cb friendly colors as fill aesthetic with ggplot — scale_fill_cb_friendly","text":"use cb friendly colors fill aesthetic ggplot","code":""},{"path":"http://bcb.io/bcbioR/reference/scale_fill_cb_friendly.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"use cb friendly colors as fill aesthetic with ggplot — scale_fill_cb_friendly","text":"","code":"scale_fill_cb_friendly(palette = \"main\", discrete = TRUE, reverse = FALSE, ...)"},{"path":"http://bcb.io/bcbioR/reference/scale_fill_cb_friendly.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"use cb friendly colors as fill aesthetic with ggplot — scale_fill_cb_friendly","text":"palette name palette returned discrete boolean, whether make palette discretely divided colors continuous reverse boolean, reverse order colors palette ... pass ggplot","code":""},{"path":"http://bcb.io/bcbioR/news/index.html","id":"bcbior-013","dir":"Changelog","previous_headings":"","what":"bcbioR 0.1.3","title":"bcbioR 0.1.3","text":"Add combatseq Add draft templates TEAseq, COSMX Adapt templates nf-core rnaseq Fix sample start number Fix rRNA rate missing Add sample plots QC Add function check nfcore samplesheet Add PCA variance analysis Minor details fixed QC RNAseq report Correct metric rRNA tRNA","code":""},{"path":"http://bcb.io/bcbioR/news/index.html","id":"bcbior-011","dir":"Changelog","previous_headings":"","what":"bcbioR 0.1.1","title":"bcbioR 0.1.1","text":"Add page github Make CHECK pass Add vignette","code":""}]
+[{"path":"http://bcb.io/bcbioR/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2024 bcbioR authors Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"http://bcb.io/bcbioR/articles/bcbioR_quick_start.html","id":"color-blind-friendly-palette","dir":"Articles","previous_headings":"","what":"Color blind friendly palette","title":"bcbioR quick start","text":"Compatible ggplot. get colors directly: full palette:","code":"set.seed(596) dsamp <- diamonds[sample(nrow(diamonds), 1000), ] ggplot(dsamp, aes(carat, price)) + geom_point(aes(colour = clarity)) + scale_color_cb_friendly() cb_friendly_cols(1:16) #> blue light_orange olive_green purple pink sky_blue #> \"#2759F6\" \"#FFD37D\" \"olivedrab3\" \"#9176C8\" \"#E93380\" \"#4FAEEB\" #> blue_grey forest_green yellow dark_purple dark_orange army_green #> \"#92A6BC\" \"#3C877B\" \"yellow\" \"#402999\" \"#D5392C\" \"#C3C380\" #> black dark_grey light_blue brown #> \"black\" \"darkgrey\" \"lightblue\" \"#661100\" library(hues) swatch(cb_friendly_cols(1:16))"},{"path":"http://bcb.io/bcbioR/articles/bcbioR_quick_start.html","id":"set-projects","dir":"Articles","previous_headings":"","what":"Set projects","title":"bcbioR quick start","text":"HCBC uses structured based directory organize projects. can set using: support multiple analyses type: RNAseq scRNAseq TEAseq COSMX get example code can use similar command: Use scrnaseq, teaseq cosmx get templates.","code":"tmp_dir=withr::local_tempdir() bcbio_templates(type=\"base\", outpath=tmp_dir) fs::dir_ls(tmp_dir, recurse=TRUE) #> /tmp/Rtmp3ZTsjG/file17d61049278d/README.md #> /tmp/Rtmp3ZTsjG/file17d61049278d/code #> /tmp/Rtmp3ZTsjG/file17d61049278d/code/placeholder.R #> /tmp/Rtmp3ZTsjG/file17d61049278d/data #> /tmp/Rtmp3ZTsjG/file17d61049278d/data/readme #> /tmp/Rtmp3ZTsjG/file17d61049278d/information.R #> /tmp/Rtmp3ZTsjG/file17d61049278d/meta #> /tmp/Rtmp3ZTsjG/file17d61049278d/meta/placeholder.R #> /tmp/Rtmp3ZTsjG/file17d61049278d/scripts #> /tmp/Rtmp3ZTsjG/file17d61049278d/scripts/placeholder #> /tmp/Rtmp3ZTsjG/file17d61049278d/skeleton.Rmd analysis_tmp=fs::path_join(c(tmp_dir, \"reports\")) bcbio_templates(type=\"rnaseq\", outpath=analysis_tmp) fs::dir_ls(analysis_tmp, recurse=TRUE) #> /tmp/Rtmp3ZTsjG/file17d61049278d/reports/DE #> /tmp/Rtmp3ZTsjG/file17d61049278d/reports/DE/DEG.Rmd #> /tmp/Rtmp3ZTsjG/file17d61049278d/reports/DE/PCA_variance_analysis.Rmd #> /tmp/Rtmp3ZTsjG/file17d61049278d/reports/DE/load_data.R #> /tmp/Rtmp3ZTsjG/file17d61049278d/reports/DE/params_de-example.R #> /tmp/Rtmp3ZTsjG/file17d61049278d/reports/DE/params_de.R #> /tmp/Rtmp3ZTsjG/file17d61049278d/reports/DE/run_markdown.R #> /tmp/Rtmp3ZTsjG/file17d61049278d/reports/QC #> /tmp/Rtmp3ZTsjG/file17d61049278d/reports/QC/QC.Rmd #> /tmp/Rtmp3ZTsjG/file17d61049278d/reports/QC/QC_nf-core.Rmd #> /tmp/Rtmp3ZTsjG/file17d61049278d/reports/QC/params_qc.R #> /tmp/Rtmp3ZTsjG/file17d61049278d/reports/QC/params_qc_nf-core-example.R #> /tmp/Rtmp3ZTsjG/file17d61049278d/reports/QC/params_qc_nf-core.R #> /tmp/Rtmp3ZTsjG/file17d61049278d/reports/QC/placeholder #> /tmp/Rtmp3ZTsjG/file17d61049278d/reports/QC/run_markdown.R #> /tmp/Rtmp3ZTsjG/file17d61049278d/reports/README.md #> /tmp/Rtmp3ZTsjG/file17d61049278d/reports/information.R #> /tmp/Rtmp3ZTsjG/file17d61049278d/reports/skeleton.Rmd"},{"path":"http://bcb.io/bcbioR/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Pantano Lorena. Author, maintainer.","code":""},{"path":"http://bcb.io/bcbioR/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Lorena P (2024). bcbioR: Templates functions guide downstream analysis data interpretation. R package version 0.1.3, http://bcb.io/bcbioR/.","code":"@Manual{, title = {bcbioR: Templates and functions to guide downstream analysis and data interpretation}, author = {Pantano Lorena}, year = {2024}, note = {R package version 0.1.3}, url = {http://bcb.io/bcbioR/}, }"},{"path":"http://bcb.io/bcbioR/index.html","id":"bcbior","dir":"","previous_headings":"","what":"Templates and functions to guide downstream analysis and data interpretation","title":"Templates and functions to guide downstream analysis and data interpretation","text":"goal bcbioR create guidelines NGS data interpretation based experience Harvard Chan Bioinformatics Core everybody contributes package.","code":""},{"path":"http://bcb.io/bcbioR/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Templates and functions to guide downstream analysis and data interpretation","text":"can install development version bcbioR GitHub :","code":"# install.packages(\"devtools\") devtools::install_github(\"bcbio/bcbioR\") devtools::install_github(\"bcbio/bcbioR\",ref = \"devel\")"},{"path":"http://bcb.io/bcbioR/index.html","id":"quick-start","dir":"","previous_headings":"","what":"Quick start","title":"Templates and functions to guide downstream analysis and data interpretation","text":"Use code generate standard project name folders. code create folders files.","code":"library(bcbioR) ## basic example code # will help you to build a folder name following HCBC naming rules bcbio_set_project()"},{"path":"http://bcb.io/bcbioR/index.html","id":"set-base-project","dir":"","previous_headings":"Quick start","what":"Set base project","title":"Templates and functions to guide downstream analysis and data interpretation","text":"use setwd() set current directory place want work. bcbioR functions automatically write whatever directory set. following code pop Rmd template populate folder HCBC data structure guidelines","code":"setwd(\"/path/to/analysis/folder\") bcbio_templates(type=\"base\", outpath=\"/path/to/analysis/folder\")"},{"path":"http://bcb.io/bcbioR/index.html","id":"set-rnaseq-report-folder","dir":"","previous_headings":"Quick start","what":"Set RNAseq report folder","title":"Templates and functions to guide downstream analysis and data interpretation","text":"code populate folder HCBC data structure guidelines Rmd code: need create reports folder prior running code. create populate reports folder.","code":"bcbio_templates(type=\"rnaseq\", outpath=\"/path/to/analysis/folder/reports\")"},{"path":"http://bcb.io/bcbioR/index.html","id":"discover-more","dir":"","previous_headings":"Quick start","what":"Discover more…","title":"Templates and functions to guide downstream analysis and data interpretation","text":"Go vignette know vignette(\"bcbioR_quick_start\",package=\"bcbioR\")","code":""},{"path":[]},{"path":"http://bcb.io/bcbioR/index.html","id":"open-an-issue","dir":"","previous_headings":"How to Contribute","what":"Open an issue","title":"Templates and functions to guide downstream analysis and data interpretation","text":"find bug want new feature want add code templates","code":""},{"path":"http://bcb.io/bcbioR/index.html","id":"modify-the-code","dir":"","previous_headings":"How to Contribute","what":"Modify the code","title":"Templates and functions to guide downstream analysis and data interpretation","text":"Clone repository Make sure devel branch Create new branch git checkout -b feature1 Modify code, add commit Push GitHub new branch Create PR branch devel Assignt PR Alex best practices developing: install devtools Use usethis::use_import_from(\"stringr\",\"str_replace_all\") add new function using code.","code":""},{"path":"http://bcb.io/bcbioR/index.html","id":"contributors","dir":"","previous_headings":"How to Contribute","what":"Contributors","title":"Templates and functions to guide downstream analysis and data interpretation","text":"Lorena Pantano Alex Bartlett Emma Berdan Heather Wick James Billingsley Zhu Zhuo Elizabeth Partan","code":""},{"path":"http://bcb.io/bcbioR/reference/bcbioR-package.html","id":null,"dir":"Reference","previous_headings":"","what":"bcbioR: Templates and functions to guide downstream analysis and data interpretation — bcbioR-package","title":"bcbioR: Templates and functions to guide downstream analysis and data interpretation — bcbioR-package","text":"Collaborative code repository Harvard Chan Bioinformatics Core.","code":""},{"path":[]},{"path":"http://bcb.io/bcbioR/reference/bcbioR-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"bcbioR: Templates and functions to guide downstream analysis and data interpretation — bcbioR-package","text":"Maintainer: Pantano Lorena lorena.pantano@gmail.com","code":""},{"path":"http://bcb.io/bcbioR/reference/bcbio_nfcore_check.html","id":null,"dir":"Reference","previous_headings":"","what":"Function to check samplesheet for nf-core — bcbio_nfcore_check","title":"Function to check samplesheet for nf-core — bcbio_nfcore_check","text":"Function check samplesheet nf-core","code":""},{"path":"http://bcb.io/bcbioR/reference/bcbio_nfcore_check.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function to check samplesheet for nf-core — bcbio_nfcore_check","text":"","code":"bcbio_nfcore_check(file)"},{"path":"http://bcb.io/bcbioR/reference/bcbio_nfcore_check.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function to check samplesheet for nf-core — bcbio_nfcore_check","text":"file path CSV file nf-core","code":""},{"path":"http://bcb.io/bcbioR/reference/bcbio_nfcore_check.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Function to check samplesheet for nf-core — bcbio_nfcore_check","text":"","code":"bcbio_nfcore_check(system.file(\"extdata\", \"rnaseq_good.csv\", package = \"bcbioR\") ) #> Rows: 6 Columns: 8 #> ── Column specification ──────────────────────────────────────────────────────── #> Delimiter: \",\" #> chr (8): sample, fastq_1, fastq_2, strandedness, tissue, sex, 4_weeks, bone_... #> #> ℹ Use `spec()` to retrieve the full column specification for this data. #> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. #> All good."},{"path":"http://bcb.io/bcbioR/reference/bcbio_set_project.html","id":null,"dir":"Reference","previous_headings":"","what":"Function to help with project name used for parent folder — bcbio_set_project","title":"Function to help with project name used for parent folder — bcbio_set_project","text":"function ask user input : numeric code PI full name technology tissue organism project description","code":""},{"path":"http://bcb.io/bcbioR/reference/bcbio_set_project.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function to help with project name used for parent folder — bcbio_set_project","text":"","code":"bcbio_set_project()"},{"path":"http://bcb.io/bcbioR/reference/bcbio_set_project.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Function to help with project name used for parent folder — bcbio_set_project","text":"string list hbc_code, project folder name","code":""},{"path":"http://bcb.io/bcbioR/reference/bcbio_set_project.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Function to help with project name used for parent folder — bcbio_set_project","text":"removes special character _. output guideline folder used can .","code":""},{"path":"http://bcb.io/bcbioR/reference/bcbio_templates.html","id":null,"dir":"Reference","previous_headings":"","what":"Function to help deploy analysis folder inside a project folder — bcbio_templates","title":"Function to help deploy analysis folder inside a project folder — bcbio_templates","text":"function contains Rmd, R, md, files help structure analysis following HCBC best-practices. rnaseq, deploy: QC DE Rmd additional files help facilitate analysis needed.","code":""},{"path":"http://bcb.io/bcbioR/reference/bcbio_templates.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function to help deploy analysis folder inside a project folder — bcbio_templates","text":"","code":"bcbio_templates(type = \"rnaseq\", outpath)"},{"path":"http://bcb.io/bcbioR/reference/bcbio_templates.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function to help deploy analysis folder inside a project folder — bcbio_templates","text":"type string indicating type analysis, supported: base rnaseq, scrnaseq, teaseq cosmx outpath string path indicating copy files ","code":""},{"path":"http://bcb.io/bcbioR/reference/bcbio_templates.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Function to help deploy analysis folder inside a project folder — bcbio_templates","text":"Normally helper files inside report folder inside project folder.","code":""},{"path":"http://bcb.io/bcbioR/reference/bcbio_templates.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Function to help deploy analysis folder inside a project folder — bcbio_templates","text":"","code":"if (FALSE) { bcbio_templates(\"rnaseq\", \"path_to_projects/project1/reports\") }"},{"path":"http://bcb.io/bcbioR/reference/bcbio_vsd_data.html","id":null,"dir":"Reference","previous_headings":"","what":"varianceStabilizingTransformation Object from Test Data — bcbio_vsd_data","title":"varianceStabilizingTransformation Object from Test Data — bcbio_vsd_data","text":"example output varianceStabilizingTransformation show different visualization code","code":""},{"path":"http://bcb.io/bcbioR/reference/bcbio_vsd_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"varianceStabilizingTransformation Object from Test Data — bcbio_vsd_data","text":"","code":"bcbio_vsd_data"},{"path":[]},{"path":"http://bcb.io/bcbioR/reference/bcbio_vsd_data.html","id":"bcbio-vsd-data","dir":"Reference","previous_headings":"","what":"bcbio_vsd_data","title":"varianceStabilizingTransformation Object from Test Data — bcbio_vsd_data","text":"VSD object DESeq2 data","code":""},{"path":"http://bcb.io/bcbioR/reference/cb_friendly_colors.html","id":null,"dir":"Reference","previous_headings":"","what":"list of colorblind-friendly colors, developed by James and client — cb_friendly_colors","title":"list of colorblind-friendly colors, developed by James and client — cb_friendly_colors","text":"list colorblind-friendly colors, developed James client","code":""},{"path":"http://bcb.io/bcbioR/reference/cb_friendly_colors.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"list of colorblind-friendly colors, developed by James and client — cb_friendly_colors","text":"","code":"cb_friendly_colors"},{"path":"http://bcb.io/bcbioR/reference/cb_friendly_colors.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"list of colorblind-friendly colors, developed by James and client — cb_friendly_colors","text":"object class character length 17.","code":""},{"path":"http://bcb.io/bcbioR/reference/cb_friendly_cols.html","id":null,"dir":"Reference","previous_headings":"","what":"fetch color from list by name — cb_friendly_cols","title":"fetch color from list by name — cb_friendly_cols","text":"fetch color list name","code":""},{"path":"http://bcb.io/bcbioR/reference/cb_friendly_cols.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"fetch color from list by name — cb_friendly_cols","text":"","code":"cb_friendly_cols(...)"},{"path":"http://bcb.io/bcbioR/reference/cb_friendly_cols.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"fetch color from list by name — cb_friendly_cols","text":"... list color names","code":""},{"path":"http://bcb.io/bcbioR/reference/cb_friendly_pal.html","id":null,"dir":"Reference","previous_headings":"","what":"access cb friendly palette by name, reversing if necessary — cb_friendly_pal","title":"access cb friendly palette by name, reversing if necessary — cb_friendly_pal","text":"access cb friendly palette name, reversing necessary","code":""},{"path":"http://bcb.io/bcbioR/reference/cb_friendly_pal.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"access cb friendly palette by name, reversing if necessary — cb_friendly_pal","text":"","code":"cb_friendly_pal(palette = \"main\", reverse = F, ...)"},{"path":"http://bcb.io/bcbioR/reference/cb_friendly_pal.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"access cb friendly palette by name, reversing if necessary — cb_friendly_pal","text":"palette name palette returned reverse boolean, reverse order colors palette ... pass ggplot","code":""},{"path":"http://bcb.io/bcbioR/reference/cb_friendly_palettes.html","id":null,"dir":"Reference","previous_headings":"","what":"define main colorblind-friendly palette as well as sub-palettes — cb_friendly_palettes","title":"define main colorblind-friendly palette as well as sub-palettes — cb_friendly_palettes","text":"define main colorblind-friendly palette well sub-palettes","code":""},{"path":"http://bcb.io/bcbioR/reference/cb_friendly_palettes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"define main colorblind-friendly palette as well as sub-palettes — cb_friendly_palettes","text":"","code":"cb_friendly_palettes"},{"path":"http://bcb.io/bcbioR/reference/cb_friendly_palettes.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"define main colorblind-friendly palette as well as sub-palettes — cb_friendly_palettes","text":"object class list length 5.","code":""},{"path":"http://bcb.io/bcbioR/reference/list_cb_friendly_cols.html","id":null,"dir":"Reference","previous_headings":"","what":"list cb friendly colors — list_cb_friendly_cols","title":"list cb friendly colors — list_cb_friendly_cols","text":"list cb friendly 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)"},{"path":"http://bcb.io/bcbioR/reference/scale_color_cb_friendly.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"use cb friendly colors as color aesthetic with ggplot — scale_color_cb_friendly","text":"palette name palette returned discrete boolean, whether make palette discretely divided colors continuous reverse boolean, reverse order colors palette ... pass ggplot","code":""},{"path":"http://bcb.io/bcbioR/reference/scale_fill_cb_friendly.html","id":null,"dir":"Reference","previous_headings":"","what":"use cb friendly colors as fill aesthetic with ggplot — scale_fill_cb_friendly","title":"use cb friendly colors as fill aesthetic with ggplot — scale_fill_cb_friendly","text":"use cb friendly colors fill aesthetic ggplot","code":""},{"path":"http://bcb.io/bcbioR/reference/scale_fill_cb_friendly.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"use cb friendly colors as fill aesthetic with ggplot — scale_fill_cb_friendly","text":"","code":"scale_fill_cb_friendly(palette = \"main\", discrete = TRUE, reverse = FALSE, ...)"},{"path":"http://bcb.io/bcbioR/reference/scale_fill_cb_friendly.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"use cb friendly colors as fill aesthetic with ggplot — scale_fill_cb_friendly","text":"palette name palette returned discrete boolean, whether make palette discretely divided colors continuous reverse boolean, reverse order colors palette ... pass ggplot","code":""},{"path":"http://bcb.io/bcbioR/news/index.html","id":"bcbior-013","dir":"Changelog","previous_headings":"","what":"bcbioR 0.1.3","title":"bcbioR 0.1.3","text":"fix duplicated gene names Add combatseq Add draft templates TEAseq, COSMX Adapt templates nf-core rnaseq Fix sample start number Fix rRNA rate missing Add sample plots QC Add function check nfcore samplesheet Add PCA variance analysis Minor details fixed QC RNAseq report Correct metric rRNA tRNA","code":""},{"path":"http://bcb.io/bcbioR/news/index.html","id":"bcbior-011","dir":"Changelog","previous_headings":"","what":"bcbioR 0.1.1","title":"bcbioR 0.1.1","text":"Add page github Make CHECK pass Add vignette","code":""}]