Deploying to gh-pages from @ 53cfeb0 🚀

pkgdown.yml

@@ -2,7 +2,7 @@ pandoc: 3.1.11
 pkgdown: 2.1.1
 pkgdown_sha: ~
 articles: {}
-last_built: 2024-10-30T15:49Z
+last_built: 2024-11-07T20:15Z
 urls:
   reference: https://cobriniklab.github.io/chevreul/reference
   article: https://cobriniklab.github.io/chevreul/articles

search.json

@@ -1 +1 @@
-[{"path":"https://cobriniklab.github.io/chevreul/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2024 chevreul 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":"https://cobriniklab.github.io/chevreul/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Kevin Stachelek. Author, maintainer. Bhavana Bhat. Author.","code":""},{"path":"https://cobriniklab.github.io/chevreul/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Stachelek K, Bhat B (2024). chevreul: Tools managing SingleCellExperiment objects projects. R package version 0.1.0, https://cobriniklab.github.io/chevreul/, https://github.com/cobriniklab/chevreul.","code":"@Manual{,   title = {chevreul: Tools for managing SingleCellExperiment objects as projects},   author = {Kevin Stachelek and Bhavana Bhat},   year = {2024},   note = {R package version 0.1.0,     https://cobriniklab.github.io/chevreul/},   url = {https://github.com/cobriniklab/chevreul}, }"},{"path":"https://cobriniklab.github.io/chevreul/index.html","id":"chevreul","dir":"","previous_headings":"","what":"Tools for managing SingleCellExperiment objects as projects","title":"Tools for managing SingleCellExperiment objects as projects","text":"package includes set Shiny apps exploring single cell RNA datasets processed SingleCellExperiment demo using human gene transcript dataset Shayler et al. (link) available also convenient functions : Clustering Dimensional Reduction Raw Sequencing Data. Integration Label Transfer Louvain Clustering Range Resolutions Cell cycle state regression labeling [!WARNING] chevreul designed full-length smart-seq based single cell data. Default settings may appropriate droplet (10x) data, though can adjusted. Keep mind best practices regarding normalization, dimensional reduction, etc. using.","code":""},{"path":"https://cobriniklab.github.io/chevreul/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Tools for managing SingleCellExperiment objects as projects","text":"can install released version chevreul github :","code":""},{"path":"https://cobriniklab.github.io/chevreul/index.html","id":"install-locally-and-run-in-three-steps","dir":"","previous_headings":"Installation","what":"Install locally and run in three steps:","title":"Tools for managing SingleCellExperiment objects as projects","text":"can install chevreul locally using following steps: can also customize location app using steps:","code":"install.packages(\"devtools\") devtools::install_github(\"cobriniklab/chevreul\") library(chevreul) create_project_db() devtools::install_github(\"cobriniklab/chevreul\") library(chevreul) create_project_db(destdir = \"/your/path/to/app\")"},{"path":"https://cobriniklab.github.io/chevreul/index.html","id":"tldr","dir":"","previous_headings":"","what":"TLDR","title":"Tools for managing SingleCellExperiment objects as projects","text":"Chevreul provides single command : construct SingleCellExperiment object filter genes minimum expression ubiquity normalize scale expression several methods packaged SingleCellExperiment","code":""},{"path":"https://cobriniklab.github.io/chevreul/index.html","id":"run-clustering-on-a-single-object","dir":"","previous_headings":"","what":"Run clustering on a single object","title":"Tools for managing SingleCellExperiment objects as projects","text":"default clustering run ten different resolutions 0.2 2.0. resolution can specified providing resolution argument numeric vector.","code":"clustered_sce <- clustering_workflow(chevreul_sce,     experiment_name = \"sce_hu_trans\",     organism = \"human\" )"},{"path":"https://cobriniklab.github.io/chevreul/index.html","id":"get-a-first-look-at-a-processed-dataset-using-an-interactive-shiny-app","dir":"","previous_headings":"","what":"Get a first look at a processed dataset using an interactive shiny app","title":"Tools for managing SingleCellExperiment objects as projects","text":"","code":"minimalChevreulApp(chevreul_sce)"},{"path":"https://cobriniklab.github.io/chevreul/reference/hello.html","id":null,"dir":"Reference","previous_headings":"","what":"Hello, World! — hello","title":"Hello, World! — hello","text":"Prints 'Hello, world!'.","code":""},{"path":"https://cobriniklab.github.io/chevreul/reference/hello.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Hello, World! — hello","text":"","code":"hello()"},{"path":"https://cobriniklab.github.io/chevreul/reference/hello.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Hello, World! — hello","text":"","code":"hello() #> [1] \"Hello, world!\""}]
+[{"path":"https://cobriniklab.github.io/chevreul/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2024 chevreul 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":"https://cobriniklab.github.io/chevreul/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Kevin Stachelek. Author, maintainer. Bhavana Bhat. Author.","code":""},{"path":"https://cobriniklab.github.io/chevreul/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Stachelek K, Bhat B (2024). chevreul: Processing, plotting, interactive eda full-length scRNA-seq SingleCellExperiments. R package version 0.1.0, https://cobriniklab.github.io/chevreul/, https://github.com/cobriniklab/chevreul.","code":"@Manual{,   title = {chevreul: Processing, plotting, and interactive eda of full-length scRNA-seq as SingleCellExperiments},   author = {Kevin Stachelek and Bhavana Bhat},   year = {2024},   note = {R package version 0.1.0,     https://cobriniklab.github.io/chevreul/},   url = {https://github.com/cobriniklab/chevreul}, }"},{"path":"https://cobriniklab.github.io/chevreul/index.html","id":"chevreul","dir":"","previous_headings":"","what":"Processing, plotting, and interactive eda of full-length scRNA-seq as SingleCellExperiments","title":"Processing, plotting, and interactive eda of full-length scRNA-seq as SingleCellExperiments","text":"package includes set Shiny apps exploring single cell RNA datasets processed SingleCellExperiment demo using human gene transcript dataset Shayler et al. (link) available also convenient functions : Clustering Dimensional Reduction Raw Sequencing Data. Integration Label Transfer Louvain Clustering Range Resolutions Cell cycle state regression labeling [!WARNING] chevreul designed full-length smart-seq based single cell data. Default settings may appropriate droplet (10x) data, though can adjusted. Keep mind best practices regarding normalization, dimensional reduction, etc. using.","code":""},{"path":"https://cobriniklab.github.io/chevreul/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Processing, plotting, and interactive eda of full-length scRNA-seq as SingleCellExperiments","text":"can install released version chevreul github :","code":""},{"path":"https://cobriniklab.github.io/chevreul/index.html","id":"install-locally-and-run-in-three-steps","dir":"","previous_headings":"Installation","what":"Install locally and run in three steps:","title":"Processing, plotting, and interactive eda of full-length scRNA-seq as SingleCellExperiments","text":"can install chevreul locally using following steps: can also customize location app using steps:","code":"install.packages(\"devtools\") devtools::install_github(\"cobriniklab/chevreul\") library(chevreul) create_project_db() devtools::install_github(\"cobriniklab/chevreul\") library(chevreul) create_project_db(destdir = \"/your/path/to/app\")"},{"path":"https://cobriniklab.github.io/chevreul/index.html","id":"tldr","dir":"","previous_headings":"","what":"TLDR","title":"Processing, plotting, and interactive eda of full-length scRNA-seq as SingleCellExperiments","text":"Chevreul provides single command : construct SingleCellExperiment object filter genes minimum expression ubiquity normalize scale expression several methods packaged SingleCellExperiment","code":""},{"path":"https://cobriniklab.github.io/chevreul/index.html","id":"run-clustering-on-a-single-object","dir":"","previous_headings":"","what":"Run clustering on a single object","title":"Processing, plotting, and interactive eda of full-length scRNA-seq as SingleCellExperiments","text":"default clustering run ten different resolutions 0.2 2.0. resolution can specified providing resolution argument numeric vector.","code":"clustered_sce <- clustering_workflow(chevreul_sce,     experiment_name = \"sce_hu_trans\",     organism = \"human\" )"},{"path":"https://cobriniklab.github.io/chevreul/index.html","id":"get-a-first-look-at-a-processed-dataset-using-an-interactive-shiny-app","dir":"","previous_headings":"","what":"Get a first look at a processed dataset using an interactive shiny app","title":"Processing, plotting, and interactive eda of full-length scRNA-seq as SingleCellExperiments","text":"","code":"minimalChevreulApp(chevreul_sce)"},{"path":"https://cobriniklab.github.io/chevreul/reference/hello.html","id":null,"dir":"Reference","previous_headings":"","what":"Hello, World! — hello","title":"Hello, World! — hello","text":"Prints 'Hello, world!'.","code":""},{"path":"https://cobriniklab.github.io/chevreul/reference/hello.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Hello, World! — hello","text":"","code":"hello()"},{"path":"https://cobriniklab.github.io/chevreul/reference/hello.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Hello, World! — hello","text":"","code":"hello() #> [1] \"Hello, world!\""}]