Initialize

.gitignore

@@ -0,0 +1,7 @@
+.Rproj.user
+.Rhistory
+.RData
+_publish.R
+_book
+_bookdown_files
+rsconnect

.travis.yml

@@ -0,0 +1,11 @@
+language: r
+cache: packages
+pandoc_version: 1.19.2.1
+
+before_script:
+  - chmod +x ./_build.sh
+  - chmod +x ./_deploy.sh
+
+script:
+  - ./_build.sh
+  - ./_deploy.sh

01-config.Rmd

@@ -0,0 +1,8 @@
+# (PART) Configuration {-} 
+
+# Configure environment 
+
+## Set up a virtual machine
+## Define variables 
+## Create directories
+

02-config-for-image-analysis.Rmd

@@ -0,0 +1,4 @@
+# (PART) Images to measurements  {-}
+# Configure tools to process images
+## Download software
+## Setup Distributed CellProfiler

03-setup-pipelines.Rmd

@@ -0,0 +1,6 @@
+# Setup pipelines and images
+## Get CellProfiler pipelines
+## Specify pipeline set
+## Prepare images
+## Create list of plates
+## Create LoadData CSVs

04-setup-jobs.Rmd

@@ -0,0 +1,4 @@
+# Setup jobs 
+## Illumination correction 
+## Quality control 
+## Analysis 

05-run-jobs.Rmd

@@ -0,0 +1,10 @@
+# Run jobs
+## Illumination correction
+### Single node
+### DCP
+## Quality control
+### Process QC results into a database for CPA
+## Analysis 
+### Single node
+### DCP
+

06-config-for-profiling.Rmd

@@ -0,0 +1,3 @@
+# (PART) Measurements to profiles  {-}
+# Configure tools to create profiles
+## Download software

07-create-profiles.Rmd

@@ -0,0 +1,11 @@
+# Create profiles
+## Create database backend
+## Annotate
+## Normalize
+## Selection variables
+## Aggregate perturbations
+## Audit
+## Convert to other formats
+## Upload data
+### Sync to S3
+### Sync from S3 to another machine

08-appendix.Rmd

@@ -0,0 +1,3 @@
+# (APPENDIX) Appendix {-} 
+# Appendix A
+## Directory structure

DESCRIPTION

@@ -0,0 +1,6 @@
+Package: placeholder
+Type: Book
+Title: Does not matter.
+Version: 0.0.1
+Imports: bookdown
+Remotes: rstudio/bookdown

LICENSE

@@ -0,0 +1,117 @@
+CC0 1.0 Universal
+
+Statement of Purpose
+
+The laws of most jurisdictions throughout the world automatically confer
+exclusive Copyright and Related Rights (defined below) upon the creator and
+subsequent owner(s) (each and all, an "owner") of an original work of
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+Certain owners wish to permanently relinquish those rights to a Work for the
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+contribute to the Commons to promote the ideal of a free culture and the
+further production of creative, cultural and scientific works, or to gain
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+For these and/or other purposes and motivations, and without any expectation
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+1. Copyright and Related Rights. A Work made available under CC0 may be
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+  vi. database rights (such as those arising under Directive 96/9/EC of the
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+  vii. other similar, equivalent or corresponding rights throughout the world
+  based on applicable law or treaty, and any national implementations thereof.
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+2. Waiver. To the greatest extent permitted by, but not in contravention of,
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+any other legal or equitable action to disrupt the quiet enjoyment of the Work
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+3. Public License Fallback. Should any part of the Waiver for any reason be
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+Affirmer's express Statement of Purpose. In addition, to the extent the Waiver
+is so judged Affirmer hereby grants to each affected person a royalty-free,
+non transferable, non sublicensable, non exclusive, irrevocable and
+unconditional license to exercise Affirmer's Copyright and Related Rights in
+the Work (i) in all territories worldwide, (ii) for the maximum duration
+provided by applicable law or treaty (including future time extensions), (iii)
+in any current or future medium and for any number of copies, and (iv) for any
+purpose whatsoever, including without limitation commercial, advertising or
+promotional purposes (the "License"). The License shall be deemed effective as
+of the date CC0 was applied by Affirmer to the Work. Should any part of the
+License for any reason be judged legally invalid or ineffective under
+applicable law, such partial invalidity or ineffectiveness shall not
+invalidate the remainder of the License, and in such case Affirmer hereby
+affirms that he or she will not (i) exercise any of his or her remaining
+Copyright and Related Rights in the Work or (ii) assert any associated claims
+and causes of action with respect to the Work, in either case contrary to
+Affirmer's express Statement of Purpose.
+
+4. Limitations and Disclaimers.
+
+  a. No trademark or patent rights held by Affirmer are waived, abandoned,
+  surrendered, licensed or otherwise affected by this document.
+
+  b. Affirmer offers the Work as-is and makes no representations or warranties
+  of any kind concerning the Work, express, implied, statutory or otherwise,
+  including without limitation warranties of title, merchantability, fitness
+  for a particular purpose, non infringement, or the absence of latent or
+  other defects, accuracy, or the present or absence of errors, whether or not
+  discoverable, all to the greatest extent permissible under applicable law.
+
+  c. Affirmer disclaims responsibility for clearing rights of other persons
+  that may apply to the Work or any use thereof, including without limitation
+  any person's Copyright and Related Rights in the Work. Further, Affirmer
+  disclaims responsibility for obtaining any necessary consents, permissions
+  or other rights required for any use of the Work.
+
+  d. Affirmer understands and acknowledges that Creative Commons is not a
+  party to this document and has no duty or obligation with respect to this
+  CC0 or use of the Work.
+
+For more information, please see
+<http://creativecommons.org/publicdomain/zero/1.0/>
+

README.md

@@ -0,0 +1,3 @@
+This is a minimal example of a book based on R Markdown and **bookdown** (https://github.com/rstudio/bookdown). Please see the page "[Get Started](https://bookdown.org/yihui/bookdown/get-started.html)" at https://bookdown.org/yihui/bookdown/ for how to compile this example.
+
+You can find the preview of this example at https://bookdown.org/yihui/bookdown-demo/

_bookdown.yml

@@ -0,0 +1,5 @@
+book_filename: "bookdown-demo"
+language:
+  ui:
+    chapter_name: "Chapter "
+delete_merged_file: true

_build.sh

@@ -0,0 +1,3 @@
+#!/bin/sh
+
+Rscript -e "bookdown::render_book('index.Rmd', 'bookdown::gitbook')"

_deploy.sh

@@ -0,0 +1,16 @@
+#!/bin/sh
+
+set -e
+
+[ -z "${GITHUB_PAT}" ] && exit 0
+[ "${TRAVIS_BRANCH}" != "master" ] && exit 0
+
+git config --global user.email "[email protected]"
+git config --global user.name "Shantanu Singh"
+
+git clone -b gh-pages https://${GITHUB_PAT}@github.com/${TRAVIS_REPO_SLUG}.git book-output
+cd book-output
+cp -r ../_book/* ./
+git add --all *
+git commit -m"Update the book" || true
+git push -q origin gh-pages

_output.yml

@@ -0,0 +1,17 @@
+bookdown::gitbook:
+  css: style.css
+  config:
+    toc:
+      before: |
+        <li><a href="./">Image-based Profiling Handbook</a></li>
+      after: |
+        <li><a href="https://github.com/rstudio/bookdown" target="blank">Published with bookdown</a></li>
+    edit: https://github.com/cytomining/profiling-handbook/edit/master/%s
+    download: ["pdf", "epub"]
+bookdown::pdf_book:
+  includes:
+    in_header: preamble.tex
+  latex_engine: xelatex
+  citation_package: natbib
+  keep_tex: yes
+bookdown::epub_book: default

book.bib

@@ -0,0 +1,10 @@
+@Book{xie2015,
+  title = {Dynamic Documents with {R} and knitr},
+  author = {Yihui Xie},
+  publisher = {Chapman and Hall/CRC},
+  address = {Boca Raton, Florida},
+  year = {2015},
+  edition = {2nd},
+  note = {ISBN 978-1498716963},
+  url = {http://yihui.name/knitr/},
+}

index.Rmd

@@ -0,0 +1,14 @@
+--- 
+title: "Image-based Profiling Handbook"
+author: "Tim Becker, Beth Cimini, Shantanu Singh"
+date: "`r Sys.Date()`"
+site: bookdown::bookdown_site
+output: bookdown::gitbook
+documentclass: book
+bibliography: [book.bib, packages.bib]
+biblio-style: apalike
+link-citations: yes
+github-repo: rstudio/bookdown-demo
+description: "This is a handbook for processing image-based profiling datasets using CellProfiler and cytominer"
+---
+

packages.bib

@@ -0,0 +1,29 @@
+@Manual{R-base,
+  title = {R: A Language and Environment for Statistical Computing},
+  author = {{R Core Team}},
+  organization = {R Foundation for Statistical Computing},
+  address = {Vienna, Austria},
+  year = {2018},
+  url = {https://www.R-project.org/},
+}
+@Manual{R-bookdown,
+  title = {bookdown: Authoring Books and Technical Documents with R Markdown},
+  author = {Yihui Xie},
+  note = {R package version 0.7.8},
+  url = {https://github.com/rstudio/bookdown},
+  year = {2018},
+}
+@Manual{R-knitr,
+  title = {knitr: A General-Purpose Package for Dynamic Report Generation in R},
+  author = {Yihui Xie},
+  year = {2018},
+  note = {R package version 1.20},
+  url = {https://CRAN.R-project.org/package=knitr},
+}
+@Manual{R-rmarkdown,
+  title = {rmarkdown: Dynamic Documents for R},
+  author = {JJ Allaire and Yihui Xie and Jonathan McPherson and Javier Luraschi and Kevin Ushey and Aron Atkins and Hadley Wickham and Joe Cheng and Winston Chang},
+  year = {2018},
+  note = {R package version 1.9},
+  url = {https://CRAN.R-project.org/package=rmarkdown},
+}

preamble.tex

@@ -0,0 +1,8 @@
+\usepackage{booktabs}
+\usepackage{amsthm}
+\makeatletter
+\def\thm@space@setup{%
+  \thm@preskip=8pt plus 2pt minus 4pt
+  \thm@postskip=\thm@preskip
+}
+\makeatother

profiling-handbook.Rproj

@@ -0,0 +1,15 @@
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+BuildType: Website

style.css

@@ -0,0 +1,14 @@
+p.caption {
+  color: #777;
+  margin-top: 10px;
+}
+p code {
+  white-space: inherit;
+}
+pre {
+  word-break: normal;
+  word-wrap: normal;
+}
+pre code {
+  white-space: inherit;
+}