Files in DataScienceILC/tlsc-dsfb26v-20_workflows
Bookdown site for workflows course
.DS_Store
.Rbuildignore
.gitignore
.unpublished/data_formatting.Rmd
.unpublished/lesson-045-rmarkdown-automate.Rmd
DESCRIPTION
FancySuppTable2.xls
LICENSE.txt
NAMESPACE
R/README.txt
README.md
Rmd/.DS_Store
Rmd/course_intro.Rmd
Rmd/course_intro.html
Rmd/flipbook_mtcars.Rmd
Rmd/flipbook_mtcars.html
Rmd/flipbook_mtcars_files/figure-html/mtcars-1.png
Rmd/flipbook_mtcars_files/figure-html/mtcars_auto_03_output-1.png
Rmd/flipbook_mtcars_files/figure-html/mtcars_auto_04_output-1.png
Rmd/flipbook_mtcars_files/figure-html/mtcars_auto_05_output-1.png
Rmd/flipbook_mtcars_files/figure-html/mtcars_auto_06_output-1.png
Rmd/flipbook_mtcars_files/figure-html/mtcars_auto_07_output-1.png
Rmd/flipbook_mtcars_files/figure-html/mtcars_non_seq-1.png
Rmd/flipbook_mtcars_files/figure-html/mtcars_non_seq_auto_02_output-1.png
Rmd/flipbook_mtcars_files/figure-html/mtcars_non_seq_auto_03_output-1.png
Rmd/flipbook_mtcars_files/figure-html/mtcars_non_seq_auto_04_output-1.png
Rmd/flipbook_mtcars_files/figure-html/mtcars_non_seq_auto_05_output-1.png
Rmd/flipbook_mtcars_files/figure-html/mtcars_non_seq_auto_06_output-1.png
Rmd/flipbook_mtcars_files/figure-html/mtcars_non_seq_auto_07_output-1.png
Rmd/flipbook_mtcars_files/figure-html/mtcars_plot-1.png
Rmd/flipbook_mtcars_files/figure-html/mtcars_plot_auto_02_output-1.png
Rmd/flipbook_mtcars_files/figure-html/mtcars_plot_auto_03_output-1.png
Rmd/flipbook_mtcars_files/figure-html/mtcars_plot_auto_04_output-1.png
Rmd/flipbook_mtcars_files/figure-html/mtcars_plot_auto_05_output-1.png
Rmd/flipbook_mtcars_files/figure-html/mtcars_plot_auto_06_output-1.png
Rmd/flipbook_mtcars_files/figure-html/mtcars_plot_user_01_output-1.png
Rmd/flipbook_mtcars_files/figure-html/mtcars_plot_user_02_output-1.png
Rmd/flipbook_mtcars_files/figure-html/mtcars_plot_user_03_output-1.png
Rmd/flipbook_mtcars_files/figure-html/mtcars_plot_user_04_output-1.png
Rmd/flipbook_mtcars_files/figure-html/mtcars_user_02_output-1.png
Rmd/flipbook_mtcars_files/figure-html/mtcars_user_03_output-1.png
Rmd/flipbook_mtcars_files/figure-html/mtcars_user_04_output-1.png
Rmd/lesson1.Rmd
Rmd/lesson2.Rmd
Rmd/lesson3.Rmd
Rmd/lesson4.Rmd
Rmd/lesson5.Rmd
Rmd/libs/remark-css-0.0.1/default.css
Rmd/libs/remark-css-0.0.1/hygge.css
Rmd/libs/remark-css-0.0.1/ninjutsu.css
Rmd/lorem.Rmd
Rmd/ocean_floor.Rmd
Rmd/steps_to_graph_from_excel_file.Rmd
_bookdown.yml
_build.sh
_deploy.sh
_output.yml
archief/lesson-980-exam.Rmd
code/README.txt
code/covid_cases.R
code/demos.R
code/extract_tables_repita.R
code/get_rmd_dependencies.R
code/publish_book.R
code/render_covid_reports_with_params.R
code/render_covid_reports_with_params.log
code/schedule_daily_task.R
code/shipman_murders.R
course_urls.RData
data-raw/.DS_Store
data-raw/Data010/2020-06-19_covid_ecdc_cases_geography.csv
data-raw/Data010/2020-06-19_md5sums_covid_ecdc_cases_geography.md5
data-raw/Data010/README.txt
data-raw/Data010/supporting/covid_ecdc_cases_geography.R
data-raw/Data010/supporting/md5sums.R
data-raw/Data010/v01/2020-05-31_covid_ecdc_cases_geography.csv
data-raw/Data010/v01/2020-05-31_md5sums_covid_ecdc_cases_geography.md5
data-raw/Data020/README.txt
data-raw/Data020/messy_excel.xlsx
data/.DS_Store
data/.gitignore
data/CE.LIQ.FLOW.062_Tidydata.xlsx
data/D020/tidy_excel.csv
data/D020/tidy_excel.csv.md5
data/D030/00-1-shipman-confirmed-victims-x.csv
data/D030/README.txt
data/README.txt
data/README_ToxRefDB_20141106.docx
data/dengue_data.csv
data/dengue_data.md5
data/dengue_data_db.csv
data/dependencies.rda
data/flu_data.csv
data/flu_data_db.csv
data/md5_examples/MD5_exampledata_1.txt
data/md5_examples/MD5_exampledata_backupcomputercrash.txt
data/md5_examples/MD5_exampledata_maybethisone.txt
data/md5_examples/MD5_exampledata_savethisone.txt
data/md5_examples/md5_examples.zip
data/md5_examples2/MD5_exampledata_1.txt
data/md5_examples2/MD5_exampledata_backupcomputercrash.txt
data/md5_examples2/MD5_exampledata_maybethisone.txt
data/md5_examples2/MD5_exampledata_savethisone.txt
data/salmonella CFU kinetics OD600 in LB van ipecs 8okt2020 kleur.xlsx
data/tidy_Kopie van salmonella CFU kinetics OD600 in LB van ipecs 8okt2020 kleur.xlsx
data/toxrefdb_nel_lel_noael_loael_summary_AUG2014_FOR_PUBLIC_RELEASE.csv
data/toxrefdb_nel_lel_noael_loael_summary_AUG2014_FOR_PUBLIC_RELEASE.md5
data/toxrefdb_nel_lel_noael_loael_summary_AUG2014_FOR_PUBLIC_RELEASE_LOCAL.md5
data/workflowsdb_flu_dengue.sql
doc/Reproducibility_and_reporting_practices_in_COVID-1.pdf
doc/Whitepaper-Scrum-voor-de-non-IT-.pdf
doc/ripeta_approach_and_criteria_definitions.pdf
extra_lessons/inanderegeplakt/lesson-022-git-and-rstudio.Rmd
extra_lessons/inanderegeplakt/lesson-032-agile-scrum.Rmd
extra_lessons/inanderegeplakt/lesson-05-git-collaboration.Rmd
extra_lessons/inanderegeplakt/lesson-06-shiny-interactive.Rmd
extra_lessons/lesson-013-represtools.Rmd
extra_lessons/lesson-042-rmarkdown-chunks.Rmd
extra_lessons/lesson-06-bookdown-portfolio.Rmd
images/.DS_Store
images/10_githubpages.png
images/10_reproScience_PlosOne.png
images/DBeaver_albums.PNG
images/DBeaver_createdb.PNG
images/DBeaver_new.png
images/DBeaver_new2.PNG
images/DBeaver_new3.PNG
images/DBeaver_new4.PNG
images/DBeaver_newtablebehere.PNG
images/DBeaver_pagila1.PNG
images/DBeaver_pagila2.PNG
images/DBeaver_pagila3.PNG
images/DBeaver_pagila4.PNG
images/DBeaver_start.PNG
images/Data-Repositories.png
images/EC_FAIR_data.png
images/InkedDBeaver_albums2.jpg
images/Light_bulb_icon_red.svg
images/Pepper.png
images/Presentatie1/Dia1.JPG
images/Presentatie1/Dia10.JPG
images/Presentatie1/Dia12.JPG
images/Presentatie1/Dia13.JPG
images/Presentatie1/Dia17.JPG
images/Presentatie1/Dia18.JPG
images/Presentatie1/Dia2.JPG
images/Presentatie1/Dia20.JPG
images/Presentatie1/Dia26.JPG
images/Presentatie1/Dia3.JPG
images/Presentatie1/Dia4.JPG
images/Presentatie1/Dia5.JPG
images/Presentatie1/Dia6.JPG
images/Presentatie1/Dia9.JPG
images/Question-mark-grey.jpg
images/Understanding-Creative-Commons-Licenses-20.png
images/automated.gif
images/bad-characters.png
images/bad_formatting_file_name_and_headers.jpg
images/build_book.PNG
images/card.jpg
images/chunk_names.jpg
images/cos-shield.png
images/covid_rmd_screenshot.jpg
images/creatvie_commons_picture.png.crdownload
images/crownsource.jpg
images/data_science_languages/Dia1.jpg
images/data_science_languages/Dia2.jpg
images/data_science_languages/Dia3.jpg
images/data_science_languages/Dia4.jpg
images/data_science_languages/InkedDia1_LI.jpg
images/docking_station_harddisk.jpg
images/dplyr_issues.png
images/final.jpg
images/final_final.png
images/git_collaboration.png
images/git_commit_diff.png
images/git_workflow.jpg
images/github_issues.png
images/gollum_climbing.jpg
images/guerrilla_analytics.jpg
images/html_br.png
images/inter_lab_messy.png
images/interlab_messy1.png
images/korok.jpg
images/laderast_ReproducibleMatrix.jpg
images/laderast_metadata.png
images/lancet_covid.png
images/lesson22_1_createRepo.png
images/lesson22_2_downloadRepo.png
images/lesson22_3_gitmenu.PNG
images/lesson22_4_commitmenu.PNG
images/lesson22_5_commitsGitHub.png
images/lesson22_6_gitCommandLine.png
images/lesson23_1_mainbranch.png
images/lesson23_2_newbranch.png
images/lesson23_3_newbranch2.png
images/lesson23_4_branchesGitHub.png
images/lesson23_5_pullrequest.png
images/lesson23_6_pullrequest2.png
images/lesson23_7_pullrequest3.png
images/lesson23_8_pullrequest4.png
images/lesson23_9_switchtomain.png
images/megatron.jpeg
images/mendeley_citationkey.PNG
images/mendeley_detailwindow.PNG
images/mendeley_folder.PNG
images/messy_excel.png
images/messy_steps.jpg
images/migrate.jpeg
images/one-does-not-simply-migrate-data.jpg
images/one_ring.jpg
images/open_data_challenges.PNG
images/openscience_principles.png
images/outputs-1-word.png
images/phd_final1.PNG
images/phd_final2.PNG
images/phd_final3.PNG
images/prime.jpeg
images/project_structure_categorical.png
images/readme.png
images/readme_updated.png
images/readxl_sticker.png
images/research_comic_phd.gif
images/rmd_printscr.png
images/rpackages_network.png
images/rstudiologo.png
images/summarizedexperiment.png
images/tidy-1.png
images/tidyverse.png
images/trump_chloroquine.png
images/understanding_science_repetition.gif
images/voorbeeldlogo2.png
images/zotero1.png
index.Rmd
lesson-00a-leeruitkomsten.Rmd
lesson-00b-prerequisites.Rmd
lesson-01-git-and-github.Rmd
lesson-02-git-branching-and-merging.Rmd
lesson-03-represdata.Rmd
lesson-04-reproducible-research.Rmd
lesson-05-relational-db.Rmd
lesson-06-rpackages.Rmd
lesson-07-rmarkdown.Rmd
lesson-08-rmarkdown-output.Rmd
lesson-09-rmarkdown-params.Rmd
lesson-10-portfolio.Rmd
lesson-998-resources.Rmd
manifest.json
references.bib
rsconnect/datascience.hu.nl/bas.vangestel/workflows_reader.dcf
rsconnect/documents/index.Rmd/datascience.hu.nl/alyanne.dehaan/data_science_for_biology_2-workflows.dcf
rsconnect/documents/index.Rmd/lesmaterialen.rstudio.hu.nl/alyanne.dehaan@hu.nl/data_science_for_biology_2-workflows.dcf
rsconnect/documents/index.Rmd/lesmaterialen.rstudio.hu.nl/alyanne.dehaan@hu.nl/workflows_2022_2023.dcf
rsconnect/documents/index.Rmd/lesmaterialen.rstudio.hu.nl/bas.vangestel@hu.nl/dsfb2_workflows_reader.dcf
style.css
tlsc-dsfb26v-20_workflows.Rproj
toxrefdb_nel_lel_noael_loael_summary_AUG2014_FOR_PUBLIC_RELEASE.md5
urls
workflows_course.rds
wrong_structure/.DS_Store
wrong_structure/Data files 001/Final Results/experiment_1_results_final.txt
wrong_structure/Data files 001/experiment_1.txt
wrong_structure/Manuscripts/me_et al , 2020_v01 - Copy.docx
wrong_structure/Manuscripts/me_et al , 2020_v02.docx
wrong_structure/Manuscripts/me_et al , 2020_v03_final_final.docx
wrong_structure/Project Documentation/applications/Application final prject x.docx
wrong_structure/Project Documentation/applications/application_final_project y.docx
wrong_structure/Volunteer responses/Patient 2.xlsx
wrong_structure/Volunteer responses/Patient_3.xlsx
wrong_structure/Volunteer responses/patient_1.xlsx
