diff --git a/core/week-6/overview.html b/core/week-6/overview.html index a2d049d..b08c60c 100644 --- a/core/week-6/overview.html +++ b/core/week-6/overview.html @@ -270,7 +270,7 @@

Learning objectives

  • Describe the purpose of a README file

  • List the key components of a README file

    • -

  • Use sessioninfo to document the software used in an R project

    • +

  • Use packages to discover the packages used in a project

  • Write a README file for a project

    • diff --git a/core/week-6/workshop.html b/core/week-6/workshop.html index 9497fd1..6fc3dd2 100644 --- a/core/week-6/workshop.html +++ b/core/week-6/workshop.html @@ -339,7 +339,10 @@

    Non-scr
    -

    Images were converted to: Manual cropping: Projection type used: etc

    +

    Images were converted to:

    +

    Manual cropping:

    +

    Projection type used:

    +

    etc

    diff --git a/search.json b/search.json index 608f0e6..4f4d849 100644 --- a/search.json +++ b/search.json @@ -50,7 +50,7 @@ "href": "core/week-6/overview.html", "title": "Overview", "section": "", - "text": "We considered how to organise reproducible data analyses in Core: Supporting Information 1. This week we will consider how to document and curate reproducible data analyses. You will add a README to your project and discover all the software you are using in R. The workshop will also include a questions and answers section.\n\nLearning objectives\nThe successful student will be able to:\n\nDescribe the purpose of a README file\nList the key components of a README file\nUse sessioninfo to document the software used in an R project\nWrite a README file for a project\n\n\n\nInstructions\n\nPrepare\n\nRevise Core: Supporting Information 1 and make a note of queries you have\n\nWorkshop\nConsolidate", + "text": "We considered how to organise reproducible data analyses in Core: Supporting Information 1. This week we will consider how to document and curate reproducible data analyses. You will add a README to your project and discover all the software you are using in R. The workshop will also include a questions and answers section.\n\nLearning objectives\nThe successful student will be able to:\n\nDescribe the purpose of a README file\nList the key components of a README file\nUse packages to discover the packages used in a project\nWrite a README file for a project\n\n\n\nInstructions\n\nPrepare\n\nRevise Core: Supporting Information 1 and make a note of queries you have\n\nWorkshop\nConsolidate", "crumbs": [ "Core Supporting Info", "Week 6: Supporting Information 2", @@ -98,7 +98,7 @@ "href": "core/week-6/workshop.html#non-scripted-parts-of-the-analysis", "title": "Workshop", "section": "Non-scripted parts of the analysis", - "text": "Non-scripted parts of the analysis\nNon-scripted parts of the analysis such as manual data cleaning or using software that does not have a script to analyse data presented in the report should be documented. This includes the steps taken, parameter settings and the decisions made. It need not be written as a narrative - you can use bullet points and be concise.\nšŸŽ¬ Go through any code you have written and edit your comments.\nšŸŽ¬ Make a text file for each non-scripted part of the analysis and document the steps taken, parameter settings and decisions made. You likely will not be able to complete now where you will be analysing data in semester 2, but you can write down ā€œplace holdersā€ where possible. For example, in using Fiji to analyse images:\n\n\n\n\n\n\nimage_processing_in_fiji.txt\n\n\n\nImages were converted to: Manual cropping: Projection type used: etc", + "text": "Non-scripted parts of the analysis\nNon-scripted parts of the analysis such as manual data cleaning or using software that does not have a script to analyse data presented in the report should be documented. This includes the steps taken, parameter settings and the decisions made. It need not be written as a narrative - you can use bullet points and be concise.\nšŸŽ¬ Go through any code you have written and edit your comments.\nšŸŽ¬ Make a text file for each non-scripted part of the analysis and document the steps taken, parameter settings and decisions made. You likely will not be able to complete now where you will be analysing data in semester 2, but you can write down ā€œplace holdersā€ where possible. For example, in using Fiji to analyse images:\n\n\n\n\n\n\nimage_processing_in_fiji.txt\n\n\n\nImages were converted to:\nManual cropping:\nProjection type used:\netc", "crumbs": [ "Core Supporting Info", "Week 6: Supporting Information 2", diff --git a/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-73-1.png b/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-73-1.png index 3cb3b5d..ea9d18f 100644 Binary files a/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-73-1.png and b/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-73-1.png differ diff --git a/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-74-1.png b/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-74-1.png index 69fb43b..078df1c 100644 Binary files a/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-74-1.png and b/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-74-1.png differ diff --git a/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-80-1.png b/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-80-1.png index 699d790..922636d 100644 Binary files a/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-80-1.png and b/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-80-1.png differ diff --git a/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-81-1.png b/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-81-1.png index 1ba309c..c795754 100644 Binary files a/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-81-1.png and b/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-81-1.png differ diff --git a/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-87-1.png b/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-87-1.png index 0da04b0..df84e9c 100644 Binary files a/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-87-1.png and b/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-87-1.png differ diff --git a/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-88-1.png b/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-88-1.png index be2fbf2..8cd3d9d 100644 Binary files a/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-88-1.png and b/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-88-1.png differ diff --git a/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-89-1.png b/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-89-1.png index 5de2ce7..50b5d95 100644 Binary files a/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-89-1.png and b/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-89-1.png differ diff --git a/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-95-1.png b/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-95-1.png index 3b92841..d69542a 100644 Binary files a/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-95-1.png and b/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-95-1.png differ diff --git a/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-96-1.png b/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-96-1.png index 0da91ae..724be5c 100644 Binary files a/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-96-1.png and b/transcriptomics/week-5/workshop_files/figure-html/unnamed-chunk-96-1.png differ