From d540928feaeb7e89d7a6afc1407ddbb292877865 Mon Sep 17 00:00:00 2001 From: Emma Rand Date: Mon, 4 Nov 2024 09:11:27 +0000 Subject: [PATCH 1/2] remove non-relevant material --- .renvignore | 10 ++ core/week-6/Y12345678.zip | Bin 49341 -> 0 bytes core/week-6/overview.qmd | 11 +- core/week-6/study_after_workshop.qmd | 10 +- core/week-6/study_before_workshop.qmd | 6 +- core/week-6/styles.css | 16 -- core/week-6/workshop.qmd | 223 +------------------------- 7 files changed, 18 insertions(+), 258 deletions(-) create mode 100644 .renvignore delete mode 100644 core/week-6/Y12345678.zip delete mode 100644 core/week-6/styles.css diff --git a/.renvignore b/.renvignore new file mode 100644 index 0000000..04a4248 --- /dev/null +++ b/.renvignore @@ -0,0 +1,10 @@ +.Rproj.user +.Rhistory +.Rdata +.httr-oauth +.DS_Store + +/.quarto/ + +transcriptomics/week-3/data-raw/ + diff --git a/core/week-6/Y12345678.zip b/core/week-6/Y12345678.zip deleted file mode 100644 index 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zkfWI+qluA;rP(F+&(XW=EHm)(^j}Bs@1BEA&Nu1)E0l;(Xu!MP`(JGC`vPuN0*&pP zv)7bM>e6sQkn zN`DFJ{QFQ~99>G`&)za#0yqB|*y#uKMQz(C7Lh9h!zTA~p0aFK_9w;%$jl|RX_q?i~RH#-N%&lZlpZgQ>w z{*M78?p*Sm9~Yyo^A9b^D2hvHeaHXvQh&KbPk}l3iVnC~nYsQ_d;B~-T~=Mvc>hKg z=Vj&Q;bIf{q2B-L=3lzw;^G^8HO$z`*wzYU;b;W5bY}#nZ?pdvVZb%#+i^aZ4qwgx zGgXHJDEnW>_3z&QpH-dl)$E^D-MLEtB44Iq4D>YyXn#fbqQ)Nn9`IjP9pe910T!bj zWi9}_1Zd~il=I_)uW{?jV4OP)HZrj>viLXQc;1ES0VDoj3rAu=5nK`Pa})n19M27? z`G`n@0lx|UAsj<~&%o8f@!U**8U8hLz|6Tey(}CR2!E>||6juK7V(2Fb810Sh%zjvvAVRSKMFG|g zhC9E>G6}T5;(IY=!UEI7uM7HH6u!F-Sh2iBj#QD Date: Mon, 4 Nov 2024 13:45:46 +0000 Subject: [PATCH 2/2] overview and before done --- core/week-2/study_before_workshop.qmd | 2 +- core/week-6/images/mentimeter_qr_code.png | Bin 0 -> 16768 bytes core/week-6/overview.qmd | 20 +++++++++++++++++--- core/week-6/study_after_workshop.qmd | 2 +- core/week-6/study_before_workshop.qmd | 21 +++++++++++++++++++-- core/week-6/workshop.qmd | 2 +- update-notes.txt | 2 +- 7 files changed, 40 insertions(+), 9 deletions(-) create mode 100644 core/week-6/images/mentimeter_qr_code.png diff --git a/core/week-2/study_before_workshop.qmd b/core/week-2/study_before_workshop.qmd index 8bdf889..6d10214 100644 --- a/core/week-2/study_before_workshop.qmd +++ b/core/week-2/study_before_workshop.qmd @@ -9,7 +9,7 @@ toc-location: right 2. 📖 Read [Workflow in RStudio](https://3mmarand.github.io/comp4biosci/workflow_rstudio.html). You may find it helpful to remind yourself about RStudio Projects. In previous years, you have submitted an "RStudio Project" as part of your BABS work. In this module, you will submit "Supporting Information" for your Project Report. The Supporting Information is a documented and organised collection of all the digital parts of your research project. This includes data (or instructions for accessing data), code and/or non-coded processing, instructions for use, computational requirements and outputs. The Supporting Information could be a single RStudio Project (like you have done previously but with better documentation) or a folder that includes an RStudio Project and other material/scripts. -3.💻 Set up the Virtual Desktop. I very strongly recommend working on +3. Set up the Virtual Desktop. I very strongly recommend working on the University computers for this work. You will be using more specialised R packages than you might be used to. 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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. ### Learning objectives The successful student will be able to: -- +- 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 + +- Write a README file for a project + + + ### Instructions 1. [Prepare](study_before_workshop.qmd) - i. + i. Revise [Core: Supporting Information 1](../week-2/overview.qmd) + and make a note of queries you have 2. [Workshop](workshop.qmd) diff --git a/core/week-6/study_after_workshop.qmd b/core/week-6/study_after_workshop.qmd index 306b379..4beb2b9 100644 --- a/core/week-6/study_after_workshop.qmd +++ b/core/week-6/study_after_workshop.qmd @@ -1,6 +1,6 @@ --- title: "Independent Study to consolidate this week" -subtitle: "Core 2" +subtitle: "Core: Supporting Information 2" toc: true toc-location: right format: diff --git a/core/week-6/study_before_workshop.qmd b/core/week-6/study_before_workshop.qmd index fc1377b..f7661f7 100644 --- a/core/week-6/study_before_workshop.qmd +++ b/core/week-6/study_before_workshop.qmd @@ -1,8 +1,25 @@ --- title: "Independent Study to prepare for workshop" -subtitle: "Core 2" +subtitle: "Core: Supporting Information 2" toc: true toc-location: right --- -1. \ No newline at end of file +1. Revise [Core: Supporting Information 1 Organising Reproducible Data + Analyses](../week-2/overview.qmd). + + i. Do you know your Supporting information will most likely be be a + structured folder which *is* either an RStudio Project or + contains an RStudio Project? + ii. Are you following the best practices code formatting and style? + If not, go through your scripts and edit. + iii. Do you have numbers hard coded where they could be variables? + iv. Are you using a sensible naming convention for files and + variables? Have you written it down? + v. Make a note of queries you have. Take some time to formulate and + write down your questions. The more specific and clear your + question is, the better answer I will be able to provide. + vi. Post your questions here: + [Menti](https://www.menti.com/m86rqcbb88) Code: 3306 3222. QR: + ![mentimeter qr + code](images/mentimeter_qr_code.png){width="400"} diff --git a/core/week-6/workshop.qmd b/core/week-6/workshop.qmd index e00f869..ba18a2c 100644 --- a/core/week-6/workshop.qmd +++ b/core/week-6/workshop.qmd @@ -1,6 +1,6 @@ --- title: "Workshop" -subtitle: "Organising Reproducible Data Analyses" +subtitle: "Supporting Information 2 Documenting and curating Reproducible Data Analyses" author: "Emma Rand" toc: true toc-depth: 4 diff --git a/update-notes.txt b/update-notes.txt index 20a181a..2fb6d29 100644 --- a/update-notes.txt +++ b/update-notes.txt @@ -86,7 +86,7 @@ Curate your and reorganise your code restart R to try. exchange projects with a friend. Do they understand? Readme -- how to make +- how to make: create a new text file in the top level of your project - what goes in - software including versions - session info