Project Report and Research Compendium 70% of which
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Oral presentation 30%
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Project Report and Research Compendium 70% of which
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70% report (i.e., 49% of the total mark)
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30% compendium (i.e., 21% of the total mark)
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70% report (i.e., 49% of the total mark)
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30% compendium (i.e., 21% of the total mark)
These slides are a guide to Research compendium.
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What is a Research Compendium?
Overview of assessment
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Stage 3 Integrated Masters students are expected to submit a Research Compendium that is a documented collection of all the digital parts of the research project including data (or access to data), code and outputs. The collection is organised and documented in such a way that reproducing all the results is straightforward for another individual.
Students will be assessed on the technical complexity, completeness and organisation of their compendium and the completeness, reproducibility and clarity of their documentation at the project and code/process level. Marking will focus on the reproducibility of the results and the clarity of the decision making processes rather than the interpretation of the results which is covered in the report. There is no word or size limit for any part of the compendium but its contents should be concise and minimal. Extraneous text, code or files will be penalised.
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What is a Research Compendium?
Overview of assessment
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Stage 3 Integrated Masters students are expected to submit a Research Compendium that is a documented collection of all the digital parts of the research project including data (or access to data), code and outputs. The collection is organised and documented in such a way that reproducing all the results is straightforward for another individual.
Students will be assessed on the technical complexity, completeness and organisation of their compendium and the completeness, reproducibility and clarity of their documentation at the project and code/process level. Marking will focus on the reproducibility of the results and the clarity of the decision making processes rather than the interpretation of the results which is covered in the report. There is no word or size limit for any part of the compendium but its contents should be concise and minimal. Extraneous text, code or files will be penalised.
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What is a Research Compendium?
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Zipped folder containing all data, code, and text associated with a research project organised and documented clearly. Any unscripted processing should be described.
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Everything needed to reproduce the results, and no more. The compendium should not be a dumping ground for data files and scripts. It needs to be curated. You may generate files that are not needed to reproduce your work and these should be removed.
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Zipped folder containing all data, code and text associated with a research project organised and documented clearly. Any unscripted processing should be described.
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Everything needed to understand what the project is and reproduce the results, and no more. The compendium should not be a dumping ground for data files and scripts. It needs to be curated. You may generate files that are not needed to reproduce your work and these should be removed.
Your compendium might be a single Quarto/RStudio Project, or it might be folder including an RStudio Project and some additional materials including the description of unscripted processing.
Ideally uses literate programming to create submitted report
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Use guidelines from Core 1 and 2
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follow the guidance in Core 1 on organisation, naming things, and documentation
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follow the guidance in Core 2 well-formatted code, consistency, modularisation and documentation
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follow the guidance in Core 1 on organisation, naming things and documentation
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follow the guidance in Core 2 on well-formatted code, consistency, modularisation and documentation
@@ -437,7 +441,7 @@
Project level documentation
as concise as possible, bullet points are good
primarily in the README file but some details may be in scripts
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title, concise description of the work, date, overview of compendium contents
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title, concise description of the work, author exam number, date, overview of compendium contents
all the software information including versions
instructions needed to reproduce the work, order of workflow, settings/parameter values for software
In this workshop we will go through an example quarto document. You will learn:
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what the YAML header is
formatting (bold, italics, headings)
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chunk options to control whether code and output are in the rendered document
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adding citations
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figures and tables with cross referencing and autonumberiung
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inline coding to report results
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special characters and equations
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to control default and individual chunk options
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how to add citations
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figures and tables with cross referencing and automatic numbering
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how to use inline coding to report results
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how to insert special characters and equations
Exercise
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🎬 make a start on your compendium
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🎬 make a start on a quarto doc
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🎬 The example RStudio project containing this code here: chaffinch. You can download the project as a zip file from there but there is some code that will do that automatically for you. Since this is an RStudio Project, do not run the code from inside a project. You may want to navigate to a particular directory or edit the destdir:
You can agree to deleting the zip. You should find RStudio restarts and you have a new project called chaffinch-xxxxxx. The xxxxxx is a commit reference - you do not need to worry about that, it is just a way to tell you which version of the repo you downloaded. You can now run the code in the project.
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🎬 Make an outline of your compendium. This could be a sketch on paper or slide or from the mindmap software you usually use. Or it could be a skeleton of folders and files on your computer.
total 228
-drwxr-xr-x 2 runner docker 4096 Dec 3 14:01 data
-drwxr-xr-x 2 runner docker 4096 Dec 3 14:01 images
--rw-r--r-- 1 runner docker 1597 Dec 3 14:01 overview.qmd
--rw-r--r-- 1 runner docker 25553 Dec 3 14:05 study_after_workshop.html
--rw-r--r-- 1 runner docker 184 Dec 3 14:01 study_after_workshop.qmd
--rw-r--r-- 1 runner docker 70839 Dec 3 14:05 study_before_workshop.html
--rw-r--r-- 1 runner docker 4807 Dec 3 14:01 study_before_workshop.ipynb
--rw-r--r-- 1 runner docker 13029 Dec 3 14:01 study_before_workshop.qmd
--rw-r--r-- 1 runner docker 58063 Dec 3 14:01 workshop.html
--rw-r--r-- 1 runner docker 8550 Dec 3 14:01 workshop.qmd
--rw-r--r-- 1 runner docker 8564 Dec 3 14:05 workshop.rmarkdown
-drwxr-xr-x 3 runner docker 4096 Dec 3 14:01 workshop_files
+drwxr-xr-x 2 runner docker 4096 Dec 4 10:05 data
+drwxr-xr-x 2 runner docker 4096 Dec 4 10:05 images
+-rw-r--r-- 1 runner docker 1597 Dec 4 10:05 overview.qmd
+-rw-r--r-- 1 runner docker 25553 Dec 4 10:09 study_after_workshop.html
+-rw-r--r-- 1 runner docker 184 Dec 4 10:05 study_after_workshop.qmd
+-rw-r--r-- 1 runner docker 70839 Dec 4 10:09 study_before_workshop.html
+-rw-r--r-- 1 runner docker 4807 Dec 4 10:05 study_before_workshop.ipynb
+-rw-r--r-- 1 runner docker 13029 Dec 4 10:05 study_before_workshop.qmd
+-rw-r--r-- 1 runner docker 58063 Dec 4 10:05 workshop.html
+-rw-r--r-- 1 runner docker 8550 Dec 4 10:05 workshop.qmd
+-rw-r--r-- 1 runner docker 8564 Dec 4 10:09 workshop.rmarkdown
+drwxr-xr-x 3 runner docker 4096 Dec 4 10:05 workshop_files
You can use more than one option at once. The -h option stands for “human readable” and makes the file sizes easier to understand for humans:
@@ -512,18 +512,18 @@
Workshop
ls-hl
total 228K
-drwxr-xr-x 2 runner docker 4.0K Dec 3 14:01 data
-drwxr-xr-x 2 runner docker 4.0K Dec 3 14:01 images
--rw-r--r-- 1 runner docker 1.6K Dec 3 14:01 overview.qmd
--rw-r--r-- 1 runner docker 25K Dec 3 14:05 study_after_workshop.html
--rw-r--r-- 1 runner docker 184 Dec 3 14:01 study_after_workshop.qmd
--rw-r--r-- 1 runner docker 70K Dec 3 14:05 study_before_workshop.html
--rw-r--r-- 1 runner docker 4.7K Dec 3 14:01 study_before_workshop.ipynb
--rw-r--r-- 1 runner docker 13K Dec 3 14:01 study_before_workshop.qmd
--rw-r--r-- 1 runner docker 57K Dec 3 14:01 workshop.html
--rw-r--r-- 1 runner docker 8.4K Dec 3 14:01 workshop.qmd
--rw-r--r-- 1 runner docker 8.4K Dec 3 14:05 workshop.rmarkdown
-drwxr-xr-x 3 runner docker 4.0K Dec 3 14:01 workshop_files
+drwxr-xr-x 2 runner docker 4.0K Dec 4 10:05 data
+drwxr-xr-x 2 runner docker 4.0K Dec 4 10:05 images
+-rw-r--r-- 1 runner docker 1.6K Dec 4 10:05 overview.qmd
+-rw-r--r-- 1 runner docker 25K Dec 4 10:09 study_after_workshop.html
+-rw-r--r-- 1 runner docker 184 Dec 4 10:05 study_after_workshop.qmd
+-rw-r--r-- 1 runner docker 70K Dec 4 10:09 study_before_workshop.html
+-rw-r--r-- 1 runner docker 4.7K Dec 4 10:05 study_before_workshop.ipynb
+-rw-r--r-- 1 runner docker 13K Dec 4 10:05 study_before_workshop.qmd
+-rw-r--r-- 1 runner docker 57K Dec 4 10:05 workshop.html
+-rw-r--r-- 1 runner docker 8.4K Dec 4 10:05 workshop.qmd
+-rw-r--r-- 1 runner docker 8.4K Dec 4 10:09 workshop.rmarkdown
+drwxr-xr-x 3 runner docker 4.0K Dec 4 10:05 workshop_files
The -a option stands for “all” and shows us all the files, including hidden files.
@@ -531,20 +531,20 @@
Workshop
ls-alh
total 236K
-drwxr-xr-x 5 runner docker 4.0K Dec 3 14:05 .
-drwxr-xr-x 6 runner docker 4.0K Dec 3 14:05 ..
-drwxr-xr-x 2 runner docker 4.0K Dec 3 14:01 data
-drwxr-xr-x 2 runner docker 4.0K Dec 3 14:01 images
--rw-r--r-- 1 runner docker 1.6K Dec 3 14:01 overview.qmd
--rw-r--r-- 1 runner docker 25K Dec 3 14:05 study_after_workshop.html
--rw-r--r-- 1 runner docker 184 Dec 3 14:01 study_after_workshop.qmd
--rw-r--r-- 1 runner docker 70K Dec 3 14:05 study_before_workshop.html
--rw-r--r-- 1 runner docker 4.7K Dec 3 14:01 study_before_workshop.ipynb
--rw-r--r-- 1 runner docker 13K Dec 3 14:01 study_before_workshop.qmd
--rw-r--r-- 1 runner docker 57K Dec 3 14:01 workshop.html
--rw-r--r-- 1 runner docker 8.4K Dec 3 14:01 workshop.qmd
--rw-r--r-- 1 runner docker 8.4K Dec 3 14:05 workshop.rmarkdown
-drwxr-xr-x 3 runner docker 4.0K Dec 3 14:01 workshop_files
+drwxr-xr-x 5 runner docker 4.0K Dec 4 10:09 .
+drwxr-xr-x 6 runner docker 4.0K Dec 4 10:08 ..
+drwxr-xr-x 2 runner docker 4.0K Dec 4 10:05 data
+drwxr-xr-x 2 runner docker 4.0K Dec 4 10:05 images
+-rw-r--r-- 1 runner docker 1.6K Dec 4 10:05 overview.qmd
+-rw-r--r-- 1 runner docker 25K Dec 4 10:09 study_after_workshop.html
+-rw-r--r-- 1 runner docker 184 Dec 4 10:05 study_after_workshop.qmd
+-rw-r--r-- 1 runner docker 70K Dec 4 10:09 study_before_workshop.html
+-rw-r--r-- 1 runner docker 4.7K Dec 4 10:05 study_before_workshop.ipynb
+-rw-r--r-- 1 runner docker 13K Dec 4 10:05 study_before_workshop.qmd
+-rw-r--r-- 1 runner docker 57K Dec 4 10:05 workshop.html
+-rw-r--r-- 1 runner docker 8.4K Dec 4 10:05 workshop.qmd
+-rw-r--r-- 1 runner docker 8.4K Dec 4 10:09 workshop.rmarkdown
+drwxr-xr-x 3 runner docker 4.0K Dec 4 10:05 workshop_files
You can move about with the cd command, which stands for “change directory”. You can use it to move into a directory by specifying the path to the directory:
[^_]{2,3} matches two or three characters that are not _ at the start of the string (^)
.+ matches one or more characters. The extract() function puts the first match into the first column, type, and the second match into the second column, conc. The remove = FALSE argument means the original column is kept.
You now have a dataframe with all the tracking data which is relatively easy to summarise and plot using tools you know.
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There is an example RStudio project containing this code here: tips. You can also download the project as a zip file from there but there is some code that will do that automatically for you. Since this is an RStudio Project, do not run the code from inside a project:
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There is an example RStudio project containing this code here: tips. You can also download the project as a zip file from there but there is some code that will do that automatically for you. Since this is an RStudio Project, do not run the code from inside a project. You may want to navigate to a particular directory or edit the destdir:
You can agree to deleting the zip. You should find RStudio restarts and you have a new project called tips-xxxxxx. The xxxxxx is a commit reference - you do not need to worry about that, it is just a way to tell you which version of the repro you downloaded. You can now run the code in the project.
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You can agree to deleting the zip. You should find RStudio restarts and you have a new project called tips-xxxxxx. The xxxxxx is a commit reference - you do not need to worry about that, it is just a way to tell you which version of the repo you downloaded. You can now run the code in the project.
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On the vertical axis are genes which are differentially expressed at the 0.01 level. On the horizontal axis are samples. We can see that the FGF-treated samples cluster together and the control samples cluster together. We can also see two clusters of genes; one of these shows genes upregulated (more yellow) in the FGF-treated samples (the pink cluster) and the other shows genes down regulated (more blue, the blue cluster) in the FGF-treated samples.
It will take a minute to run and display. On the vertical axis are genes which are differentially expressed at the 0.01 level. On the horizontal axis are cells. We can see that cells of the same type don’t cluster that well together. We can also see two clusters of genes but the pattern of gene is not as clear as it was for the frogs and the correspondence with the cell clusters is not as strong.