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index.Rmd
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---
title: "BIOINF3005/7160: Transcriptomics Applications"
subtitle: "Course Homepage"
output:
html_document:
toc: yes
toc_float: yes
keep_md: yes
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(
echo = FALSE,
message = FALSE,
warning = FALSE
)
```
```{r}
library(tidyverse)
library(lubridate)
library(pander)
library(kableExtra)
options(knitr.kable.NA = '')
panderOptions("table.style", "rmarkdown")
panderOptions("table.split.table", Inf)
panderOptions("missing", "")
```
```{r}
pracs <- tribble(
~Week, ~`Week Starting`, ~Lecture, ~Lecturer, ~LecUrl, ~Practical, ~PracUrl,
1, "2020-03-02", "Introduction", "Stephen Pederson", "lectures/1_Introduction.pdf", "Introduction to R and `rmarkdown`", "practicals/1_IntroR.html",
NA_integer_, NA_character_, NA_character_, NA_character_, NA_character_, "Manipulating Text in R", "practicals/1_Using_stringr.html",
2, "2020-03-09", "**Adelaide Cup Day**", "No Lecture", "", "Using the tidyverse", "practicals/2_Tidyverse.html",
NA_integer_, NA_character_, NA_character_, NA_character_, NA_character_, "Plotting Data with the `tidyverse`", "practicals/2.2_Tidyverse.html",
3, "2020-03-16", "Early Transcriptomic Techniques", "Stephen Pederson", "lectures/2_EarlyTranscriptomics.pdf", "Data Types in R", "practicals/3.1_DataTypes.html",
NA_integer_, NA_character_, NA_character_, NA_character_, NA_character_, "Additional Visualisation", "practicals/3.2_MoreVisualisation.html",
4, "2020-03-23", "Microarrays and Statistics for Quantification", "Stephen Pederson", "lectures/3_MicroarrayTechnology.pdf", "The Bioconductor Project", "practicals/4.1_Bioconductor.html",
NA_integer_, NA_character_, NA_character_, NA_character_, NA_character_, "Genomic Ranges", "practicals/4.2_GenomicRanges.html",
5, "2020-03-30", "Statistics For Transcriptomics", "Stephen Pederson", "lectures/4_Statistics.pdf", "Basic Statistics in R", "practicals/5.1_Statistics.html",
NA_integer_, NA_character_, NA_character_, NA_character_, NA_character_, "Differential Expression", "practicals/5.2_MoreStatistics.html",
6, "2020-04-06", "RNA-Seq", "Zhipeng Qu", "lectures/Lecture5_RNASeq_ZQ_2020.pdf", "Using Limma For Differential Expression", "practicals/6.1_Limma.html",
NA_integer_, "2020-04-13", "**Mid-Semester Break**", "No Lecture", "", "", "",
NA_integer_, "2020-04-20", "**Mid-Semester Break**", "No Lecture", "", "", "",
7, "2020-04-27", "Alignment and Quantification", "Zhipeng Qu", "lectures/Lecture6_Alignment_Quantification_ZQ_2020.pdf", "More Complex Designs", "practicals/7.1_More_Complex_Designs.html",
NA_integer_, NA_character_, NA_character_, NA_character_, NA_character_, "More Complex Designs (2)", "practicals/7.2_More_Complex_Designs2.html",
8, "2020-05-04", "Statistics for RNA-Seq", "Stephen Pederson", "lectures/7_Stats_For_RNASeq.pdf", "Alignments and Visualisation", "practicals/8.1_Alignments.html",
NA_integer_, NA_character_, NA_character_, NA_character_, NA_character_, "Alignments and Visualisation", "practicals/8.2_Scripting_Alignments.html",
9, "2020-05-11", "Enrichment Analysis", "Stephen Pederson", "lectures/8_EnrichmentTesting.pdf", "Differential Expression Using edgeR", "practicals/9.1_edgeR.html",
NA_integer_, NA_character_, NA_character_, NA_character_, NA_character_, "Enrichment Strategies", "practicals/9.2_EnrichmentAnalysis.html",
10, "2020-05-18", "Network Analysis", "Zhipeng Qu", "lectures/Lecture10_Network_Analysis_ZQ_2020.pdf", "WGCNA_part1", "practicals/10.1_WGCNA_part1.html",
NA_integer_, NA_character_, NA_character_, NA_character_, NA_character_, "WGCNA_part2", "practicals/10.2_WGCNA_part2.html",
11, "2020-05-25", "Single Cell RNA-Seq", "Stephen Pederson", "lectures/10_scRNA.pdf", "scRNA", "practicals/11.1_scRNA.html",
NA_integer_, NA_character_, NA_character_, NA_character_, NA_character_, "scRNA", "practicals/11.1_scRNA.html#removing_other_low_quality_cells",
12, "2020-06-01", "Transcriptome Assembly", "Terry Bertozzi", "lectures/11_Transcriptome_Assembly.pdf", "Using StringTie to Define New Transcripts", "practicals/12_Stringtie.html",
NA_integer_, NA_character_, NA_character_, NA_character_, NA_character_, "Assignment and Project Questions", "",
13, "2020-06-07", "Cancer Applications", "Dan Thomas", "", "", ""
)
```
# Timetable
- **Lectures**
- Monday 9:10am - 10:00am, Ingkarni Wardli, Room B17
- **Practicals**
- Wednesday 9:10am - 11:00am, Johnson Building, Room 111
- Friday 9:10am - 11:00am, Johnson Building, Room 111
Lectures for this course are held on a Monday, and will clash with **two Public Holidays** in Semester 1.
1. Week 2, March 9^th^, Adelaide Cup Day: **No Lecture in Week 2**
2. Week 13, June 7^th^, Queen's Birthday: An alternative lecture time may be found for this week. This will be announced closer to the date.
```{r}
pracs %>%
mutate(
`Week Starting` = as_date(`Week Starting`),
Lecture = case_when(
is.na(Lecture) ~ NA_character_,
!grepl("\\*\\*", Lecture) ~ paste0("[", Lecture, "](", LecUrl, ")", " (", Lecturer, ")"),
grepl("\\*\\*", Lecture) ~ paste0(Lecture, " (", Lecturer, ")")
),
Practical = paste0("[", Practical, "](", PracUrl, ")")
) %>%
dplyr::select(starts_with("Week"), Lecture, Practical) %>%
kable() %>%
kable_styling(
bootstrap_options = c("striped", "hover", "condensed", "responsive")
)
```
# Assessments
```{r}
ass <- tribble(
~Url, ~Topic, ~`Due Date`, ~Solutions,
"assignments/A1.html", "Introductory Work", "2020-03-24", "assignments/A1_Solutions.html",
"assignments/A2.html", "Gene Expression", "2020-04-09", "assignments/A2_Solutions.html",
"assignments/A3.html", "Differential Analysis", "2020-05-12", "assignments/A3_Solutions.html",
"assignments/A4.html", "Enrichment Analysis", "2020-05-26", "assignments/A4_Solutions.html",
"assignments/A5.html", "WGCNA and scRNA", "2020-06-09","assignments/A5_Solutions.html",
"assignments/A6.html", "Transcriptome Assembly", "2020-06-19", "assignments/A6_Solutions.html"
) %>%
mutate(
Assessment = paste("Assessment", seq_len(nrow(.)) )
)
```
## Assessment Tasks
```{r}
ass %>%
mutate(
Solutions = case_when(
Solutions == "" ~ "",
Solutions != "" ~ paste0("[", Assessment, " Solutions](", Solutions, ")")
),
Assessment = paste0("[", Assessment, "](", Url, ")")
) %>%
dplyr::select(Assessment, Topic, `Due Date`, Solutions) %>%
kable() %>%
kable_styling(
bootstrap_options = c("striped", "hover", "condensed", "responsive")
)
```
## Major Project
For the postgraduate students, an additional Major Project is included as part of your curriculum.
The details of this project are available [here](assignments/MajorProject.html)
## Assessment Checklist
Have you:
- [ ] Answered all the questions?
- [ ] Followed naming conventions for Assessments?
- [ ] Checked that you have not breached the [Academic Honesty Policy](http://www.adelaide.edu.au/policies/230/).
- [ ] Identified the work as yours?
- Emails should have the course and assessment task names.
- Documents should be named with your name, the course name and the assessment task.
- Printed documents should have you name and the course and assessment task in the text/footer/header.
- [ ] Used appropriate electronic communication with assessors?
- Emails should have a meaningful subject.
- [ ] Handed in the assignment before the due time (see MyUni)?
# Useful Links
[How To Ask Questions The Smart Way](http://www.catb.org/esr/faqs/smart-questions.html)
[How to write a good bug report](https://musescore.org/en/developers-handbook/how-write-good-bug-report-step-step-instructions)