Biology 720

Mondays 12:30-2:20pm BSB 105 2019

This class will provide students with a brief introduction to UNIX and to the R statistical environment. Each week problem sets will be given to provide students with necessary practice on the class material. The problems will be related to common bioinformatics tasks where appropriate.

We recommend, but do not require, students buy “Bioinformatics Data Skills" by Vince Buffalo, Orielly Publ. (You may also be interested in Practical Computing for Biologists by Haddock & Dunn, Sinauer).

We require that those with a Windows laptop install the mobaxterm software before coming to class (apple users can ignore this). If there are problems doing this, bring your laptop to LSB 522 well before class. geno data


You can preview,
https://www.youtube.com/watch?v=id3DGvljhT4

Contact Dr. Brian Golding (Golding@McMaster.CA, LSB 533) for more information.


Week 1: Some commands
Week 2: Redirection, nano, head, tail
Week 3: Some utilities
Week 3: Some regex
Week 4: Some shell stuff
Week 5: Some practical utilities



For Dr. Evans part of the course on using R for bioinformatics, he will
be making use of the fantastic resources of DataCamp. See
https://www.datacamp.com/home.




Week 2: exercise answers
Week 3: exercises answers
Week 4: exercises answers
Week 5: exercises answers

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R and R-studio
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Nov4 2019 lecture notes
Problem Set 1; due Nov 11

Class_problems_Nov_4_and_11
Nov11_2019_lecture_notes.pdf
Problem_set_2

Class_problems_Nov_18
Nov18_2019_lecture_notes.pdf
Problem_set_3

Class_problems_Nov_25
Nov25_2019_lecture_notes.pdf
Problem_set_4

Dec2_2019_lecture_notes.pdf

Lecture Notes

R_lecture_1_calculator_vectors_datatypes.R
R_lecture_2_matrices_and_arrays.R
R_lecture_3_reading_and_writing_data.R
R_lecture_4_scripts_ and_loops.R
R_lecture_5_functions.R
R_lecture_6_ggplot.R