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