Course Modules: 201910-Spring 2019-BINF-3121-001-Statistics for Bioinformatics

Week 1 - R Introduction - Jan 14

Week 1 - R Introduction - Jan 14 Week 1 - R Introduction - Jan 14

Context Module Sub Header

Slides & Notes 1

context_module_sub_header 1564712 0

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External Url

Introduction to the class Introduction to the class 2

external_url 1564713 0

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
External Url

Introduction to R and RStudio Introduction to R and RStudio 3

external_url 1564714 0

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Context Module Sub Header

Assignments 4

context_module_sub_header 1564715 0

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Assignment

Install RStudio, R Install RStudio, R 5 5

assignment 1564716 1

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
External Url

How to: Install R and RStudio How to: Install R and RStudio 6

external_url 1564717 0

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Context Module Sub Header

Stanford OLI Probstat - Reading & Quiz 10

context_module_sub_header 1564718 0

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Assignment

Stanford OLI Probstat - Part 1 - Exploratory Data Analysis Stanford OLI Probstat - Part 1 - Exploratory Data Analysis 11

assignment 1564719 1

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Quiz

Quiz - Stanford OLI Probstat - Part 1 - Exploratory Data Analysis Quiz - Stanford OLI Probstat - Part 1 - Exploratory Data Analysis 21 12

quiz 1564720 1

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete

Week 2 - Functions & Vectors - Jan 21 (no class - MLK holiday)

Week 2 - Functions & Vectors - Jan 21 (no class - MLK holiday) Week 2 - Functions & Vectors - Jan 21 (no class - MLK holiday)

Context Module Sub Header

At home: R tutorial and quiz 1

context_module_sub_header 1564721 0

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Assignment

R Tutorial - Functions & vectors R Tutorial - Functions & vectors 2

assignment 1564722 1

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Quiz

Quiz - R Tutorial - Functions & vectors Quiz - R Tutorial - Functions & vectors 13 3

quiz 1564723 1

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Context Module Sub Header

Stanford OLI ProbStat Reading and Quiz 5

context_module_sub_header 1564725 0

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Assignment

Stanford OLI Probstat - Part 2 - Probability 1 Stanford OLI Probstat - Part 2 - Probability 1 6

assignment 1564726 1

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Quiz

Quiz - Stanford OLI Probstat - Part 2 - Probability 1 Quiz - Stanford OLI Probstat - Part 2 - Probability 1 40 7

quiz 1564727 1

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete

Week 3 - Matrices & data frames - Jan 28

Week 3 - Matrices & data frames - Jan 28 Week 3 - Matrices & data frames - Jan 28

Context Module Sub Header

In-class: R tutorial and quiz 1

context_module_sub_header 1564728 0

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Attachment

In-class practice & review: Functions and Vectors In-class practice & review: Functions and Vectors 2

attachment 1564724 0

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Assignment

R tutorial - Matrices & data frames R tutorial - Matrices & data frames 3

assignment 1564729 1

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Quiz

Quiz - R Tutorial - Matrices & data frames Quiz - R Tutorial - Matrices & data frames 6 4

quiz 1564730 1

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Context Module Sub Header

Assignment 5

context_module_sub_header 1564731 0

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Quiz

Quiz: Using R for exploratory data analysis Quiz: Using R for exploratory data analysis 45 6

quiz 1564732 1

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete

Week 4 - Reading & analyzing data - Feb 4

Week 4 - Reading & analyzing data - Feb 4 Week 4 - Reading & analyzing data - Feb 4

Context Module Sub Header

In-class: R tutorial and quiz 1

context_module_sub_header 1564733 0

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Assignment

R Tutorial - Reading & analyzing data R Tutorial - Reading & analyzing data 2

assignment 1564734 1

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Quiz

Quiz - R Tutorial - Reading & analyzing data Quiz - R Tutorial - Reading & analyzing data 11 3

quiz 1564735 1

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Context Module Sub Header

Assignments 4

context_module_sub_header 1564736 0

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Assignment

Install knitr, upload a knitted Markdown Install knitr, upload a knitted Markdown 5 5

assignment 1564737 1

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Context Module Sub Header

Stanford OLI ProbStat Reading and Quiz 8

context_module_sub_header 1564738 0

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Assignment

Stanford OLI Probstat - Part 3 - Probability 2 Stanford OLI Probstat - Part 3 - Probability 2 9

assignment 1564739 1

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Quiz

Quiz - Stanford OLI Probstat - Part 3 - Probability 2 Quiz - Stanford OLI Probstat - Part 3 - Probability 2 41 10

quiz 1564740 1

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete

Week 5 - Writing reports with Markdown - Feb 11

Week 5 - Writing reports with Markdown - Feb 11 Week 5 - Writing reports with Markdown - Feb 11

Context Module Sub Header

Notes and Slides 1

context_module_sub_header 1564741 0

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Page

Data Analysis Report - What to include, how to write it Data Analysis Report - What to include, how to write it 2

wiki_page 1614065 0

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Attachment

Background Info: BED file format for describing gene models Background Info: BED file format for describing gene models 3

attachment 1564743 0

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Context Module Sub Header

Data Analysis 4

context_module_sub_header 1564744 0

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Assignment

Distribution of gene lengths in two Brassicas: Camelina sativa and Arabidopsis thaliana Distribution of gene lengths in two Brassicas: Camelina sativa and Arabidopsis thaliana 50 5

assignment 1564745 1

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Attachment

howToReadBedFiles.R howToReadBedFiles.R 6

attachment 1564746 0

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Context Module Sub Header

Example Markdown 7

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Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Page

Example Markdown and knitted Markdown Example Markdown and knitted Markdown 8

wiki_page 1614066 0

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete

Week 6 - Conditional probability - Feb 18

Week 6 - Conditional probability - Feb 18 Week 6 - Conditional probability - Feb 18

Assignment

Writing functions in R - getProbDisease Writing functions in R - getProbDisease 20 1

assignment 1564749 1

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Quiz

Quiz: Probability of disease given a positive test result Quiz: Probability of disease given a positive test result 20 3

quiz 1747546 1

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete

Week 7 - Sample means - Feb 25

Week 7 - Sample means - Feb 25 Week 7 - Sample means - Feb 25

Context Module Sub Header

In-class assignment 1

context_module_sub_header 1564751 0

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Assignment

Using R built-in distribution functions to solve sample mean problems Using R built-in distribution functions to solve sample mean problems 40 2

assignment 1564752 1

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Attachment

Example.zip Example.zip 3

attachment 1564753 0

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Context Module Sub Header

Notes and Slides 4

context_module_sub_header 1564754 0

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Attachment

UsingBuiltinProbDistributions.pdf UsingBuiltinProbDistributions.pdf 5

attachment 1564755 0

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Attachment

07-PointEstimators.pptx 07-PointEstimators.pptx 6

attachment 1564756 0

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Context Module Sub Header

Stanford OLI ProbStat Reading and Quiz 7

context_module_sub_header 1564757 0

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Quiz

Quiz - Stanford OLI Probstat - Part 4 - Inference 1 Quiz - Stanford OLI Probstat - Part 4 - Inference 1 42 8

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Assignment

Stanford OLI Probstat - Part 4 - Inference 1 Stanford OLI Probstat - Part 4 - Inference 1 9

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Page

Data sets (.RData files) for Quiz Data sets (.RData files) for Quiz 10

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Context Module Sub Header

Reading 11

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Assignment

All significance tests are the same All significance tests are the same 0 12

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Week 8 - Inference I - Mar 4 (no class - spring break)

Week 8 - Inference I - Mar 4 (no class - spring break) Week 8 - Inference I - Mar 4 (no class - spring break)

Context Module Sub Header

Notes and Slides 1

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Attachment

Z score test Z score test 2

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Attachment

One sample t test One sample t test 3

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Attachment

Two sample t test - paired & unpaired Two sample t test - paired & unpaired 4

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Context Module Sub Header

Example Data Sets 5

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Attachment

DrunkDrivers.txt DrunkDrivers.txt 6

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Context Module Sub Header

Stanford OLI ProbStat Reading and Quiz 7

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Assignment

Stanford OLI Probstat - Part 5 - Inference 2 Stanford OLI Probstat - Part 5 - Inference 2 8

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Quiz

Quiz -Stanford OLI Probstat - Part 5 - Inference 2 Quiz -Stanford OLI Probstat - Part 5 - Inference 2 45 9

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Context Module Sub Header

Reading 10

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Assignment

Check your understanding of a p value Check your understanding of a p value 0 11

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Week 9 - Inference II - Mar 11

Week 9 - Inference II - Mar 11 Week 9 - Inference II - Mar 11

Context Module Sub Header

Notes & Slides 1

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Page

Slides: Comparing groups - Background for ProbStat Inference II Quiz Slides: Comparing groups - Background for ProbStat Inference II Quiz 2

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Attachment

Comparing 3+ groups - ANOVA Comparing 3+ groups - ANOVA 3

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Page

Mid-term review and practice Mid-term review and practice 4

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Attachment

Midterm Review Problems .docx Midterm Review Problems .docx 5

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Context Module Sub Header

Example Data 7

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Attachment

flicker.txt flicker.txt 8

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Context Module Sub Header

Code 9

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Attachment

Inference1.Rmd Inference1.Rmd 10

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Attachment

FlickerTesting.Rmd FlickerTesting.Rmd 11

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Week 10 - Midterm Exam - Mar 18

Week 10 - Midterm Exam - Mar 18 Week 10 - Midterm Exam - Mar 18

Context Module Sub Header

Stanford OLI Probstat 1

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Quiz

Stanford ProbStat Final Quiz Stanford ProbStat Final Quiz 145 2

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Context Module Sub Header

Assignments 4

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Page

Install and test limma, affy Install and test limma, affy 5

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Assignment

Install and test affy, limma Install and test affy, limma 10 6

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Week 11 - DNA microarrays & limma - Mar 25

Week 11 - DNA microarrays & limma - Mar 25 Week 11 - DNA microarrays & limma - Mar 25

Context Module Sub Header

Data Analysis - In Class 1

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Page

DNA microarray data analysis example - programmed cell death experiment DNA microarray data analysis example - programmed cell death experiment 2

wiki_page 1564791 0

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Quiz

Quiz - DNA microarray data analysis example - programmed cell death experiment Quiz - DNA microarray data analysis example - programmed cell death experiment 25 3

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Context Module Sub Header

Background 6

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Page

DNA microarrays - background reading DNA microarrays - background reading 7

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Page

Links to resources Links to resources 8

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Week 12 - Linear models - Apr 1

Week 12 - Linear models - Apr 1 Week 12 - Linear models - Apr 1

Context Module Sub Header

Background - watch & do before class 1

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Page

Linear models introduction Linear models introduction 2

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Quiz

Quiz on background materials - linear models Quiz on background materials - linear models 36 3

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Context Module Sub Header

Data analysis - in class 4

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Page

Files needed for today Files needed for today 5

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Assignment

Optional Assignment - Linear models practice Markdown Optional Assignment - Linear models practice Markdown 0 6

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Context Module Sub Header

Resources mentioned in class 7

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External Url

Prof. Kasper Hansen's video explaining S4 classes in Bioconductor Prof. Kasper Hansen's video explaining S4 classes in Bioconductor 8

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External Url

Video: Linear Models as Matrix Multiplication I (Prof. Irizarry) Video: Linear Models as Matrix Multiplication I (Prof. Irizarry) 9

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External Url

Video: Linear Models as Matrix Multiplication II (Prof. Irizarry) Video: Linear Models as Matrix Multiplication II (Prof. Irizarry) 10

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External Url

Expressing design formula in R (Prof. Irizarry) Expressing design formula in R (Prof. Irizarry) 11

external_url 1564806 0

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External Url

Prof. Kasper Hansen's free course "Bioconductor for Genomic Data Science" Prof. Kasper Hansen's free course "Bioconductor for Genomic Data Science" 12

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External Url

Factors in R (UC Berkeley State 133 class) Factors in R (UC Berkeley State 133 class) 13

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Week 13 - RNA-Seq - Apr 8

Week 13 - RNA-Seq - Apr 8 Week 13 - RNA-Seq - Apr 8

Context Module Sub Header

Data Analysis 1

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Page

RNA-Seq slides and notes RNA-Seq slides and notes 2

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Page

Link to R code Link to R code 3

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Attachment

counts.txt counts.txt 4

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Attachment

samples.txt samples.txt 5

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Attachment

gene_description.txt gene_description.txt 6

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Quiz

RNA-Seq - Compare expression between sample types RNA-Seq - Compare expression between sample types 26 7

quiz 1782281 1

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Context Module Sub Header

Project options 9

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Assignment

Data Analysis Project - Student's choice Data Analysis Project - Student's choice 200 10

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Page

Use co-expression analysis to find new players in a biological process (stomata development) Use co-expression analysis to find new players in a biological process (stomata development) 11

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Page

Which genes are expressed everywhere and never change? Which genes are expressed everywhere and never change? 12

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Page

Find the most highly-expressed genes for biotechnology applications Find the most highly-expressed genes for biotechnology applications 13

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Page

Can the R subread package process RNA-Seq data on a consumer-grade computer? Can the R subread package process RNA-Seq data on a consumer-grade computer? 14

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Page

Reproduce a published microarray study of dicamba (an herbicide) and compare results Reproduce a published microarray study of dicamba (an herbicide) and compare results 15

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Week 14 - Data analysis project - Apr 15

Week 14 - Data analysis project - Apr 15 Week 14 - Data analysis project - Apr 15

Assignment

Choose a project Choose a project 10 1

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Week 15 - In-class data analysis - Apr 22

Week 15 - In-class data analysis - Apr 22 Week 15 - In-class data analysis - Apr 22

Week 16 - In-class data analysis - Apr 29

Week 16 - In-class data analysis - Apr 29 Week 16 - In-class data analysis - Apr 29

Course Modules

Week 1 - R Introduction - Jan 14

Slides & Notes 1

Assignments 4

Stanford OLI Probstat - Reading & Quiz 10

Week 2 - Functions & Vectors - Jan 21 (no class - MLK holiday)

At home: R tutorial and quiz 1

Stanford OLI ProbStat Reading and Quiz 5

Week 3 - Matrices & data frames - Jan 28

In-class: R tutorial and quiz 1

Assignment 5

Week 4 - Reading & analyzing data - Feb 4

In-class: R tutorial and quiz 1

Assignments 4

Stanford OLI ProbStat Reading and Quiz 8

Week 5 - Writing reports with Markdown - Feb 11

Notes and Slides 1

Data Analysis 4

Example Markdown 7

Week 6 - Conditional probability - Feb 18

Week 7 - Sample means - Feb 25

In-class assignment 1

Notes and Slides 4

Stanford OLI ProbStat Reading and Quiz 7

Reading 11

Week 8 - Inference I - Mar 4 (no class - spring break)

Notes and Slides 1

Example Data Sets 5

Stanford OLI ProbStat Reading and Quiz 7

Reading 10

Week 9 - Inference II - Mar 11

Notes & Slides 1

Example Data 7

Code 9

Week 10 - Midterm Exam - Mar 18

Stanford OLI Probstat 1

Assignments 4

Week 11 - DNA microarrays & limma - Mar 25

Data Analysis - In Class 1

Background 6

Week 12 - Linear models - Apr 1

Background - watch & do before class 1

Data analysis - in class 4

Resources mentioned in class 7

Week 13 - RNA-Seq - Apr 8

Data Analysis 1

Project options 9

Week 14 - Data analysis project - Apr 15

Week 15 - In-class data analysis - Apr 22

Week 16 - In-class data analysis - Apr 29