From ae8cc7e5966c17cec57b2cc5f02036f2ad219c1c Mon Sep 17 00:00:00 2001 From: Natalie Elphick Date: Sun, 4 May 2025 21:23:32 -0700 Subject: [PATCH] update for May 2025 --- docs/Intro_to_R_data_analysis_part_1.html | 44 +++++++++++-------- docs/Intro_to_R_data_analysis_part_2.html | 35 +++++++-------- .../Intro_to_R_data_analysis_part_1.Rmd | 39 +++++++++------- .../Intro_to_R_data_analysis_part_2.Rmd | 27 +++++------- 4 files changed, 75 insertions(+), 70 deletions(-) diff --git a/docs/Intro_to_R_data_analysis_part_1.html b/docs/Intro_to_R_data_analysis_part_1.html index 2cfd342..ab81985 100644 --- a/docs/Intro_to_R_data_analysis_part_1.html +++ b/docs/Intro_to_R_data_analysis_part_1.html @@ -3,7 +3,7 @@ - + Introduction to R Data Analysis @@ -2571,8 +2571,8 @@ class CountdownTimer {

Introduction to R Data Analysis

Part 1

-

Natalie Elphick

-

January 27th, 2025

+

Natalie Gill

+

May 5th, 2025

@@ -2583,10 +2583,8 @@ class CountdownTimer {

Introductions

-

Natalie Elphick
+

Natalie Gill
Bioinformatician II

-

Michela Traglia
-Senior Statistician

Poll 1

@@ -2652,8 +2650,8 @@ the end of the workshop to continue at your own pace.
@@ -2883,7 +2881,7 @@ value?

  • “1.5” - Numeric
  • “A” - Character
  • 1L - Integer
    • -
  • TRUE - Boolean
    • +
  • TRUE - Boolean/Logical
    • @@ -2923,7 +2921,7 @@ types/structures (ex. nested lists)

    10 min break

    -
    +
    10:00
    @@ -3092,7 +3090,7 @@ correct format

    Why use Tidyverse Packages?

      -
    • Most of the work in data analysis is getting data into the correct +
    • Much of the work in data analysis is getting data into the correct format to create outputs (plots and tables)
    • The tidyverse collection of packages simplifies this process
        @@ -3108,6 +3106,17 @@ graphics)

        End of Part 1

        +
        +
        +

        Schedule for Part 2

        +
          +
        1. Introduction to Tidyverse
          2. +
        2. Filtering and reformatting data
          3. +
        3. Plotting data
          4. +
        4. Hands on data analysis
          5. +
        5. AI tips for R
          6. +
        6. Where to get help
          7. +

        Workshop survey

        @@ -3118,15 +3127,12 @@ survey so we can continue to improve these workshops

        Upcoming Workshops

        -

        Introduction -to Unix Command Line
        -February 10-February 11, 2025 1:00-3:00pm PST

        -

        Introduction -to RNA-Seq Analysis
        -February 13-February 14, 2025 1:00-4:00pm PST

        -

        Intermediate +

        Introduction +to RNA-Seq
        +May 12-May 13, 2025 1:00-4:00pm PDT

        +

        Intermediate RNA-Seq Analysis Using R
        -February 20, 2025 9:00am-12:00pm PST

        +May 19, 2025 1:00-4:00pm PDT

        • Check this link at for the full schedule
          • diff --git a/docs/Intro_to_R_data_analysis_part_2.html b/docs/Intro_to_R_data_analysis_part_2.html index 3c8a716..be40c2e 100644 --- a/docs/Intro_to_R_data_analysis_part_2.html +++ b/docs/Intro_to_R_data_analysis_part_2.html @@ -3,7 +3,7 @@ - + Introduction to R Data Analysis @@ -2795,8 +2795,8 @@ border: 0;

          Introduction to R Data Analysis

          Part 2

          -

          Natalie Elphick

          -

          January 28th, 2025

          +

          Natalie Gill

          +

          May 6th, 2025

          @@ -2807,10 +2807,8 @@ border: 0;

          Introductions

          -

          Natalie Elphick
          +

          Natalie Gill
          Bioinformatician II

          -

          Min-Gyoung Shin
          -Bioinformatician III

          @@ -2820,7 +2818,7 @@ Bioinformatician III

        • Filtering and reformatting data
        • Plotting data
        • Hands on data analysis
          • -
        • ChatGPT tips for R
          • +
        • AI tips for R
        • Where to get help
          • @@ -3046,7 +3044,7 @@ modified by adding layers

          10 min break

          -
          +
          10:00
          @@ -4254,15 +4252,15 @@ part2_filled_out.html
    -
    -

    ChatGPT Tips for R

    +
    +

    AI Tips for R

    General Tips

    • Follow any relevant institutional guidelines on using LLMs
      • -
    • Always confirm ChatGPT’s outputs are correct
      • +
    • Always confirm the outputs are correct
    • Provide as much detail as possible about the problem in the 1st prompt
    • Use separate chats for separate tasks/projects
      • @@ -4274,7 +4272,7 @@ prompt
      • Commented R code yields better responses
      • Provide the code and error message in the same prompt
        • -
      • ChatGPT can work well to convert syntax and improve your code: +
      • LLMs can work well to convert syntax and improve your code:
        • “Turn this loop into a function : [your code]”
        • “Is there a better way to do this : [your code]”
          • @@ -4364,15 +4362,12 @@ survey so we can continue to improve these workshops

    Upcoming Workshops

    -

    Introduction -to Unix Command Line
    -February 10-February 11, 2025 1:00-3:00pm PST

    -

    Introduction -to RNA-Seq Analysis
    -February 13-February 14, 2025 1:00-4:00pm PST

    -

    Intermediate +

    Introduction +to RNA-Seq
    +May 12-May 13, 2025 1:00-4:00pm PDT

    +

    Intermediate RNA-Seq Analysis Using R
    -February 20, 2025 9:00am-12:00pm PST

    +May 19, 2025 1:00-4:00pm PDT

    • Check this link at for the full schedule
      • diff --git a/intro-r-data-analysis/Intro_to_R_data_analysis_part_1.Rmd b/intro-r-data-analysis/Intro_to_R_data_analysis_part_1.Rmd index d433254..3337184 100644 --- a/intro-r-data-analysis/Intro_to_R_data_analysis_part_1.Rmd +++ b/intro-r-data-analysis/Intro_to_R_data_analysis_part_1.Rmd @@ -1,8 +1,8 @@ --- title: "Introduction to R Data Analysis" subtitle: "Part 1" -author: "Natalie Elphick" -date: "January 27th, 2025" +author: "Natalie Gill" +date: "May 5th, 2025" knit: (function(input, ...) { rmarkdown::render( input, @@ -26,13 +26,9 @@ knitr::opts_chunk$set(comment = "") ## Introductions -**Natalie Elphick** +**Natalie Gill** Bioinformatician II -**Michela Traglia** -Senior Statistician - - ## Poll 1 @@ -83,7 +79,7 @@ Keep at it—progress comes with persistence! ## R - An open source language developed for statistical computing by **R**oss Ihaka and **R**obert Gentleman -- Inspired by the **S** language developed at Bell labs in 1976 to make interactive data analysis easier +- Developed at Bell labs in 1976 to make interactive data analysis easier - The first official version was released in 2000 ## Why use R for data analysis? @@ -266,7 +262,7 @@ NA + 1 1. "1.5" - Numeric 2. "A" - Character 3. 1L - Integer -4. TRUE - Boolean +4. TRUE - Boolean/Logical @@ -466,7 +462,7 @@ packages ## Why use Tidyverse Packages? -- Most of the work in data analysis is getting data into the correct format to create outputs (plots and tables) +- Much of the work in data analysis is getting data into the correct format to create outputs (plots and tables) - The tidyverse collection of packages simplifies this process - Intuitive syntax - Comprehensive (data manipulation, cleaning, modeling and graphics) @@ -476,19 +472,30 @@ packages # End of Part 1 + +## Schedule for Part 2 + +1. Introduction to Tidyverse +2. Filtering and reformatting data +3. Plotting data +4. Hands on data analysis +5. AI tips for R +6. Where to get help + + + ## Workshop survey - Please fill out our [workshop survey](https://www.surveymonkey.com/r/bioinfo-training) so we can continue to improve these workshops ## Upcoming Workshops -[Introduction to Unix Command Line](https://gladstone.org/events/introduction-unix-command-line-2) -February 10-February 11, 2025 1:00-3:00pm PST +[Introduction to RNA-Seq](https://gladstone.org/events/introduction-rna-seq-0) +May 12-May 13, 2025 1:00-4:00pm PDT -[Introduction to RNA-Seq Analysis](https://gladstone.org/events/introduction-rna-seq-analysis-8) -February 13-February 14, 2025 1:00-4:00pm PST -[Intermediate RNA-Seq Analysis Using R](https://gladstone.org/events/intermediate-rna-seq-analysis-using-r-6) -February 20, 2025 9:00am-12:00pm PST +[Intermediate RNA-Seq Analysis Using R](https://gladstone.org/events/intermediate-rna-seq-analysis-using-r-7) +May 19, 2025 1:00-4:00pm PDT + - Check [this link](https://gladstone.org/events?series=data-science-training-program) at for the full schedule diff --git a/intro-r-data-analysis/Intro_to_R_data_analysis_part_2.Rmd b/intro-r-data-analysis/Intro_to_R_data_analysis_part_2.Rmd index 9c0ebe4..b914f00 100644 --- a/intro-r-data-analysis/Intro_to_R_data_analysis_part_2.Rmd +++ b/intro-r-data-analysis/Intro_to_R_data_analysis_part_2.Rmd @@ -1,8 +1,8 @@ --- title: "Introduction to R Data Analysis" subtitle: "Part 2" -author: "Natalie Elphick" -date: "January 28th, 2025" +author: "Natalie Gill" +date: "May 6th, 2025" knit: (function(input, ...) { rmarkdown::render( input, @@ -28,11 +28,9 @@ knitr::opts_chunk$set(comment = "")
      *Press the ? key for tips on navigating these slides*
      # Introductions -**Natalie Elphick** +**Natalie Gill** Bioinformatician II -**Min-Gyoung Shin** -Bioinformatician III # Schedule @@ -40,7 +38,7 @@ Bioinformatician III 2. Filtering and reformatting data 3. Plotting data 4. Hands on data analysis -5. ChatGPT tips for R +5. AI tips for R 6. Where to get help @@ -239,12 +237,13 @@ Steps: -# ChatGPT Tips for R +# AI Tips for R + ## General Tips - Follow any relevant institutional guidelines on using LLMs -- Always confirm ChatGPT's outputs are correct +- Always confirm the outputs are correct - Provide as much detail as possible about the problem in the 1st prompt - Use separate chats for separate tasks/projects - Try the 'Custom Instructions' function @@ -253,7 +252,7 @@ Steps: - Commented R code yields better responses - Provide the code and error message in the same prompt -- ChatGPT can work well to convert syntax and improve your code: +- LLMs can work well to convert syntax and improve your code: - "Turn this loop into a function : [your code]" - "Is there a better way to do this : [your code]" - Check out the file: `example_code/1_convert_syntax_example.R` for an example use case @@ -306,14 +305,12 @@ Code templates can be used to avoid typing the same code over and over again. ## Upcoming Workshops -[Introduction to Unix Command Line](https://gladstone.org/events/introduction-unix-command-line-2) -February 10-February 11, 2025 1:00-3:00pm PST +[Introduction to RNA-Seq](https://gladstone.org/events/introduction-rna-seq-0) +May 12-May 13, 2025 1:00-4:00pm PDT -[Introduction to RNA-Seq Analysis](https://gladstone.org/events/introduction-rna-seq-analysis-8) -February 13-February 14, 2025 1:00-4:00pm PST +[Intermediate RNA-Seq Analysis Using R](https://gladstone.org/events/intermediate-rna-seq-analysis-using-r-7) +May 19, 2025 1:00-4:00pm PDT -[Intermediate RNA-Seq Analysis Using R](https://gladstone.org/events/intermediate-rna-seq-analysis-using-r-6) -February 20, 2025 9:00am-12:00pm PST - Check [this link](https://gladstone.org/events?series=data-science-training-program) at for the full schedule