From 03f07124d1ade08820d4245e2df9264e45128bbc Mon Sep 17 00:00:00 2001 From: Natalie Elphick Date: Fri, 24 Jan 2025 12:32:34 -0800 Subject: [PATCH] update for Jan 2025 --- docs/Intro_to_R_data_analysis_part_1.html | 32 +- docs/Intro_to_R_data_analysis_part_2.html | 336 +----------------- .../Intro_to_R_data_analysis_part_1.Rmd | 23 +- .../Intro_to_R_data_analysis_part_2.Rmd | 23 +- .../intro-r-data-analysis.Rproj | 1 + 5 files changed, 60 insertions(+), 355 deletions(-) diff --git a/docs/Intro_to_R_data_analysis_part_1.html b/docs/Intro_to_R_data_analysis_part_1.html index 67bdaa8..617a1ff 100644 --- a/docs/Intro_to_R_data_analysis_part_1.html +++ b/docs/Intro_to_R_data_analysis_part_1.html @@ -2572,7 +2572,7 @@ class CountdownTimer {

Introduction to R Data Analysis

Part 1

Natalie Elphick

-

November 11th, 2024

+

January 27th, 2025

@@ -2584,7 +2584,9 @@ class CountdownTimer {

Introductions

Natalie Elphick
-Bioinformatician I

+Bioinformatician II

+

Michela Traglia
+Senior Statistician

Poll 1

@@ -2921,7 +2923,7 @@ types/structures (ex. nested lists)

10 min break

-
+
10:00
@@ -3091,7 +3093,7 @@ correct format

Why use Tidyverse Packages?

  • Most of the work in data analysis is getting data into the correct -format to create outputs
    • +format to create outputs (plots and tables)
  • The tidyverse collection of packages simplifies this process
    • Intuitive syntax
      • @@ -3110,21 +3112,21 @@ graphics)

      Workshop survey

        -
      • Please fill out our workshop survey so we -can continue to improve these workshops
        • +
      • Please fill out our workshop +survey so we can continue to improve these workshops

      Upcoming Workshops

      -

      Introduction -to scATAC-seq Data Analysis
      -November 14 - November 15, 2024 1:00-4:00pm PST

      -

      Introduction -to Linear Mixed Effects Models
      -November 18-November 19, 2024 1:00-3:00pm PST

      -

      scATAC-seq -and scRNA-seq Data Integration
      -November 22, 2024 1:00-4:00pm PST

      +

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

      • 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 45a78e8..3c8a716 100644 --- a/docs/Intro_to_R_data_analysis_part_2.html +++ b/docs/Intro_to_R_data_analysis_part_2.html @@ -2796,7 +2796,7 @@ border: 0;

        Introduction to R Data Analysis

        Part 2

        Natalie Elphick

        -

        November 12th, 2024

        +

        January 28th, 2025

      @@ -2808,7 +2808,7 @@ border: 0;

      Introductions

      Natalie Elphick
      -Bioinformatician I

      +Bioinformatician II

      Min-Gyoung Shin
      Bioinformatician III

      @@ -3046,7 +3046,7 @@ modified by adding layers

      10 min break

      -
      +
      10:00
      @@ -3072,313 +3072,12 @@ and recently extinct mammals compiled from literature

      Taxonomic Rank

      -

      - - - - - - - - - - - - - লাল শিয়াল - (ভালপেস ভালপেস) - Rotfuchs - (Vulpes vulpes) - Zorro rojo - (Vulpes vulpes) - - မြေခွေးနီ (Vulpes vulpes) - обыкновенная лисица - (Vulpes vulpes) - - රතු හිවලා (වුල්පෙස් වුල්පෙස්) - Rödräv - (Vulpes vulpes) - - लाल लोमड़ी - वुल्पेस वुल्पेस - Црвена лисица - (Vulpes vulpes) - Red fox - (Vulpes vulpes) - - - অধিজগৎজগৎপর্বশ্রেণিবর্গগোত্রগণ - প্রজাতি - DomäneReichStammKlasseOrdnungFamilieGattung - Art - DominioReinoFiloClaseOrdenFamiliaGénero - Especie - နယ်ပယ်လောကမျိုးပေါင်းစုမျိုးပေါင်းမျိုးစဉ်မျိုးရင်းမျိုးစု - မျိုးစိတ် - ДоменЦарствоТипКлассОтрядСемействоРод - Вид - වසමරාජධානියවංශයවර්ගයගෝත්‍රයකුලයගණය - විශේෂය - DomänRikeFylumKlassOrdningFamiljSläkte - Art - - अधिजगत्जगत् संघवर्गगणकुटुम्बवंश - जाति - ДоменЦарствоКоленоКласаРедСемејствоРод - Вид - DomainKingdomPhylumClassOrderFamilyGenus - Species - - - সুকেন্দ্রিকপ্রাণীমেরুদণ্ডীস্তন্যপায়ীশ্বাপদক্যানিডেভালপেস - ভালপেস ভালপেস - EucariotaAnimaliaCordadosMamíferosCarnívoraCánidosVulpes - Vulpes vulpes - ယူကာရုတ်တိရစ္ဆာန်ကော်ဒိတ်နို့တိုက်သတ္တဝါကာနီဗိုရာခွေးမျိုးရင်းVulpes - Vuples vulpes - ЭукариотыЖивотныеХордовыеМлекопитающиеХищныеПсовыеVulpes - Vulpes vulpes - යුකේරියාඇනිමේලියාකෝඩේටාමමාලියාකානිවෝරාකානිඩේවුල්පෙස් - Vuples vulpes - EukaryoterDjurRyggsträngsdjurDäggdjurRovdjurHunddjurVulpes - Vulpes vulpes - - सुकेन्द्रकप्राणीरज्जुकीस्तनधारी मांसाहारीश्वानवुल्पेस - वुल्पेस वुल्पेस - ЕукариотиЖивотниХордовиЦицачиЅверовиКучињаЛисици - Црвена лисица - EukaryaAnimaliaChordataMammaliaCarnivoraCanidaeVulpes - Vulpes vulpes - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

      +

      Taxonomy

      Data Preview

      - +
      @@ -4627,7 +4326,7 @@ reach out to the authors using their preferred method

      Code templates can be used to avoid typing the same code over and over again.

      @@ -4658,21 +4358,21 @@ data analysis

      Workshop survey

        -
      • Please fill out our workshop survey so we -can continue to improve these workshops
        • +
      • Please fill out our workshop +survey so we can continue to improve these workshops

      Upcoming Workshops

      -

      Introduction -to scATAC-seq Data Analysis
      -November 14 - November 15, 2024 1:00-4:00pm PST

      -

      Introduction -to Linear Mixed Effects Models
      -November 18-November 19, 2024 1:00-3:00pm PST

      -

      scATAC-seq -and scRNA-seq Data Integration
      -November 22, 2024 1:00-4:00pm PST

      +

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

      • 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 cb8f4f6..d433254 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 @@ -2,7 +2,7 @@ title: "Introduction to R Data Analysis" subtitle: "Part 1" author: "Natalie Elphick" -date: "November 11th, 2024" +date: "January 27th, 2025" knit: (function(input, ...) { rmarkdown::render( input, @@ -27,8 +27,10 @@ knitr::opts_chunk$set(comment = "") ## Introductions **Natalie Elphick** -Bioinformatician I +Bioinformatician II +**Michela Traglia** +Senior Statistician @@ -464,7 +466,7 @@ packages ## Why use Tidyverse Packages? -- Most of the work in data analysis is getting data into the correct format to create outputs +- Most 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) @@ -475,19 +477,18 @@ packages # End of Part 1 ## Workshop survey -- Please fill out our [workshop survey](https://www.surveymonkey.com/r/F75J6VZ) so we can continue to improve these workshops +- 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 scATAC-seq Data Analysis](https://gladstone.org/events/introduction-scatac-seq-data-analysis) -November 14 - November 15, 2024 1:00-4:00pm PST +[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 Linear Mixed Effects Models](https://gladstone.org/events/introduction-linear-mixed-effects-models-0) -November 18-November 19, 2024 1:00-3:00pm PST - -[scATAC-seq and scRNA-seq Data Integration](https://gladstone.org/events/scatac-seq-and-scrna-seq-data-integration) -November 22, 2024 1:00-4:00pm PST +[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 - 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 f51e042..9c0ebe4 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 @@ -2,7 +2,7 @@ title: "Introduction to R Data Analysis" subtitle: "Part 2" author: "Natalie Elphick" -date: "November 12th, 2024" +date: "January 28th, 2025" knit: (function(input, ...) { rmarkdown::render( input, @@ -29,7 +29,7 @@ knitr::opts_chunk$set(comment = "") # Introductions **Natalie Elphick** -Bioinformatician I +Bioinformatician II **Min-Gyoung Shin** Bioinformatician III @@ -282,10 +282,11 @@ For any bioinformatics specific questions feel free to reach out to the Gladston Code templates can be used to avoid typing the same code over and over again. -- These are templates that we are using to automate things like plot appearance and documentation: +- These are templates can be used to automate things like plot appearance and documentation: - [.Rmd Template](https://www.dropbox.com/scl/fi/a9cnyqdajgabbfcxbmm6y/RMD_template.Rmd?rlkey=yntfpo6aptw9b4pgjyzpe5ubi&dl=1) - [.R Script Template](https://www.dropbox.com/scl/fi/cy43b8b1x3nzn17esnmmt/Rscript_template.R?rlkey=zn7b0g8nn0s9213blh70fjjsx&dl=1) +- Customize these for your use case to save time ## R Resources @@ -301,21 +302,21 @@ Code templates can be used to avoid typing the same code over and over again. # End of Part 2 ## Workshop survey -- Please fill out our [workshop survey](https://www.surveymonkey.com/r/F75J6VZ) so we can continue to improve these workshops +- 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 scATAC-seq Data Analysis](https://gladstone.org/events/introduction-scatac-seq-data-analysis) -November 14 - November 15, 2024 1:00-4:00pm PST +[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 Linear Mixed Effects Models](https://gladstone.org/events/introduction-linear-mixed-effects-models-0) -November 18-November 19, 2024 1:00-3:00pm PST - -[scATAC-seq and scRNA-seq Data Integration](https://gladstone.org/events/scatac-seq-and-scrna-seq-data-integration) -November 22, 2024 1:00-4:00pm PST +[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 - 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-r-data-analysis.Rproj b/intro-r-data-analysis/intro-r-data-analysis.Rproj index 8e3c2eb..4ff6824 100644 --- a/intro-r-data-analysis/intro-r-data-analysis.Rproj +++ b/intro-r-data-analysis/intro-r-data-analysis.Rproj @@ -1,4 +1,5 @@ Version: 1.0 +ProjectId: 36e3c0a4-0d16-4039-b4e3-a68991d533c3 RestoreWorkspace: Default SaveWorkspace: Default