# R Shiny Transcriptomics App 2021 **URL:** http://staging.stemaway.com/c/certificates/summer-2021-certificates/r-shiny-transcriptomics-app-2021/253.md [Latest](http://staging.stemaway.com/latest.md) · [Categories](http://staging.stemaway.com/categories.md) · [Tags](http://staging.stemaway.com/tags.md) --- ## [Ddas - Bioinformatics (Level 2) Pathway](http://staging.stemaway.com/t/ddas-bioinformatics-level-2-pathway/9283)
**Author:** [@ddas](http://staging.stemaway.com/u/ddas)\ **Replies:** 0
Introduction to creating Bioinformatics Apps (Transcriptomics) using the R Shiny Framework --- ## [Shreya Vora- Bioinformatics Module 2](http://staging.stemaway.com/t/shreya-vora-bioinformatics-module-2/8335)
**Author:** [@Shreya\_Vora](http://staging.stemaway.com/u/Shreya_Vora)\ **Replies:** 0\ **Last updated:** [June 20, 2021, 5:39pm UTC](http://staging.stemaway.com/t/shreya-vora-bioinformatics-module-2/8335 "2021-06-20T17:39:08Z")
Technical: I created a metadata using the GEO database. I used excel to get some data from the larger database and then imported it into R Studio I downloaded several packages for module 3 I also built an app in R Stud… --- ## [Self-Assessment: Module 4 Maryam Momeni](http://staging.stemaway.com/t/self-assessment-module-4-maryam-momeni/9153)
**Author:** [@Maryam](http://staging.stemaway.com/u/Maryam)\ **Replies:** 0\ **Last updated:** [August 7, 2021, 7:43pm UTC](http://staging.stemaway.com/t/self-assessment-module-4-maryam-momeni/9153 "2021-08-07T19:43:49Z")
Module 4 Technical area: Collaborating in testing the Shiny app Removing outliers from datasets Getting the annotations from Databases Removing duplicated Probe IDs and the genes which don’t have any corresponding Pro… --- ## [Self-Assessment: Module 5 Maryam Momeni](http://staging.stemaway.com/t/self-assessment-module-5-maryam-momeni/9199)
**Author:** [@Maryam](http://staging.stemaway.com/u/Maryam)\ **Replies:** 0\ **Last updated:** [August 15, 2021, 6:50pm UTC](http://staging.stemaway.com/t/self-assessment-module-5-maryam-momeni/9199 "2021-08-15T18:50:27Z")
Module 5: Technical area: Implementing Gene ontology for colorectal cancer and plotting Implementing KEGG pathways enrichment analysis for up-regulated genes of colorectal cancer and showing that in barplot and dot pl… --- ## [Bioinformatics-Level1-Module6- Maryam](http://staging.stemaway.com/t/bioinformatics-level1-module6-maryam/9240)
**Author:** [@Maryam](http://staging.stemaway.com/u/Maryam)\ **Replies:** 0\ **Last updated:** [August 25, 2021, 12:07pm UTC](http://staging.stemaway.com/t/bioinformatics-level1-module6-maryam/9240 "2021-08-25T12:07:46Z")
Module 6‎: Technical Area • Export the up-regulated genes from R • Further analysis on up-regulated genes ‎ Tools • Enrichr • Metascape • GEPIA Soft Skills • Analy… --- ## [Bioinformatics -Level1-Module 7-Maryam](http://staging.stemaway.com/t/bioinformatics-level1-module-7-maryam/9241)
**Author:** [@Maryam](http://staging.stemaway.com/u/Maryam)\ **Replies:** 0\ **Last updated:** [August 25, 2021, 2:20pm UTC](http://staging.stemaway.com/t/bioinformatics-level1-module-7-maryam/9241 "2021-08-25T14:20:44Z")
Module 7:‎ (Capstone project) Technical Area • Reading datasets and meta-data in R • Quality control • Normalization and background correction • Batch effect removal • Annotation and gene filteration • KEGG pathwa… --- ## [Self-Assessment: Module 3 Maryam Momeni](http://staging.stemaway.com/t/self-assessment-module-3-maryam-momeni/9009)
**Author:** [@Maryam](http://staging.stemaway.com/u/Maryam)\ **Replies:** 0\ **Last updated:** [July 22, 2021, 8:11pm UTC](http://staging.stemaway.com/t/self-assessment-module-3-maryam-momeni/9009 "2021-07-22T20:11:25Z")
Overview: Technical area: Learning how to work with different quality control packages and finding outliers. Learning how to Normalizing, background correcting, and log transforming data. Being familiar with biomaRt a… --- ## [Bioinformatics-Level2-Module3-Huikun Li](http://staging.stemaway.com/t/bioinformatics-level2-module3-huikun-li/9227)
**Author:** [@Huikun\_Li](http://staging.stemaway.com/u/Huikun_Li)\ **Replies:** 0\ **Last updated:** [August 21, 2021, 6:35am UTC](http://staging.stemaway.com/t/bioinformatics-level2-module3-huikun-li/9227 "2021-08-21T06:35:24Z")
Technical Skills: Completed Quality Control stage of the Transcriptomics Pipeline using arrayQualityMetrics Experimented with different quality control functions Gave a presentation about the outputs with Disha to our… --- ## [Bioinformatics-Level2-Module4-Huikun Li](http://staging.stemaway.com/t/bioinformatics-level2-module4-huikun-li/9228)
**Author:** [@Huikun\_Li](http://staging.stemaway.com/u/Huikun_Li)\ **Replies:** 0\ **Last updated:** [August 21, 2021, 6:40am UTC](http://staging.stemaway.com/t/bioinformatics-level2-module4-huikun-li/9228 "2021-08-21T06:40:20Z")
Technical Skills: Completed DEG identification/ visual representation stage of the Transcriptomics Pipeline using limma, pheatmap, and EnhancedVolcano Made a heatmap that grouped by sample types (cancer vs. control) f… --- ## [Bioinformatics-Level2-Module5-Huikun Li](http://staging.stemaway.com/t/bioinformatics-level2-module5-huikun-li/9229)
**Author:** [@Huikun\_Li](http://staging.stemaway.com/u/Huikun_Li)\ **Replies:** 0\ **Last updated:** [August 21, 2021, 6:45am UTC](http://staging.stemaway.com/t/bioinformatics-level2-module5-huikun-li/9229 "2021-08-21T06:45:33Z")
Technical Skills: Differential expression analysis by Limma package Plotting a volcano plot in which the differentially expressed genes are identified Plotting a Heatmap with expression values Tools Used: RShiny/RSt… --- ## [Bioinformatics-Level2-Module6-Huikun Li](http://staging.stemaway.com/t/bioinformatics-level2-module6-huikun-li/9230)
**Author:** [@Huikun\_Li](http://staging.stemaway.com/u/Huikun_Li)\ **Replies:** 0\ **Last updated:** [August 21, 2021, 6:50am UTC](http://staging.stemaway.com/t/bioinformatics-level2-module6-huikun-li/9230 "2021-08-21T06:50:00Z")
Technical Skills: Completed Functional Analysis using Web Tools stage of the Transcriptomics Pipeline using DAVID, StringDB, and GEPIA Learned how to use GitHub Tools Used: RShiny/RStudio GitHub and GitHub Pages Sl… --- ## [Bioinformatics-Level2-Module7-Huikun Li](http://staging.stemaway.com/t/bioinformatics-level2-module7-huikun-li/9231)
**Author:** [@Huikun\_Li](http://staging.stemaway.com/u/Huikun_Li)\ **Replies:** 0\ **Last updated:** [August 21, 2021, 6:55am UTC](http://staging.stemaway.com/t/bioinformatics-level2-module7-huikun-li/9231 "2021-08-21T06:55:44Z")
Technical Skills: Learned about how to use GitHub to edit the content of for our GitHub page Design app logo Learned how to upload the image on GitHub Page Learned how to change the format on the web page Tools Used: … --- ## [Samuel\_bharti - Bioinformatics (Level 2) Pathway](http://staging.stemaway.com/t/samuel-bharti-bioinformatics-level-2-pathway/9141)
**Author:** [@Samuel\_bharti](http://staging.stemaway.com/u/Samuel_bharti)\ **Replies:** 0\ **Last updated:** [August 6, 2021, 7:59pm UTC](http://staging.stemaway.com/t/samuel-bharti-bioinformatics-level-2-pathway/9141 "2021-08-06T19:59:07Z")
Self-assessments will be added here. --- ## [Shreya\_Vora - Bioinformatics (Level 2) Pathway](http://staging.stemaway.com/t/shreya-vora-bioinformatics-level-2-pathway/8143)
**Author:** [@Shreya\_Vora](http://staging.stemaway.com/u/Shreya_Vora)\ **Replies:** 0\ **Last updated:** [June 14, 2021, 6:06am UTC](http://staging.stemaway.com/t/shreya-vora-bioinformatics-level-2-pathway/8143 "2021-06-14T06:06:07Z")
Technical Area: Downloading R and R studio and also the associated packages Understanding why R is an important language Reading a research article, and learning how to understand the figures in a research paper Tools… --- ## [Modupe - Bioinformatics (Level 2) Pathway](http://staging.stemaway.com/t/modupe-bioinformatics-level-2-pathway/8291)
**Author:** [@Modupe](http://staging.stemaway.com/u/Modupe)\ **Replies:** 0\ **Last updated:** [June 18, 2021, 2:26am UTC](http://staging.stemaway.com/t/modupe-bioinformatics-level-2-pathway/8291 "2021-06-18T02:26:04Z")
Week 1 --- ## [Huikun\_Li - Bioinformatics (Level 2) Pathway](http://staging.stemaway.com/t/huikun-li-bioinformatics-level-2-pathway/9226)
**Author:** [@Huikun\_Li](http://staging.stemaway.com/u/Huikun_Li)\ **Replies:** 0\ **Last updated:** [August 21, 2021, 6:29am UTC](http://staging.stemaway.com/t/huikun-li-bioinformatics-level-2-pathway/9226 "2021-08-21T06:29:29Z")
Technical Skills: Developed overall understanding of the project in order to drive the people and task management of our deliverable Tools Used: RShiny/RStudio Google Calendar Trello STEM-Away Forums Slack Soft Ski… --- ## [Maryam - Bioinformatics (Level 2) Pathway](http://staging.stemaway.com/t/maryam-bioinformatics-level-2-pathway/8780)
**Author:** [@Maryam](http://staging.stemaway.com/u/Maryam)\ **Replies:** 6\ **Last updated:** [September 7, 2021, 6:19pm UTC](http://staging.stemaway.com/t/maryam-bioinformatics-level-2-pathway/8780 "2021-09-07T18:19:43Z")
Module 1: Technical Area Installing R and R Studio Learning fundamentals of working with R like variables, different structures, functions, and packages Drawing plots by general functions, ggplot2, and EnhancedVolcano… --- ## [Sneha\_Raj - Bioinformatics (Level 2) Pathway](http://staging.stemaway.com/t/sneha-raj-bioinformatics-level-2-pathway/8797)
**Author:** [@Sneha\_Raj](http://staging.stemaway.com/u/Sneha_Raj)\ **Replies:** 6\ **Last updated:** [August 23, 2021, 4:03am UTC](http://staging.stemaway.com/t/sneha-raj-bioinformatics-level-2-pathway/8797 "2021-08-23T04:03:03Z")
Module 1 Self-Assessment Technical Area Installed RStudio and additional packages Learned R syntax, functions, and arguments Reviewed reading academic literature Learned to plot data using ggplot Tools RStudio ggpl… --- ## [Nikita\_Krishnan - Bioinformatics (Level 2) Pathway](http://staging.stemaway.com/t/nikita-krishnan-bioinformatics-level-2-pathway/8150)
**Author:** [@Nikita\_Krishnan](http://staging.stemaway.com/u/Nikita_Krishnan)\ **Replies:** 7\ **Last updated:** [August 10, 2021, 4:02pm UTC](http://staging.stemaway.com/t/nikita-krishnan-bioinformatics-level-2-pathway/8150 "2021-08-10T16:02:06Z")
My self-assessments will be posted here. --- ## [Veyssi - Bioinformatics (Level 2) Pathway](http://staging.stemaway.com/t/veyssi-bioinformatics-level-2-pathway/8144)
**Author:** [@veyssi](http://staging.stemaway.com/u/veyssi)\ **Replies:** 7\ **Last updated:** [August 8, 2021, 2:05am UTC](http://staging.stemaway.com/t/veyssi-bioinformatics-level-2-pathway/8144 "2021-08-08T02:05:05Z")
Bioinformatics Week 1 Module 1 Overview: Technical Area: Installing RStudio, along with packages in R Explored ggplot2 and bioinformatics packages. Learned basic R fundamentals such as syntax and debugging. Understan… --- ## [Ashlesha.patil - Bioinformatics (Level 2) Pathway](http://staging.stemaway.com/t/ashlesha-patil-bioinformatics-level-2-pathway/8147)
**Author:** [@ashlesha.patil](http://staging.stemaway.com/u/ashlesha.patil)\ **Replies:** 5\ **Last updated:** [August 5, 2021, 2:05pm UTC](http://staging.stemaway.com/t/ashlesha-patil-bioinformatics-level-2-pathway/8147 "2021-08-05T14:05:55Z")
Week 1 Self-Assessment Things Learnt: Technical Skills Refreshing my skills in R, R studio and basics of GitHubReading and evauluating the Long et al., 2019 paper on lung cancer Understanding how R shiny works and the… --- ## [Roman\_Ramirez - Bioinformatics (Level 2) Pathway](http://staging.stemaway.com/t/roman-ramirez-bioinformatics-level-2-pathway/8305)
**Author:** [@Roman\_Ramirez](http://staging.stemaway.com/u/Roman_Ramirez)\ **Replies:** 7\ **Last updated:** [August 1, 2021, 7:11pm UTC](http://staging.stemaway.com/t/roman-ramirez-bioinformatics-level-2-pathway/8305 "2021-08-01T19:11:04Z")
My self-assessments are posted as replies to this thread. --- ## [Disha - Bioinformatics (Level 2) Pathway](http://staging.stemaway.com/t/disha-bioinformatics-level-2-pathway/8276)
**Author:** [@disha](http://staging.stemaway.com/u/disha)\ **Replies:** 6\ **Last updated:** [August 1, 2021, 1:42am UTC](http://staging.stemaway.com/t/disha-bioinformatics-level-2-pathway/8276 "2021-08-01T01:42:36Z")
Technical Skills: Refreshed my knowledge of the Transcriptomics Pipeline/how to read and analyze a bioinformatics paper Experimented with RShiny interactive plotting Analyzed UX requirements of planned educational app … --- ## [Ivanlam27 - Bioinformatics (Level 2) Pathway](http://staging.stemaway.com/t/ivanlam27-bioinformatics-level-2-pathway/8108)
**Author:** [@ivanlam27](http://staging.stemaway.com/u/ivanlam27)\ **Replies:** 7\ **Last updated:** [July 31, 2021, 9:04am UTC](http://staging.stemaway.com/t/ivanlam27-bioinformatics-level-2-pathway/8108 "2021-07-31T09:04:47Z")
Things that have learnt (Week 1): Technical Dissect the key features that were used in the Long et al., 2019’s paper, how they presented the quantitative data into visual representation Criticise the paper and learn mor… --- ## [Ananya\_Kaushik - Bioinformatics (Level 2) Pathway](http://staging.stemaway.com/t/ananya-kaushik-bioinformatics-level-2-pathway/8110)
**Author:** [@Ananya\_Kaushik](http://staging.stemaway.com/u/Ananya_Kaushik)\ **Replies:** 6\ **Last updated:** [July 30, 2021, 4:09am UTC](http://staging.stemaway.com/t/ananya-kaushik-bioinformatics-level-2-pathway/8110 "2021-07-30T04:09:05Z")
Week 1 Self Assessment Things Learnt: Technical: Reading a scientific paper- Analysing the different methods used for study and how to interpret their results to draw meaningful conclusions Installing R and RStudio a… --- ## [Bioinformatics (Level 1)- Shreya Vora](http://staging.stemaway.com/t/bioinformatics-level-1-shreya-vora/8494)
**Author:** [@Shreya\_Vora](http://staging.stemaway.com/u/Shreya_Vora)\ **Replies:** 6\ **Last updated:** [July 30, 2021, 5:05am UTC](http://staging.stemaway.com/t/bioinformatics-level-1-shreya-vora/8494 "2021-07-30T05:05:36Z")
Module 1: Technical Area: Downloading R and R studio and also the associated packages Understanding why R is an important language Reading a research article, and learning how to understand the figures in a research p… --- ## [Aditi\_3 - Bioinformatics (Level 2) Pathway](http://staging.stemaway.com/t/aditi-3-bioinformatics-level-2-pathway/8444)
**Author:** [@aditi\_3](http://staging.stemaway.com/u/aditi_3)\ **Replies:** 6\ **Last updated:** [July 30, 2021, 4:19am UTC](http://staging.stemaway.com/t/aditi-3-bioinformatics-level-2-pathway/8444 "2021-07-30T04:19:19Z")
Module 1 Overview: Technical Area: R programming (reviewing visualization, coding, and debugging on RStudio) Process of reading and understanding research papers, highlighting key points and evaluating results Gettin… --- ## [Austin\_Yang1 - Bioinformatics (Level 2) Pathway](http://staging.stemaway.com/t/austin-yang1-bioinformatics-level-2-pathway/8745)
**Author:** [@Austin\_Yang1](http://staging.stemaway.com/u/Austin_Yang1)\ **Replies:** 1\ **Last updated:** [July 19, 2021, 2:49am UTC](http://staging.stemaway.com/t/austin-yang1-bioinformatics-level-2-pathway/8745 "2021-07-19T02:49:19Z")
Overview: Technical Area: Reviewing R, which had become a bit rusty over the school year Explored new packages in R, which may potentially be useful when offering technical guidance Reviewed my responsibilities as PM … --- ## [Marc\_Abdallah - Bioinformatics (Level 2) Pathway](http://staging.stemaway.com/t/marc-abdallah-bioinformatics-level-2-pathway/8346)
**Author:** [@Marc\_Abdallah](http://staging.stemaway.com/u/Marc_Abdallah)\ **Replies:** 1\ **Last updated:** [June 28, 2021, 3:49pm UTC](http://staging.stemaway.com/t/marc-abdallah-bioinformatics-level-2-pathway/8346 "2021-06-28T15:49:46Z")
Week 2 Self-Assessment Things Learned: Technical Skills Using the Bioconductor packages to load data into R. Creating a basic RShiny application Tools: R Studio R shiny Bioconductor Trello Soft Skills Communica… --- ## [Xgeng - Bioinformatics (Level 2) Pathway](http://staging.stemaway.com/t/xgeng-bioinformatics-level-2-pathway/8243)
**Author:** [@xgeng](http://staging.stemaway.com/u/xgeng)\ **Replies:** 2\ **Last updated:** [June 25, 2021, 10:03pm UTC](http://staging.stemaway.com/t/xgeng-bioinformatics-level-2-pathway/8243 "2021-06-25T22:03:40Z")
My self-assessments will be posted here [Next page](http://staging.stemaway.com/c/certificates/summer-2021-certificates/r-shiny-transcriptomics-app-2021/253.md?page=1)