BioinfoClass_Spring_2026

Wistar Bioinformatics Class Spring 2026

The Wistar Bioinformatics Class is a 15-week research training program for PCOM students interested in learning scientific biological data analysis.

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Schedule

Webpage mirror Bioinfo Class Spring 2026

GitHub mirror Bioinfo Class Spring 2026

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Zoom lint to BIOM 643

Bioinformatics - Tuesdays 2-3:30 https://pcom.zoom.us/j/95474182052?pwd=zYZpNnN0hOQe2VcqaVoZmAbMJAriL5.1

Bioinformatics - Thursdays 2-3:30 https://pcom.zoom.us/j/94375316257?pwd=0K4oCIOIa60iaoJhbGxdVdXFMTeHFA.1

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Getting Started

Programs to Install

1. Slack https://slack.com/ our slack name is wistar_bioinfo_spring2026 Join Slack bioinfo group or email me jmadzo@wistar.org

2. R: https://cloud.r-project.org/ to download and install R.

3. RStudio: https://rstudio.com/products/rstudio/download/ and download the FREE version.

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Lecture Material

Week 1 Orientation and Basics R

Welcome and Introduction to Rmarkdown and RStudio

• Introduction to Bioinformatics Research
• Introduction to Rmarkdown and RStudio
• slides

• demo dplyr / tidyverse qmd

• in class changes notebook qmd
• html version html

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Week 2 Markdown and more Basics R

Markdown

resource about Markdown

• html version html

• MarkDown notebook demo qmd

Data organization and Plotting in R

• slides
• notebook demo qmd
• html version html

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Week 3: Statistics I: Scientific Foundations

Tuesday

• slides

Thursday: practice section on basic statistic

• notebook demo qmd

• html version html

• R color palette pdf

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Week 4:

Tuesday - Statistics II: Clustering and Linear Model

• slides

Thursday - practice section on basic statistic continue

• demo Clustering qmd and its html

• demo LM qmd and its html

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Week 5: Introduction to Next Generation Sequencing

Tuesday - Theoretical basis for sequencing

• slides lecture presented by Sonali Majumdar (Managing Director, Genomics Facility at Wistar Institute)

Thursday - Introduction to RNA-seq

• slides theory behind RNA-seq

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Week 6: Gene Regulation

Tuesday - Overview of Regulation of Gene expression

• slides lecture presented by Sandra Deliard (Associate Staff Scientist at Wistar Institute)

Thursday - RNAseq practice

• notebook
• data
• metadata

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Week 7: Gene Regulation II

Tuesday - Epigenetic Regulation of Gene expression

• slides lecture presented by Alessandro Gardini (Associate Professor, Genomics Facility Scientific Director Wistar Institute)

Thursday - Stats of RNAseq: PCA / Linear Models

PCA practice

• PCA

  T-test vs. Linear models

• t-test vs lm

Common Statistical tests are LMs (Linear Models)

• how to teach stat

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Week 8: Non-coding RNA

Tuesday - Non-coding RNA and Transposable Elements (TE)

• slide lecture presented by Simon Chu (Caspar Wistar Fellow, Wistar Institute)

Thursday - midterm review

• practice part 1

Week 9: Example of Machine Learning on biological datasets

Tuesday - Machine Learning on datasets of hERV

• slide lecture presented by Andrew Patterson (Computational Biologist, Wistar Institute)

Thursday - midterm review

• practice part 2

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Midterm assigment

Exampe RStudio files

• data files:
  • wine_data_set

notebook

• qmd
• html

Assigment

fill in this quarto markdown (qmd) template file with your answers and send it to me

• qmd blank

• html blank

• data files: you will need to download folowing data:
  • mice_weights_and_diet
  • tissue_gene_expression

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Please, send me back your filled up Quarto Markdown (qmd) document to jmadzo@wistar.org

notes:

• please, provide verbal answer (one sentence) for statatistical questions: Is there or isn’t there statistically significant difference in values/parameters/features you testing

• beside qmd file, try to make html document as well (it will be useful for your future reference)

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Solution:

here will be expected solution in html

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Week 10: Spatial Transcriptomics / Intro to Linux

• slides lecture presented by Andrew Kossenkov (Associate Profesor, Wistar Institute)

Thursday - Introduction to Linux

• slides

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Week 11: Post-transcriptional Gene Regulation from RNA-seq / Intro to Linux

• slides lecture presented by Bin Tian (Profesor, Wistar Institute)

Thursday - Introduction to Linux

• slides