INTERNSHIP Internship Fall/Sum/Spring 2023-24 (4 students) **Undergraduate and High School Class & Lab.

Fall, Spring Semester 2023-24: Undergraduate students **Yash Singh, *Abhay Raheja, *Mohit Sai, **Riya Chadha, **Arnav Madderla – Georgia Institute of Technology, Atlanta, USA, Forsyth Central High School, Paul Duke STEM High School. 2024 Southeast Regional Clinical & Translational Science Conference, Atlanta, Identifying Diagnostic & Prognostic Biomarker Signatures in Lung Cancer, Yash Singh, Abhay Raheja, Mohit Sai, Karuna Mittal, & Shrikant Pawar. GitHub Poster

https://georgiactsa.org/_includes/documents/sections/research/cmdts/2024-abstract-book-final-pw.pdf

https://georgiactsa.org/research/cmdts/statewide-conference/2024.html

https://github.com/spawar2/INTERNSHIP

https://campuspress.yale.edu/shrikantpawar/files/2024/03/Poster-b7b266ed34d9474c.pptx

Internship 2023 (Learning Objectives):

• Session 1 (R, data banks, GitHub Intro): https://youtu.be/3ReIQmFWxas

• Github: https://github.com/spawar2/INTERNSHIP

• Session 2 (Databank Querying): https://youtu.be/tRb-_1aA57U

• Session 3 (External R packages/libraries): https://youtu.be/TJpo9apXo8k

• Session 4 (Microarray data read and visualization in R): https://youtu.be/OhXCJ_eU99Q

• Session 5 (Normalization (Affy, Oligo, Limma-RMA, Quantile, Mas5.0), GitHub uploads): https://youtu.be/DKNva3GCWQ0

• Session 6 (Fold Change Analysis): https://youtu.be/QF_X2PqDO1k

• Session 7 (Project preparation): https://youtu.be/3f5wU8niK5c

• Session 8 (Project preparation): https://youtu.be/9whLbYgicsw

• Session 9 (Project preparation): https://youtu.be/viKm2czflmY

• Session 10 (Project preparation): https://youtu.be/NaZl5zwMroc

• Session 11 (Project preparation): https://youtu.be/fBWLUOIJnow

• Session 12 (Project preparation): https://youtu.be/svZcYXwA8cU

• Session13 (Project preparation): https://youtu.be/yqmtLN5yqhw

• Session 14 (Project preparation): https://youtu.be/BF_8YEhcZMI

• Session 15 (Project preparation): https://youtu.be/5aLXmYRrf5E

• Session 16 (Project preparation): https://youtu.be/acHnwp4fqZs

• Session 17 (Project preparation): https://youtu.be/eayldhE1jRw

• Session 18 (Project preparation): https://youtu.be/AdiMhOXXSHw

• Session 19 (Project preparation): https://youtu.be/FKp9a0YSUyw

• Session 20 (Project preparation): https://youtu.be/pqSZEnwYLrw

• Session 21 (Project preparation): https://youtu.be/vyLSq2q6oi8

• Session 22 (Project preparation): https://youtu.be/nWywx6ODc-8

• Session 23.1 (Project preparation): https://youtu.be/ahe_bGYYcec

• Session 23.2 (Project preparation): https://youtu.be/f1wj1xjFHcw

• Session 24 (Project preparation): https://youtu.be/-nF8B5KAwE4

• Session 24 (Project preparation): https://youtu.be/g7h50jorUZs

​

2024:

• Session 1.1 (Introduction to R: Simple manipulations; numbers and vectors, Missing values, Objects, their modes and attributes, Ordered and unordered factors, Arrays and matrices, Lists and data frames, Reading data from files, Probability distributions, Grouping, loops and conditional execution, Custom functions, Statistical models, Graphical procedures: Bar plots, scatterplots, volcano plots, Venn diagrams, Pie charts, Density plots, Line plots, hypothesis testing with T-test, correlation, ANOVA, regression), Gene Expression Omnibus (GEO) datasets mining, Microarray data analysis: Read, Pre-processing/Normalization (Affy, Oligo, Limma-RMA, Quantile, Mas5.0), Visualization: Heat maps, box plots, Fold change expression analysis, Gene Set Enrichment Analysis (GSEA), Pathways and protein downstream interactome analysis: https://youtu.be/M4YK6UbJR10

• Session 1.2 (Introduction to R: Simple manipulations; numbers and vectors, Missing values, Objects, their modes and attributes, Ordered and unordered factors, Arrays and matrices, Lists and data frames, Reading data from files, Probability distributions, Grouping, loops and conditional execution, Custom functions, Statistical models, Graphical procedures: Bar plots, scatterplots, volcano plots, Venn diagrams, Pie charts, Density plots, Line plots, hypothesis testing with T-test, correlation, ANOVA, regression), Gene Expression Omnibus (GEO) datasets mining, Microarray data analysis: Read, Pre-processing/Normalization (Affy, Oligo, Limma-RMA, Quantile, Mas5.0), Visualization: Heat maps, box plots, Fold change expression analysis, Gene Set Enrichment Analysis (GSEA), Pathways and protein downstream interactome analysis: https://youtu.be/T6wQL4h5eEs

• Session 2.1 (Introduction to R: Simple manipulations; numbers and vectors, Missing values, Objects, their modes and attributes, Ordered and unordered factors, Arrays and matrices, Lists and data frames, Reading data from files, Probability distributions, Grouping, loops and conditional execution, Custom functions, Statistical models, Graphical procedures: Bar plots, scatterplots, volcano plots, Venn diagrams, Pie charts, Density plots, Line plots, hypothesis testing with T-test, correlation, ANOVA, regression), Gene Expression Omnibus (GEO) datasets mining, Microarray data analysis: Read, Pre-processing/Normalization (Affy, Oligo, Limma-RMA, Quantile, Mas5.0), Visualization: Heat maps, box plots, Fold change expression analysis, Gene Set Enrichment Analysis (GSEA), Pathways and protein downstream interactome analysis: https://youtu.be/riK08jGANk4

• Session 2.2 (Introduction to R: Simple manipulations; numbers and vectors, Missing values, Objects, their modes and attributes, Ordered and unordered factors, Arrays and matrices, Lists and data frames, Reading data from files, Probability distributions, Grouping, loops and conditional execution, Custom functions, Statistical models, Graphical procedures: Bar plots, scatterplots, volcano plots, Venn diagrams, Pie charts, Density plots, Line plots, hypothesis testing with T-test, correlation, ANOVA, regression), Gene Expression Omnibus (GEO) datasets mining, Microarray data analysis: Read, Pre-processing/Normalization (Affy, Oligo, Limma-RMA, Quantile, Mas5.0), Visualization: Heat maps, box plots, Fold change expression analysis, Gene Set Enrichment Analysis (GSEA), Pathways and protein downstream interactome analysis: https://youtu.be/8H9t8y1gBBs

• Session 3.1 (Introduction to R: Simple manipulations; numbers and vectors, Missing values, Objects, their modes and attributes, Ordered and unordered factors, Arrays and matrices, Lists and data frames, Reading data from files, Probability distributions, Grouping, loops and conditional execution, Custom functions, Statistical models, Graphical procedures: Bar plots, scatterplots, volcano plots, Venn diagrams, Pie charts, Density plots, Line plots, hypothesis testing with T-test, correlation, ANOVA, regression), Gene Expression Omnibus (GEO) datasets mining, Microarray data analysis: Read, Pre-processing/Normalization (Affy, Oligo, Limma-RMA, Quantile, Mas5.0), Visualization: Heat maps, box plots, Fold change expression analysis, Gene Set Enrichment Analysis (GSEA), Pathways and protein downstream interactome analysis: https://youtu.be/pBh-nsV1-_g

• Session 3.2 (Introduction to R: Simple manipulations; numbers and vectors, Missing values, Objects, their modes and attributes, Ordered and unordered factors, Arrays and matrices, Lists and data frames, Reading data from files, Probability distributions, Grouping, loops and conditional execution, Custom functions, Statistical models, Graphical procedures: Bar plots, scatterplots, volcano plots, Venn diagrams, Pie charts, Density plots, Line plots, hypothesis testing with T-test, correlation, ANOVA, regression), Gene Expression Omnibus (GEO) datasets mining, Microarray data analysis: Read, Pre-processing/Normalization (Affy, Oligo, Limma-RMA, Quantile, Mas5.0), Visualization: Heat maps, box plots, Fold change expression analysis, Gene Set Enrichment Analysis (GSEA), Pathways and protein downstream interactome analysis: https://youtu.be/NybXXfLb20g

• INTERNSHIP 4 (Introduction to R: Simple manipulations; numbers and vectors, Missing values, Objects, their modes and attributes, Ordered and unordered factors, Arrays and matrices, Lists and data frames, Reading data from files, Probability distributions, Grouping, loops and conditional execution, Custom functions, Statistical models, Graphical procedures: Bar plots, scatterplots, volcano plots, Venn diagrams, Pie charts, Density plots, Line plots, hypothesis testing with T-test, correlation, ANOVA, regression), Gene Expression Omnibus (GEO) datasets mining, Microarray data analysis: Read, Pre-processing/Normalization (Affy, Oligo, Limma-RMA, Quantile, Mas5.0), Visualization: Heat maps, box plots, Fold change expression analysis, Gene Set Enrichment Analysis (GSEA), Pathways and protein downstream interactome analysis: https://youtu.be/x6vfIOzlj9s

• Session 5 (Introduction to R: Simple manipulations; numbers and vectors, Missing values, Objects, their modes and attributes, Ordered and unordered factors, Arrays and matrices, Lists and data frames, Reading data from files, Probability distributions, Grouping, loops and conditional execution, Custom functions, Statistical models, Graphical procedures: Bar plots, scatterplots, volcano plots, Venn diagrams, Pie charts, Density plots, Line plots, hypothesis testing with T-test, correlation, ANOVA, regression), Gene Expression Omnibus (GEO) datasets mining, Microarray data analysis: Read, Pre-processing/Normalization (Affy, Oligo, Limma-RMA, Quantile, Mas5.0), Visualization: Heat maps, box plots, Fold change expression analysis, Gene Set Enrichment Analysis (GSEA), Pathways and protein downstream interactome analysis: https://youtu.be/Y0LUUIDLKFQ

• Session 6 (Introduction to R: Simple manipulations; numbers and vectors, Missing values, Objects, their modes and attributes, Ordered and unordered factors, Arrays and matrices, Lists and data frames, Reading data from files, Probability distributions, Grouping, loops and conditional execution, Custom functions, Statistical models, Graphical procedures: Bar plots, scatterplots, volcano plots, Venn diagrams, Pie charts, Density plots, Line plots, hypothesis testing with T-test, correlation, ANOVA, regression), Gene Expression Omnibus (GEO) datasets mining, Microarray data analysis: Read, Pre-processing/Normalization (Affy, Oligo, Limma-RMA, Quantile, Mas5.0), Visualization: Heat maps, box plots, Fold change expression analysis, Gene Set Enrichment Analysis (GSEA), Pathways and protein downstream interactome analysis: https://youtu.be/UC-wJ_CCUcs

• Session 7 (Introduction to R: Simple manipulations; numbers and vectors, Missing values, Objects, their modes and attributes, Ordered and unordered factors, Arrays and matrices, Lists and data frames, Reading data from files, Probability distributions, Grouping, loops and conditional execution, Custom functions, Statistical models, Graphical procedures: Bar plots, scatterplots, volcano plots, Venn diagrams, Pie charts, Density plots, Line plots, hypothesis testing with T-test, correlation, ANOVA, regression), Gene Expression Omnibus (GEO) datasets mining, Microarray data analysis: Read, Pre-processing/Normalization (Affy, Oligo, Limma-RMA, Quantile, Mas5.0), Visualization: Heat maps, box plots, Fold change expression analysis, Gene Set Enrichment Analysis (GSEA), Pathways and protein downstream interactome analysis: https://youtu.be/o4KAY94XMLg

• Session 8.1 (Introduction to R: Simple manipulations; numbers and vectors, Missing values, Objects, their modes and attributes, Ordered and unordered factors, Arrays and matrices, Lists and data frames, Reading data from files, Probability distributions, Grouping, loops and conditional execution, Custom functions, Statistical models, Graphical procedures: Bar plots, scatterplots, volcano plots, Venn diagrams, Pie charts, Density plots, Line plots, hypothesis testing with T-test, correlation, ANOVA, regression), Gene Expression Omnibus (GEO) datasets mining, Microarray data analysis: Read, Pre-processing/Normalization (Affy, Oligo, Limma-RMA, Quantile, Mas5.0), Visualization: Heat maps, box plots, Fold change expression analysis, Gene Set Enrichment Analysis (GSEA), Pathways and protein downstream interactome analysis: https://youtu.be/VuYKgOrRc7c

• Session 8.2 (Introduction to R: Simple manipulations; numbers and vectors, Missing values, Objects, their modes and attributes, Ordered and unordered factors, Arrays and matrices, Lists and data frames, Reading data from files, Probability distributions, Grouping, loops and conditional execution, Custom functions, Statistical models, Graphical procedures: Bar plots, scatterplots, volcano plots, Venn diagrams, Pie charts, Density plots, Line plots, hypothesis testing with T-test, correlation, ANOVA, regression), Gene Expression Omnibus (GEO) datasets mining, Microarray data analysis: Read, Pre-processing/Normalization (Affy, Oligo, Limma-RMA, Quantile, Mas5.0), Visualization: Heat maps, box plots, Fold change expression analysis, Gene Set Enrichment Analysis (GSEA), Pathways and protein downstream interactome analysis: https://youtu.be/T7o6-EsdmTA

• Session 9 (Introduction to R: Simple manipulations; numbers and vectors, Missing values, Objects, their modes and attributes, Ordered and unordered factors, Arrays and matrices, Lists and data frames, Reading data from files, Probability distributions, Grouping, loops and conditional execution, Custom functions, Statistical models, Graphical procedures: Bar plots, scatterplots, volcano plots, Venn diagrams, Pie charts, Density plots, Line plots, hypothesis testing with T-test, correlation, ANOVA, regression), Gene Expression Omnibus (GEO) datasets mining, Microarray data analysis: Read, Pre-processing/Normalization (Affy, Oligo, Limma-RMA, Quantile, Mas5.0), Visualization: Heat maps, box plots, Fold change expression analysis, Gene Set Enrichment Analysis (GSEA), Pathways and protein downstream interactome analysis: https://youtu.be/TZlxPD7s0xw

• Session 10.1 (Introduction to R: Simple manipulations; numbers and vectors, Missing values, Objects, their modes and attributes, Ordered and unordered factors, Arrays and matrices, Lists and data frames, Reading data from files, Probability distributions, Grouping, loops and conditional execution, Custom functions, Statistical models, Graphical procedures: Bar plots, scatterplots, volcano plots, Venn diagrams, Pie charts, Density plots, Line plots, hypothesis testing with T-test, correlation, ANOVA, regression), Gene Expression Omnibus (GEO) datasets mining, Microarray data analysis: Read, Pre-processing/Normalization (Affy, Oligo, Limma-RMA, Quantile, Mas5.0), Visualization: Heat maps, box plots, Fold change expression analysis, Gene Set Enrichment Analysis (GSEA), Pathways and protein downstream interactome analysis: https://youtu.be/HFN-9By_VYU

• Session 10.2 (Introduction to R: Simple manipulations; numbers and vectors, Missing values, Objects, their modes and attributes, Ordered and unordered factors, Arrays and matrices, Lists and data frames, Reading data from files, Probability distributions, Grouping, loops and conditional execution, Custom functions, Statistical models, Graphical procedures: Bar plots, scatterplots, volcano plots, Venn diagrams, Pie charts, Density plots, Line plots, hypothesis testing with T-test, correlation, ANOVA, regression), Gene Expression Omnibus (GEO) datasets mining, Microarray data analysis: Read, Pre-processing/Normalization (Affy, Oligo, Limma-RMA, Quantile, Mas5.0), Visualization: Heat maps, box plots, Fold change expression analysis, Gene Set Enrichment Analysis (GSEA), Pathways and protein downstream interactome analysis: https://youtu.be/MxycWaDeGfQ

• Session 11.1 (Introduction to R: Simple manipulations; numbers and vectors, Missing values, Objects, their modes and attributes, Ordered and unordered factors, Arrays and matrices, Lists and data frames, Reading data from files, Probability distributions, Grouping, loops and conditional execution, Custom functions, Statistical models, Graphical procedures: Bar plots, scatterplots, volcano plots, Venn diagrams, Pie charts, Density plots, Line plots, hypothesis testing with T-test, correlation, ANOVA, regression), Gene Expression Omnibus (GEO) datasets mining, Microarray data analysis: Read, Pre-processing/Normalization (Affy, Oligo, Limma-RMA, Quantile, Mas5.0), Visualization: Heat maps, box plots, Fold change expression analysis, Gene Set Enrichment Analysis (GSEA), Pathways and protein downstream interactome analysis: https://youtu.be/4s16eW-g_0I

• Session 11.2 (Introduction to R: Simple manipulations; numbers and vectors, Missing values, Objects, their modes and attributes, Ordered and unordered factors, Arrays and matrices, Lists and data frames, Reading data from files, Probability distributions, Grouping, loops and conditional execution, Custom functions, Statistical models, Graphical procedures: Bar plots, scatterplots, volcano plots, Venn diagrams, Pie charts, Density plots, Line plots, hypothesis testing with T-test, correlation, ANOVA, regression), Gene Expression Omnibus (GEO) datasets mining, Microarray data analysis: Read, Pre-processing/Normalization (Affy, Oligo, Limma-RMA, Quantile, Mas5.0), Visualization: Heat maps, box plots, Fold change expression analysis, Gene Set Enrichment Analysis (GSEA), Pathways and protein downstream interactome analysis: https://youtu.be/6MW48-4DO7k

• Session 12 (Introduction to R: Simple manipulations; numbers and vectors, Missing values, Objects, their modes and attributes, Ordered and unordered factors, Arrays and matrices, Lists and data frames, Reading data from files, Probability distributions, Grouping, loops and conditional execution, Custom functions, Statistical models, Graphical procedures: Bar plots, scatterplots, volcano plots, Venn diagrams, Pie charts, Density plots, Line plots, hypothesis testing with T-test, correlation, ANOVA, regression), Gene Expression Omnibus (GEO) datasets mining, Microarray data analysis: Read, Pre-processing/Normalization (Affy, Oligo, Limma-RMA, Quantile, Mas5.0), Visualization: Heat maps, box plots, Fold change expression analysis, Gene Set Enrichment Analysis (GSEA), Pathways and protein downstream interactome analysis: https://youtu.be/2a1CnkK9-pI

• Session 13 (Introduction to R: Simple manipulations; numbers and vectors, Missing values, Objects, their modes and attributes, Ordered and unordered factors, Arrays and matrices, Lists and data frames, Reading data from files, Probability distributions, Grouping, loops and conditional execution, Custom functions, Statistical models, Graphical procedures: Bar plots, scatterplots, volcano plots, Venn diagrams, Pie charts, Density plots, Line plots, hypothesis testing with T-test, correlation, ANOVA, regression), Gene Expression Omnibus (GEO) datasets mining, Microarray data analysis: Read, Pre-processing/Normalization (Affy, Oligo, Limma-RMA, Quantile, Mas5.0), Visualization: Heat maps, box plots, Fold change expression analysis, Gene Set Enrichment Analysis (GSEA), Pathways and protein downstream interactome analysis: https://youtu.be/Ln785EYIoz8

• Session 14 (Introduction to R: Simple manipulations; numbers and vectors, Missing values, Objects, their modes and attributes, Ordered and unordered factors, Arrays and matrices, Lists and data frames, Reading data from files, Probability distributions, Grouping, loops and conditional execution, Custom functions, Statistical models, Graphical procedures: Bar plots, scatterplots, volcano plots, Venn diagrams, Pie charts, Density plots, Line plots, hypothesis testing with T-test, correlation, ANOVA, regression), Gene Expression Omnibus (GEO) datasets mining, Microarray data analysis: Read, Pre-processing/Normalization (Affy, Oligo, Limma-RMA, Quantile, Mas5.0), Visualization: Heat maps, box plots, Fold change expression analysis, Gene Set Enrichment Analysis (GSEA), Pathways and protein downstream interactome analysis: https://youtu.be/PDow3EbvaBo

• Affymetrix Microarray Analysis: https://campuspress.yale.edu/shrikantpawar/files/2024/04/Screenshot-2024-04-11-at-8.37.25%E2%80%AFPM-0074b268184f12d7-300x210.png

• https://campuspress.yale.edu/shrikantpawar/files/2024/04/Screenshot-2024-04-16-at-7.02.42%E2%80%AFPM-1a3b150cfde2cf5b-300x214.png

• Box Plot Raw Microarray Data: https://campuspress.yale.edu/shrikantpawar/files/2024/04/Raw-Intensity-Plot-a65cbec9805028bc.pdf

• Session 15.1 (Introduction to R: Simple manipulations; numbers and vectors, Missing values, Objects, their modes and attributes, Ordered and unordered factors, Arrays and matrices, Lists and data frames, Reading data from files, Probability distributions, Grouping, loops and conditional execution, Custom functions, Statistical models, Graphical procedures: Bar plots, scatterplots, volcano plots, Venn diagrams, Pie charts, Density plots, Line plots, hypothesis testing with T-test, correlation, ANOVA, regression), Gene Expression Omnibus (GEO) datasets mining, Microarray data analysis: Read, Pre-processing/Normalization (Affy, Oligo, Limma-RMA, Quantile, Mas5.0), Visualization: Heat maps, box plots, Fold change expression analysis, Gene Set Enrichment Analysis (GSEA), Pathways and protein downstream interactome analysis: https://youtu.be/_PVck8bxzjE

• Session 15.2 (Introduction to R: Simple manipulations; numbers and vectors, Missing values, Objects, their modes and attributes, Ordered and unordered factors, Arrays and matrices, Lists and data frames, Reading data from files, Probability distributions, Grouping, loops and conditional execution, Custom functions, Statistical models, Graphical procedures: Bar plots, scatterplots, volcano plots, Venn diagrams, Pie charts, Density plots, Line plots, hypothesis testing with T-test, correlation, ANOVA, regression), Gene Expression Omnibus (GEO) datasets mining, Microarray data analysis: Read, Pre-processing/Normalization (Affy, Oligo, Limma-RMA, Quantile, Mas5.0), Visualization: Heat maps, box plots, Fold change expression analysis, Gene Set Enrichment Analysis (GSEA), Pathways and protein downstream interactome analysis: https://youtu.be/jFvuX3eRJEo

• Session 16 (Introduction to R: Simple manipulations; numbers and vectors, Missing values, Objects, their modes and attributes, Ordered and unordered factors, Arrays and matrices, Lists and data frames, Reading data from files, Probability distributions, Grouping, loops and conditional execution, Custom functions, Statistical models, Graphical procedures: Bar plots, scatterplots, volcano plots, Venn diagrams, Pie charts, Density plots, Line plots, hypothesis testing with T-test, correlation, ANOVA, regression), Gene Expression Omnibus (GEO) datasets mining, Microarray data analysis: Read, Pre-processing/Normalization (Affy, Oligo, Limma-RMA, Quantile, Mas5.0), Visualization: Heat maps, box plots, Fold change expression analysis, Gene Set Enrichment Analysis (GSEA), Pathways and protein downstream interactome analysis: https://youtu.be/T7hAMi0yax0

• Robust Multiarray Normalization (RMA) Normalized Plot: https://campuspress.yale.edu/shrikantpawar/files/2024/04/Normalized-Plot-Liver-Cancer-Sample-e2d0f1eadc1de028.pdfhttps://campuspress.yale.edu/shrikantpawar/files/2024/04/Screenshot-2024-04-25-at-6.56.26%E2%80%AFPM-6a468125d3479726-300x197.png

• https://campuspress.yale.edu/shrikantpawar/files/2024/04/Screenshot-2024-04-25-at-6.57.03%E2%80%AFPM-2e27b3455cb79227-300x179.png

• Session 17.1 (Introduction to R: Simple manipulations; numbers and vectors, Missing values, Objects, their modes and attributes, Ordered and unordered factors, Arrays and matrices, Lists and data frames, Reading data from files, Probability distributions, Grouping, loops and conditional execution, Custom functions, Statistical models, Graphical procedures: Bar plots, scatterplots, volcano plots, Venn diagrams, Pie charts, Density plots, Line plots, hypothesis testing with T-test, correlation, ANOVA, regression), Gene Expression Omnibus (GEO) datasets mining, Microarray data analysis: Read, Pre-processing/Normalization (Affy, Oligo, Limma-RMA, Quantile, Mas5.0), Visualization: Heat maps, box plots, Fold change expression analysis, Gene Set Enrichment Analysis (GSEA), Pathways and protein downstream interactome analysis: https://youtu.be/5w9GooLRBi4

• Session 17.2 (Introduction to R: Simple manipulations; numbers and vectors, Missing values, Objects, their modes and attributes, Ordered and unordered factors, Arrays and matrices, Lists and data frames, Reading data from files, Probability distributions, Grouping, loops and conditional execution, Custom functions, Statistical models, Graphical procedures: Bar plots, scatterplots, volcano plots, Venn diagrams, Pie charts, Density plots, Line plots, hypothesis testing with T-test, correlation, ANOVA, regression), Gene Expression Omnibus (GEO) datasets mining, Microarray data analysis: Read, Pre-processing/Normalization (Affy, Oligo, Limma-RMA, Quantile, Mas5.0), Visualization: Heat maps, box plots, Fold change expression analysis, Gene Set Enrichment Analysis (GSEA), Pathways and protein downstream interactome analysis: https://youtu.be/Pp9-jBHfYuA

• https://github.com/spawar2/INTERNSHIP/blob/main/Dummy-Plot.pdf

• Boxplots in R: https://github.com/spawar2/INTERNSHIP/blob/main/May%209.png

• Session 18 (Introduction to R: Simple manipulations; numbers and vectors, Missing values, Objects, their modes and attributes, Ordered and unordered factors, Arrays and matrices, Lists and data frames, Reading data from files, Probability distributions, Grouping, loops and conditional execution, Custom functions, Statistical models, Graphical procedures: Bar plots, scatterplots, volcano plots, Venn diagrams, Pie charts, Density plots, Line plots, hypothesis testing with T-test, correlation, ANOVA, regression), Gene Expression Omnibus (GEO) datasets mining, Microarray data analysis: Read, Pre-processing/Normalization (Affy, Oligo, Limma-RMA, Quantile, Mas5.0), Visualization: Heat maps, box plots, Fold change expression analysis, Gene Set Enrichment Analysis (GSEA), Pathways and protein downstream interactome analysis: https://youtu.be/oFOSaewJ_-o

• https://github.com/spawar2/INTERNSHIP/blob/main/Breast-Cancer-Analysis.R

• https://github.com/spawar2/INTERNSHIP/blob/main/Cluster.csv

• https://github.com/spawar2/INTERNSHIP/blob/main/Control.csv

• https://github.com/spawar2/INTERNSHIP/blob/main/Cytoscape-Session.cys

• https://github.com/spawar2/INTERNSHIP/blob/main/Final.xlsx

• https://github.com/spawar2/INTERNSHIP/blob/main/Fold_change.csv

• Gene Set Enrichment Analysis (GSEA) Plot: https://github.com/spawar2/INTERNSHIP/blob/main/GSEAplot.pdf

• https://github.com/spawar2/INTERNSHIP/blob/main/Heatamp.csv

• https://github.com/spawar2/INTERNSHIP/blob/main/Heatmap.pdf

• https://github.com/spawar2/INTERNSHIP/blob/main/May%209.png

• https://github.com/spawar2/INTERNSHIP/blob/main/Prostate-Cancer-Analysis.R

• https://github.com/spawar2/INTERNSHIP/blob/main/Prostate-Heatmap.pdf

• https://github.com/spawar2/INTERNSHIP/blob/main/dotplot.pdf

• https://github.com/spawar2/INTERNSHIP/blob/main/gseaplot.pdf

• https://github.com/spawar2/INTERNSHIP/blob/main/string_interactions.csv.png