Publications by Snijesh V P
How to retrieve data using SRA Toolkit
Retrieve data using SRA Toolkit Snijesh V P The SRA Toolkit is a set of software tools used to interact with the Sequence Read Archive (SRA), which is a public repository that stores high-throughput sequencing data. Managed by the National Center for Biotechnology Information (NCBI), the SRA contains raw reads from various sequencing platform...
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Dissecting the steps in ssGSEA analysis
Load Required Library # Load the required library options(warn=-1) #suppress warnings sw = suppressPackageStartupMessages #suppress startup message shhhhhhhhhh.... sw(library(dplyr)) sw(library(GSVA)) Create Gene Expression Matrix We create a matrix named genetable with gene expression values and set column and row names accordingly. # Create...
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Identification of differentially expressed genes using limma
Identification of Differentially Expressed Genes using limma Snijesh V P 2024-07-31 Required Packages limma dplyr Step 1: Read Expression Data # Read expression data df = read.delim("raw_expression_data.txt", row.names = 1, header = TRUE) # Read sample information target = read.delim("sample_info.txt") Expression Data: Load the gene express...
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How to retrieve KEGG compounds for each pathways
Introduction This document demonstrates how to retrieve compounds for each pathway entry from the KEGG database using the KEGGREST R package. We will get the list of pathway IDs for Homo sapiens and then retrieve and concatenate the compounds for each pathway into a single data frame. Load Required Package First, we need to load the KEGGREST p...
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Limma and DESeq2
Outputs from Limma and DESeq2 Snijesh V P 2024-02-12 Explanation of limma Output Columns The output file of limma typically includes the following columns: logFC (logarithm of fold change): This column represents the logarithm of the fold change in gene expression between two groups. It indicates the magnitude and direction of the change in ...
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Dates to Gene symbols
Gene Information Let’s take a look at the gene information: # Displaying the data frame knitr::kable(gene_info_data) Date Symbol Accession Alias Name 1-Sep SEPTIN1 1731 SEPT1 septin 1 2-Sep SEPTIN2 4735 SEPT2 septin 2 3-Sep SEPTIN3 55964 SEPT3 septin 3 4-Sep SEPTIN4 5414 SEPT4 septin 4 5-Sep SEPTIN5 5413 SEPT5 septin 5 6-Sep SEPTIN6 23157...
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PAM50 Breast Cancer Subtype Classification
Molecular Subtyping Analysis with PAM50 Classifier In this analysis, we will use the molecular.subtyping function from the genefu package to apply the PAM50 classifier to RNA-seq data. # Load the PAM50 classifier and robust parameters library(genefu) library(dplyr) library(pheatmap) data(pam50) data(pam50.robust) # Read the expression data...
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Odds Ratio in Statistics
Odds Ratio in Statistics Snijesh V P 2024-02-03 Introduction The odds ratio (OR) is a statistical measure used to quantify the strength and direction of the association between two categorical variables. It is commonly employed in epidemiology, medicine, and other fields where researchers are interested in understanding the relationship betwee...
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Quadrant Plots
How to create Quadrant Plots in R Snijesh V P 2024-02-02 Quadrant Plot Data # Load the data data(iris) head(iris) ## Sepal.Length Sepal.Width Petal.Length Petal.Width Species ## 1 5.1 3.5 1.4 0.2 setosa ## 2 4.9 3.0 1.4 0.2 setosa ## 3 4.7 3.2 1...
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