Generate a gene counts matrix when featureCounts run separately on individual aligned files
Make discoveries with your data
SAMtools for manipulation of BAM files
NCBI E-utilities for downloading the single or large number of sequences from the NCBI sequence database
VCF fields information
bulk and single-cell RNA-seq expression units, count normalization, formula, examples in Python, gene quantification, batch effects, and between-sample and w...
Downloading FASTQ files from NCBI SRA database
t-SNE using sklearn package. This article explains the basics of t-SNE, differences between t-SNE and PCA, example using scRNA-seq data, and results interpre...
High-through sequencing coverage calculation and coverage recommendations
Heatmap and hierarchical clustering visualization in Python
Performing and visualizing the Principal component analysis (PCA) from PCA function and scratch in Python
PCA using sklearn package. This article explains the basics of PCA, sample size requirement, data standardization, and interpretation of the PCA results
Volcano plot using bioinfokit package. This article explains the visualization of volcano plots for gene expression data
Multiple hypothesis testing and corrections, type I and II errors, false discovery rate, Bonferroni correction, and Benjamini/Hochberg correction