Create a gene counts matrix from featureCounts
Generate a gene counts matrix when featureCounts run separately on individual aligned files
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Parsing and analyzing BAM files
SAMtools for manipulation of BAM files
Entrez programming utilities for downloading the nucleotide and protein sequences from NCBI
NCBI E-utilities for downloading the single or large number of sequences from the NCBI sequence database
A guide to understanding the variant information fields in variant call format (VCF) file
VCF fields information
Gene expression units explained: RPM, RPKM, FPKM, TPM, DESeq, TMM, SCnorm, GeTMM, and ComBat-Seq
bulk and single-cell RNA-seq expression units, count normalization, formula, examples in Python, gene quantification, batch effects, and between-sample and w...
How to use NCBI SRA Toolkit effectively?
Downloading FASTQ files from NCBI SRA database
t-SNE in Python [single cell RNA-seq example and hyperparameter optimization]
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...
Sequencing coverage and breadth of coverage
High-through sequencing coverage calculation and coverage recommendations
Heatmap in Python
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 in Python
Volcano plot using bioinfokit package. This article explains the visualization of volcano plots for gene expression data
Multiple hypothesis testing problem in Bioinformatics
Multiple hypothesis testing and corrections, type I and II errors, false discovery rate, Bonferroni correction, and Benjamini/Hochberg correction