A guide to understanding the variant information fields in variant call format (VCF) file
VCF fields information
Make discoveries with your data
Recent posts
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...
bedtools for genomics analysis
bedtools for comparative analysis of genomic datasets
How to use NCBI SRA Toolkit effectively?
Downloading FASTQ files from NCBI SRA database
UMAP dimension reduction algorithm in Python (with example)
How to reduce and visualize high-dimensional data using UMAP in Python
t-SNE in Python for visualization of high-dimensional data
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...
K-means Clustering in Python: Detailed Guide With Example
This article how to perform and visualize the K-means Clustering in Python
Sequencing coverage and breadth of coverage
High-through sequencing coverage calculation and coverage recommendations
pheatmap: create annotated heatmaps in R (detailed guide)
How to create and customize heatmap using pheatmap package in R
Interactive Heatmap in Python (using hvPlot and Bokeh)
Visualize interactive heatmap using hvPlot and Bokeh
Heatmap in Python
Heatmap and hierarchical clustering visualization in Python
Principal component analysis (PCA) and visualization using Python (Detailed guide with example)
PCA using sklearn package. This article explains the basics of PCA, sample size requirement, data standardization, and interpretation of the PCA results
