Make discoveries with your data

Create a gene counts matrix from featureCounts

1 minute read

Generate a gene counts matrix when featureCounts run separately on individual aligned files

Parsing and analyzing BAM files

6 minute read

SAMtools for manipulation of BAM files

Entrez programming utilities for downloading the nucleotide and protein sequences from NCBI

5 minute read

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

7 minute read

VCF fields information

Gene expression units explained: RPM, RPKM, FPKM, TPM, DESeq, TMM, SCnorm, GeTMM, and ComBat-Seq

15 minute read

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

8 minute read

bedtools for comparative analysis of genomic datasets

How to use NCBI SRA Toolkit effectively?

7 minute read

Downloading FASTQ files from NCBI SRA database

UMAP dimension reduction algorithm in Python (with example)

6 minute read

How to reduce and visualize high-dimensional data using UMAP in Python

t-SNE in Python for visualization of high-dimensional data

8 minute read

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...