Make discoveries with your data

Two-pass alignment of RNA-seq reads with STAR

4 minute read

Complete tutorial on how to use STAR aligner in two-pass mode for mapping RNA-seq reads to genome

Aligning RNA-seq reads with STAR (Complete tutorial)

8 minute read

Complete tutorial on how to use STAR aligner for mapping RNA-seq reads to genome

Linux for Bioinformatics (for beginners)

15 minute read

Learn Linux command lines for Bioinformatics analysis

Survival analysis in R (Kaplan–Meier, Cox proportional hazards, and Log-rank test methods)

10 minute read

Detailed introduction of survival analysis and its calculations in R

Differential gene expression analysis using edgeR (comprehensive tutorial)

8 minute read

Perform differential gene expression analysis of RNA-seq data using EdgeR

Differential gene expression analysis using DESeq2 (comprehensive tutorial)

9 minute read

Perform differential gene expression analysis of RNA-seq data using DESeq2

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

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