Two-pass alignment of RNA-seq reads with STAR
Complete tutorial on how to use STAR aligner in two-pass mode for mapping RNA-seq reads to genome
Make discoveries with your data
Recent posts
Aligning RNA-seq reads with STAR (Complete tutorial)
Complete tutorial on how to use STAR aligner for mapping RNA-seq reads to genome
Linux for Bioinformatics (for beginners)
Learn Linux command lines for Bioinformatics analysis
Survival analysis in R (Kaplan–Meier, Cox proportional hazards, and Log-rank test methods)
Detailed introduction of survival analysis and its calculations in R
Differential gene expression analysis using edgeR (comprehensive tutorial)
Perform differential gene expression analysis of RNA-seq data using EdgeR
Differential gene expression analysis using DESeq2 (comprehensive tutorial)
Perform differential gene expression analysis of RNA-seq data using DESeq2
Create a gene counts matrix from featureCounts
Generate a gene counts matrix when featureCounts run separately on individual aligned files
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...
bedtools for genomics analysis
bedtools for comparative analysis of genomic datasets
