Transcriptomics
Bulk, single-cell, spatial, and non-coding RNA sequencing computational analysis workflows.
RNA-Seq Analysis Step-by-Step: From FASTQ to Differential Expression
Step-by-step computational workflow from raw FASTQ reads to differential expression in reference-guided RNA-seq.
Read guide →DESeq2 vs edgeR: Comparing Statistical Methods for RNA-Seq Differential Expression
Head-to-head comparison of negative binomial normalization, dispersion shrinkage, and statistical modeling in DESeq2 vs edgeR.
Read guide →Single-Cell RNA-Seq Analysis Workflow: End-to-End Computational Guide
Complete single-cell RNA-seq pipeline covering droplet filtering, normalization with SCTransform, clustering, and marker annotation.
Read guide →Spatial Transcriptomics Analysis Explained: Spatially Resolved Gene Expression Workflows
Spatially resolved transcriptomics guide integrating histological tissue images with 10x Visium spot deconvolution and spatial variable genes.
Read guide →De Novo RNA-Seq Transcriptome Assembly: Complete Workflow for Non-Model Organisms
Reconstructing full-length transcript catalogs for non-model organisms without a reference genome using Trinity and TransDecoder.
Read guide →Long Non-Coding RNA-Seq Analysis Explained: Identification, Coding Potential, and Function
Systematic identification, coding potential filtering via CPC2/CNCI, and cis-trans target prediction for long non-coding RNAs.
Read guide →Small RNA and MicroRNA-Seq Analysis Explained: Detection, Target Prediction, and Profiling
Small RNA sequencing analysis covering 3' adapter clipping, hairpin quantification in miRBase, and novel miRNA discovery with miRDeep2.
Read guide →Alternative Splicing and Percent Spliced-In (PSI) Analysis: Computational Methods and Tools
Quantifying Percent Spliced-In (PSI), alternative exon skipping, and splice junction regulation using rMATS and SUPPA2.
Read guide →Epigenomics
Chromatin accessibility, histone post-translational modifications, and DNA methylation profiling.
ATAC-Seq vs ChIP-Seq: Choosing the Right Epigenomic Assay for Your Research
Comparative analysis of open chromatin accessibility profiling versus target-specific histone and transcription factor mapping.
Read guide →Single-Cell ATAC-Seq Analysis Explained: From Barcoded FASTQ to Epigenomic Landscapes
Resolving single-cell chromatin accessibility, TF-IDF / LSI dimensionality reduction, pseudo-bulk peak calling, and motif enrichment.
Read guide →SNAP-ChIP Spike-In Calibration Explained: Quantitative Epigenomics and Histone PTM Profiling
Quantitative ChIP-seq calibration using recombinant designer nucleosomes to measure antibody cross-reactivity and normalize global PTM shifts.
Read guide →DNA Methylation and Whole-Genome Bisulfite Sequencing (WGBS) Analysis Workflow
Whole-genome bisulfite sequencing (WGBS) workflow covering Bismark alignment, non-CpG conversion QC, and DMR calling.
Read guide →Genomics
Whole-genome variant calling, population genomics, and chromosome-level de novo genome assembly.
WGS vs WES: Technical, Financial, and Diagnostic Comparison for Genomic Research
Technical, financial, and diagnostic comparison between whole-genome sequencing and whole-exome sequencing.
Read guide →DNA-Seq Variant Calling Workflow: Best Practices from FASTQ to Annotated VCF
GATK Best Practices germline and somatic variant discovery pipeline from BWA-MEM2 alignment to Ensembl VEP clinical annotation.
Read guide →RAD-Seq Population Genomics Workflow: Restriction Site Associated DNA Sequencing
Fractional genome sequencing for non-model population genetics, restriction enzyme digestion, and Stacks 2 SNP cataloging.
Read guide →De Novo Genome Assembly Guide: Short Reads vs Long Reads and Hybrid Strategies
De novo genome assembly guide comparing short-read de Bruijn graphs against PacBio HiFi and Nanopore string graphs with Hi-C scaffolding.
Read guide →Metagenomics
Targeted amplicon vs shotgun metagenomic profiling, taxonomic classification, and metabolic modeling.
16S vs Shotgun Metagenomics: Choosing the Right Microbiome Sequencing Strategy
Choosing between targeted 16S amplicon profiling and untargeted whole-metagenome shotgun sequencing for microbiome studies.
Read guide →Shotgun Metagenomics Analysis Workflow: Taxonomic Profiling and Functional Metagenomics
Comprehensive taxonomic classification with Kraken 2 / MetaPhlAn 4, functional pathway profiling with HUMAnN 3, and MAG binning.
Read guide →Microarray
High-density probe hybridization data analysis, robust multi-array normalization, and linear modeling in R.
Differential Gene Expression Analysis Microarray in R: Step-by-Step Bioconductor Workflow
End-to-end Bioconductor workflow in R executing RMA background correction, normalization, and empirical Bayes linear modeling in limma.
Read guide →Looking for Hands-On Bioinformatics Training or Custom Pipelines?
Our team provides eighteen 30-day online workshops, structured research internships, and commercial NGS analysis services for universities, healthcare institutions, and biotechnology companies.