Guides to analyzing omics data well
Practical guides from our bioinformaticians and cell biologists: best-practice workflows, platform comparisons, and the mistakes we see most often in single-cell, spatial, bulk, imaging and discovery analyses.
- Single-cell
Single-cell RNA-seq analysis: a best-practice workflow from FASTQ to figures
A step-by-step scRNA-seq workflow: alignment, empty droplets, ambient RNA, doublets, QC, integration, annotation, pseudobulk DE and trajectories.
- Single-cell
12 mistakes that ruin single-cell RNA-seq analyses, and how experts avoid them
The scRNA-seq errors we fix most: pseudoreplication, doublets called new cell types, ambient RNA, over-integration, fixed QC cutoffs, UMAP myths.
- Buying guide
How much does bioinformatics analysis cost? A 2026 pricing guide
2026 costs for scRNA-seq, RNA-seq, Visium HD, Xenium, ATAC-seq and Cell Painting analysis, and how hourly, per-sample and salary pricing compare.
- Spatial
Visium HD vs Xenium vs CosMx vs MERSCOPE: choosing a spatial transcriptomics platform
Visium HD, Xenium, CosMx, MERSCOPE and GeoMx compared: resolution, gene coverage, sample types, analysis challenges and which to choose.
- Single-cell
Pseudobulk differential expression in single-cell RNA-seq: why cells are not replicates
Why cell-level tests produce false positives in scRNA-seq, how pseudobulk aggregation works, when to use mixed models, and a practical DESeq2/edgeR workflow.
- Spatial
Visium HD data analysis: from 2 µm bins to cells, domains and niches
How to analyze Visium HD: QC and tissue masking, 8 µm bins vs nucleus segmentation, RCTD or cell2location deconvolution, domains and niches.
- Single-cell
Doublets and ambient RNA in single-cell data: how to detect and remove them
How doublets and ambient RNA distort scRNA-seq and snRNA-seq results, and how to remove them with scDblFinder, DoubletFinder, CellBender, SoupX and EmptyDrops.
- Single-cell
Batch correction and data integration in single-cell RNA-seq: Harmony, scVI, Seurat and when to use each
Integrate scRNA-seq samples without erasing biology: choosing Harmony, scVI, scANVI or Seurat, scIB benchmarking and avoiding over-correction.
- Single-cell
How to design a single-cell experiment so the analysis succeeds
Plan scRNA-seq studies that succeed: biological replicates, cells per sample, sequencing depth, cells vs nuclei, multiplexing and batch layout.
- Spatial
Xenium data analysis: segmentation, QC and the pitfalls that create false biology
How to analyze 10x Xenium data: transcript QC, re-segmentation with Baysor or Proseg, panel-aware annotation, neighborhoods and niches.
- Epigenomics
snATAC-seq and 10x Multiome analysis: from fragments to regulatory networks
snATAC-seq and 10x Multiome analysis: fragment QC, TSS enrichment, iterative LSI, per-cell-type peaks, chromVAR, footprints and SCENIC+ networks.
- Bulk sequencing
Bulk RNA-seq differential expression done right: DESeq2, edgeR, limma and batch effects
Bulk RNA-seq best practices: QC, Salmon vs STAR, design matrices, DESeq2 vs edgeR vs limma-voom, batch effects, shrinkage and enrichment pitfalls.
- Imaging and phenomics
Cell Painting analysis: from images to phenotypic profiles and mechanism of action
A Cell Painting analysis pipeline: illumination correction, segmentation, features, plate effects, normalization, mAP, hit calling and MoA.
- Imaging and phenomics
Cell tracking in live-cell imaging: segmentation, linking, lineages and validation
How to track cells in time-lapse microscopy: Cellpose segmentation, TrackMate and ultrack linking, lineage trees, accuracy checks, common errors.
- Proteomics
Protein-protein interaction analysis: scoring AP-MS and BioID, building networks, modeling structures
Analyzing protein-protein interaction data: SAINT and CRAPome scoring for AP-MS and BioID, quantitative interactomics, networks, AlphaFold-Multimer.
- Discovery
Computational target discovery with multi-omics: how to build an evidence-weighted shortlist
How biotech teams prioritize drug targets: human genetics, single-cell and spatial specificity, CRISPR dependency, tractability and safety.
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