End-To-End RNA-Seq Analysis

Dseqr runs multi-sample single-cell and bulk RNA-seq analyses from counts → pathways → hits.

Open-source MIT Licensed. GitHub v0.21

Multi sample support

Runs pseudobulk differential expression analyses. For each cluster, compare a set of test samples to a set of control samples.

Sensible defaults

Follows recommendations from the OSCA handbook so that you can focus on biology, not bioinformatics.

Multiple integration algos

Integrate samples with harmony, Azimuth, and FastMNN.

Flexible QC

Start with default filtering or DIY (or both). Custom metrics and subsetting allow you to further refine your QC based on mitochondrial/ribosomal percent, library size, doublet score, or gene expression.

Automated labeling

Quickly transfer labels from previously annotated datasets or built-in references. Easily discover and fix annotation mistakes by comparing any two clusters.

Free to use

To keep Dseqr free, our servers shut down 48 hours after the last time someone opens the app. Your analyses persist between shutdowns, not your footprint.