Example gallery

Browse live charts and Python source, or try a notebook workflow. The user guide teaches the grammar they use.

Association plots

Manhattan plots and brush-linked views of genome-wide associations.

Manhattan plotHapMap · simulated association statistics Brush-linked Manhattan plotHapMap · simulated association statistics

Differential analysis

Differential-effect views such as volcano and MA plots.

RNA-seq volcano plotAirway dexamethasone experiment RNA-seq MA plotAirway dexamethasone experiment Variant association volcano plotHapMap · simulated association statistics

Single-cell expression

Single-cell UMAPs, marker heatmaps, and expression tracks with AnnData.

PBMC UMAPPBMC3k · Cell types PBMC UMAP panelsPBMC3k · Markers and cell types PBMC marker matrixPBMC3k · 12 marker genes PBMC cell heatmapPBMC3k · 2,638 cells PBMC expression tracksPBMC3k · AnnData

Expression and heatmaps

Clustered expression matrices with aligned trees and annotations.

Clustered heatmap with dendrogramsDepMap · 60 cell lines and 72 genes

Regulatory model interpretation

PISA effects and DynSeq contribution scores for interpreting regulatory models.

Reference and alternate allele contributionsSPI1 binding-QTL data Zoom-adaptive allele contributionsSPI1 binding-QTL data PISA squid plotDrosophila sog enhancer · dm6 PISA interaction matrixDrosophila sog enhancer · dm6

Multi-track genome browsers

Compose signal, sequence, and annotation tracks on a shared genomic axis.

GC content with gene annotationsHuman reference and RefSeq · hg38 Linked genome browser tracksHuman reference, ENCODE and RefSeq · hg38 Genome browser from imported chartsHuman reference and read tracks · hg38

Read alignments and RNA splicing

BAM alignments, direct-RNA reads, coverage, and splice-junction views.

ONT direct-RNA coverage and alignmentsRNF7 · HEK293T WT vs METTL3 knockout Splice junctions with a sashimi plotIGV RNA-seq example data BAM coverage and read pileup1000 Genomes NA12878 · hg18 BAM read alignmentsGIAB HG002 · chromosome 20

Genome annotations

Cytobands, regulatory intervals, and gene annotations from GFF3 and RefSeq.

Chromosome ideogramHuman cytobands · hg38 GFF3 gene annotationsGENCODE · hg38 Gene annotations with prioritized labelsRefSeq · hg38 Candidate regulatory elementsENCODE cCREs · hg38

Sequences, alignments, and logos

Reference sequences, reading frames, multiple-sequence alignments, and logos.

Six-frame translationHuman reference genome · hg38 DNA sequence trackHuman reference genome · hg38 Multiple sequence alignment16S rRNA sequences Brush-linked protein alignment34 P53 protein sequences DNA sequence logoExample nucleotide counts

Mutation position plots

Mutation-position views such as lollipop, rainfall, and variant tracks.

DNMT3A mutation lollipop plotTCGA acute myeloid leukemia PIK3CA mutation lollipop plotTCGA breast cancer Mutation rainfall plotTCGA breast cancer Variant classificationsClinVar · hg38

Oncoprints and cohort summaries

Cohort-level alteration matrices and related summaries.

Mutation oncoplotTCGA acute myeloid leukemia Oncoplot with pathways and clinical tracksTCGA acute myeloid leukemia Lung cancer oncoprintTCGA lung adenocarcinoma

Copy-number plots

Genome-wide copy-number and allele-specific signal views.

Allele-specific copy-number profileASCAT · simulated sample S96 Copy-number segmentationASCAT · simulated sample S96 Interactive purity and ploidy fittingASCAT · simulated samples Structural variants and copy numberHCC1954 breast cancer cell line Ovarian cancer GISTIC landscapeTCGA ovarian cancer

Set intersections

Set-membership combinations and intersection-size summaries.

Mutation intersections with an UpSet plotUpSetR glioblastoma cohort

Basic charts and composition

Marks, encodings, transforms, layering, and chart composition.

Scatter plotSine and cosine example HeatmapSynthetic example data Horizontal stacked barsBarley yields · Vega datasets Layered lollipop plotSynthetic sine wave Layered charts with independent scalesGenomeSpy chromosome 19 example Point shapes and stylesSynthetic grid Positive and negative barsSynthetic wave Drawing intervals with rulesSynthetic interval data Coverage and interval pileupSynthetic intervals Connecting intervalsSynthetic interval pairs Vertically stacked plotsSine and cosine example

Interaction and exploration

Brushing, zoom-dependent displays, scrolling, and dense-data exploration.

Heatmap with zoomable valuesSynthetic wave pattern Points that grow when zooming200,000 generated points Brush-linked penguin summariesPalmer Penguins Brush a million-point torus1,000,000 generated points Scrollable plotSine and cosine example Zoomable t-SNE scatter plotGenomeSpy example embedding

Interactive workflows

Try these demos in your browser, or download a notebook to use the results in Python.

Annotate genomic intervals

Save named regions to an annotation track and export BED.

Annotate genomic intervals

Select genes for follow-up

Brush a volcano plot and export the selected genes.

Select genes for follow-up

Pick individual genes

Click or Shift-click points to collect selected gene records.

Pick individual genes

Edit a sequence

Choose nucleotides in a letter grid and compare with the reference.

Edit a sequence