Explore a curated suite of visualization tools and analysis pipelines — hover over any card to learn more, then click to get started.
Scanpy · Seurat
Build a single-cell pipeline stage by stage on Scanpy or Seurat. Quality control and doublet filtering feed dimensionality reduction, clustering, cell-type annotation, and trajectory or RNA velocity — each stage streaming a live run log and figures.
DESeq2 · limma · limma-voom · edgeR
Compare two sample groups with DESeq2, edgeR, limma-voom, or limma. Choose a metadata column and groups to generate differential results, volcano/MA plots, a heatmap, and key diagnostics.
Dimensionality Reduction
Reduce high-dimensional expression data to principal components. Reveals sample clustering, batch effects, and major sources of variation in your dataset.
Kaplan-Meier Curves
Assess the association between gene expression and patient survival outcomes. Generates Kaplan-Meier curves to compare survival probabilities between high and low expression groups.
Coefficients Sized by Significance
Encodes correlation direction by colour and significance or abundance by bubble size, with grouped and faceted layouts; every column role is its own control, so uploads with other headers map without renaming.
View provenanceSpearman Tiles + Pairwise Scatters
Combines density-coloured lower panels with Spearman coefficient tiles for compact exploration of two to twelve numeric variables.
View provenanceLog-Log Fit + Group Residuals
Fits a completeness-corrected log-log regression with group marginal distributions and an inset residual box-plot comparison.
View provenanceTwo Cohorts, Two Dendrograms
Compares two cohorts with Pearson heatmap tiles, independent hierarchical orders, paired edge labels, and aligned top and bottom dendrograms.
View provenanceAnnotated Clustered Matrix
Displays a clustered numeric matrix with row annotations, searchable group filtering, dendrogram controls, and a zero-centred diverging scale.
View provenanceSubstitution Energy by Site
Maps mutation energy across sites and amino-acid substitutions, with smooth or tiled cells and an aligned mean-energy trace.
View provenanceTwo Datasets in Opposite Halves
Compares two feature-correlation matrices in one triangle: the first dataset fills the upper half and the second the lower, as significance-filtered circles or split cells, with shared or independent palettes.
View provenanceModule Blocks + Significance Mask
Applies log10 preprocessing by default, then draws a square correlation matrix grouped by variable_group, with optional clustering and significance blanking tested on the sample observations.
View provenancePearson Triangle + Abundance Bars
Combines a five-class summary, clustered bile-acid correlations and raw-concentration abundance bars in one aligned figure. Sample and bile-acid IDs are limited to 128 Unicode characters, group values to 32; control characters are rejected.
View provenanceRotated Triangle Below Dendrogram
Rotates a hierarchically clustered correlation matrix into a compact triangle with a matched dendrogram and group-coloured labels.
View provenanceShared Identifier Overlap
Compares exact identifier overlap among two, three, or four selected groups, with explicit membership counts and publication-ready styling.
View provenanceSet Intersection Sizes
Ranks exact intersections across many sets using coordinated size bars and a membership matrix, with binary-matrix and directional differential-expression modes.
View provenanceSplits and Merges Across Stages
Tracks weighted observations through three or more ordered stages, revealing how categories split, merge, and propagate downstream.
View provenanceRing Heatmaps + Shared Features
Links circular expression profiles to shared-feature membership, with Venn or UpSet views for comparing intersections among gene sets.
View provenanceScreen Hits by Decision Boundary
Highlights CRISPR screening hits with hyperbolic or rectangular decision boundaries, helping distinguish strong guide-level effects from background signals.
View provenanceFeature Effects per Comparison
Shows feature-level differential-abundance effects as deterministic beeswarm points, supporting a single gradient view or multiple comparison panels.
View provenanceLog2 Fold Change vs Significance
Plots effect size against statistical significance to identify up- and down-regulated features, with single, mirrored, cluster-faceted, and overview layouts.
View provenanceMean Level and Percent Detected
Encodes effect direction by color and magnitude by bubble size across features, targets, and groups, with faceted or separated-row layouts.
View provenanceTwo-contrast Effect Concordance
Compares fold changes from two contrasts on shared axes, highlighting top hits or features significant in both comparisons.
View provenancePolysome vs Total RNA Changes
Contrasts total-RNA and polysome-RNA fold changes to classify transcriptional, translational, and buffering responses.
View provenanceEffect Sizes with Asterisk Marks
Combines effect magnitude and statistical significance in a grouped heatmap, with layouts for facet panels or visual separator rows.
View provenanceActive vs Repressed per State
Displays transcription-factor activity across cell states as active and repressed tile rows split into TF-set facets, with a significance dot per tile and an optional summary strip.
View provenanceCo-activation vs Co-repression
Compares activation and repression scores for paired transcription factors in a symmetric heatmap, making direction, magnitude, and pair-specific balance easy to inspect.
View provenanceDE Hits + Pathway Summaries
Pairs a differential-expression volcano plot with pathway enrichment summaries or an enrichment network to connect individual hits with biological programs.
View provenanceMember Positions + GSEA Curves
Adds ranked gene-set enrichment trajectories and rug marks to a volcano plot, showing where pathway members fall across differential results.
View provenanceCell Type · Time · Condition Rings
Wraps UMAP coordinates with multidimensional sample annotations so cell type, time point, and condition can be reviewed together.
View provenancePCoA/NMDS Separation + PERMANOVA
Displays PCoA or NMDS coordinates together with marginal box plots per group and a PERMANOVA panel, revealing group separation and axis-wise spread in one view. Each row is one sample; the method column selects which ordination the variant draws, and the two-factor variant colours the points by group and shapes them by a second factor column, with box plots for each factor on both axes.
View provenanceGroup Metric + Sample Ordination
Combines NMDS sample ordination with violin distributions of diversity or distance metrics for a coordinated group-level comparison.
View provenanceCircular Clades and Tip Tracks
Renders a rooted phylogenetic tree with categorical rings, clade markers, point tracks, and heatmap-style tip annotations.
View provenanceThree-component Mixtures
Transforms three non-negative components into ternary coordinates and supports categorical, continuous-gradient, or category-plus-size point encodings.
View provenancePer-patient Treatment History
Places clinical metadata, treatments, surgery, recurrence, dense multi-site sampling, and death on patient-level longitudinal timelines.
View provenanceTreatment Lanes + Best Response
Shows metadata tracks, treatment intervals, best response, and stop status along one lane per patient, with standard or trial-grouped layouts. Rows use the canonical headers of the sample file: treatment rows carry start, end, treatment, stop_reason and ongoing; event rows carry event_time and response (SD, PR or CR); the five metadata columns fill the tracks and the legend.
View provenanceInterval Estimates + Result Table
Displays precomputed beta, hazard-ratio, odds-ratio, or risk-ratio estimates with confidence intervals beside an aligned result table. Ratio estimates are drawn on a log axis with the reference at 1; betas on a linear axis with the reference at 0. The beta_threshold layout shades Moderate and High bands at two thresholds, single_hr_grouped stacks rows under a header per group and colours points by the p-value threshold, and dual_hr draws exactly two groups per outcome side by side.
View provenanceBack-to-back Cohort Composition
Compares two sides with back-to-back stacked bars, supporting raw counts or within-side percentages while retaining category composition.
View provenanceMirrored Densities per Feature
Mirrors continuous-value distributions for two sides across features, making differences in shape, spread, and threshold crossing visible.
View provenanceSubject Lines Under Group Means
Connects repeated observations from the same sample or subject across time while retaining group-level summaries: per-group mean with SE, SD or 95% CI bars, optional per-subject trajectories, shaded phase windows read from a phase column, and per-time-point post-hoc labels (t-test or Wilcoxon, multiplicity-adjusted) when exactly two groups are present.
View provenanceGroup Trends with Uncertainty
Shows grouped trajectories over time with ribbons, error bars, or facets to compare central trends and uncertainty. The table carries time and value, an optional symmetric error or explicit lower/upper bounds, and optional group, facet and display_style columns; replicate rows at one time point are averaged. Reference lines are drawn only when Reference X or Reference Y is set.
View provenanceSite Composition on a Basemap
Maps sample counts or compositions to locations on a world or China basemap as pies, bubbles or a choropleth with pies. Rows are typed by record_type: point locations, composition slices, and optional polygon and line overlays with vertex_order. Category and zone colour objects, axis limits and the bubble size range are available to API callers.
View provenanceVolcano + Pathway Overlap Clusters
Pairs a dense differential-expression volcano with a clustered pathway-overlap network, with an alternate circos-network layout.
View provenanceIsotype Mix + Hypermutation Rate
Summarizes B-cell receptor composition and somatic hypermutation metrics in a coordinated multi-panel figure.
View provenanceTwo Measures on Separate Axes
Combines primary bars with a secondary line/point series or nested bars when two related measures require distinct scales.
View provenanceTreatment Groups per Trait
Arranges values as petal-like radial bars and optionally adds error ranges and significance annotations.
View provenanceValues Grouped by Sector
Shows ordered values as radial bars with group colors, value gradients, or both for compact circular comparison.
View provenanceMagnitude Ring + Composition Core
Places radial bars around a central composition pie to compare category-level magnitude with the overall proportion structure.
View provenanceParent-child Levels + Magnitude
Displays hierarchical categories around a circle as radial bars or bubbles, preserving parent-child structure and magnitude.
View provenanceProportions Across Nested Groups
Displays category composition as grouped stacked bars with sectioned or faceted layouts for multi-level comparisons.
View provenancePer-sample Counts + Group Share
Combines stacked dot counts with an inset pie summary so detailed observations and overall composition can be read together.
View provenancePost-hoc Mean Comparisons
Compares grouped means with uncertainty and post-hoc significance annotations for Tukey, LSD, or Dunnett testing results.
View provenanceSide-by-side Group Distributions
Compares continuous distributions through paired, grouped, overlaid, or faceted-IQR violin layouts.
View provenanceControl vs Treatment Panels
Compares reference and specialized groups with source-matched violin or box summaries, independent panel scales, title strips, gradients, and p-value annotations.
View provenanceLinked Subjects Across Conditions
Summarizes paired observations with box plots and subject-level connections, with optional facets for repeated comparisons.
View provenancePolar-sector Violins or Boxes
Bends violin or box distributions into radial sectors for compact comparison of multiple groups or features.
View provenanceFeature Estimates in a Ring
Places association estimates as lollipops around a circle, supporting compact comparison of many features and groups.
View provenanceMulti-track Cohort Overview
Organizes sample metadata and quantitative tracks around a circle for a compact, multi-layer cohort overview.
View provenanceObserved vs Expected Interval
Connects observed and expected values with dumbbells while displaying an expected interval for direction and magnitude assessment.
View provenanceCell Closeness vs Gene Expression
Combines spatial cell-neighborhood proximity with expression summaries to relate physical context to molecular signal.
View provenanceFitted Slopes with Identity Line
Creates faceted bubble-scatter panels with fitted regressions, enabling side-by-side comparison of trends across groups.
View provenanceDirection and Binned Magnitude
Encodes a categorical matrix with bubble color and size so direction, magnitude, and significance can be compared across cells.
View provenanceTaxon Fold Changes by Order
Plots differential OTU effects across ordered taxa as Manhattan-style bubbles, encoding direction, significance, and abundance.
View provenancePressure-response Regressions
Combines ecosystem-change measurements with fitted regressions and marginal summaries to compare coordinated responses.
View provenanceJittered Points + Test Brackets
Shows categorical groups as jittered points with optional publication-style significance brackets. Columns are fixed: category, group, sample_id, value, plus optional comparison_group and p_value for explicit brackets; without p-values the publication style computes a paired test between the first two groups per category. Groups matching the hollow pattern are drawn as open circles.
View provenanceWithin-pair Differences + Test
Compares paired measurements in a scatter plot and summarizes within-pair differences in an inset histogram. Requires subject, control and treat columns; an optional significant column (yes/no) overrides the difference threshold and an optional label column annotates named subjects. A paired Wilcoxon or t test is reported unless the test method is none.
View provenanceLinear Fit + Pearson Statistics
Fits an annotated linear relationship (r, P value, confidence band and quadrant arrows) or a per-group polynomial summary with mean-and-sd whiskers to x/y points. Columns are fixed: x and y are required; group, label and highlight are optional, and only highlighted rows are labelled.
View provenanceX/Y Error Bars + Count Histogram
Compares a count histogram and KDE above a log-scale scatter with bidirectional uncertainty, spectral classes, and magnitude markers. Groups outside the eleven spectral classes are placed by the numeric color_value column; marker shape follows the magnitude cut points 13 and 15.
View provenanceSpline, Logistic and LOESS Fits
Draws grouped (x, y) trajectories as raw lines on a log10 axis, smoothing splines, natural cubic x-splines or four-parameter logistic fits, or compares two groups pair by pair with a LOESS trend and a marginal density inset. Groups take a cold-to-hot colour ladder unless groupColors overrides them; the paired style needs a pair_id shared by both groups.
View provenanceRepeated Measures Around a Cycle
Displays grouped profiles as circular lines or circular bars to compare repeated measurements around an ordered cycle.
View provenanceTime Course + Endpoint Means
Pairs longitudinal trajectories with endpoint bars, linking within-subject change to final group-level outcomes. Rows tagged record_type = time feed the line panel and record_type = endpoint the bar panel; each group is summarised as mean with SE, SD or 95 percent CI error from at least two samples per condition, and a significance or p_value column is drawn once per condition.
View provenanceStacked Densities by Group
Stacks density ridges across groups or markers and can add rugs, facets, and significance annotations.
View provenanceProbability Isolines + Boundaries
Maps one dense joint distribution with probability contours, diagonal conservation boundaries, and labelled feature classes; filled facets and joint marginals remain optional variants.
View provenanceGroup Links + Outer Totals
Connects groups with a chord diagram and adds aligned outer bars to show group-specific totals or attributes.
View provenanceComposition and Total per Point
Draws composition pies at scatter coordinates and separates them into facets for multivariate spatial or ecological comparison.
View provenanceRanked Method Benchmarking
Builds a table-like mixed heatmap: each row draws a tile, circle, bar or text, ranked within its column onto the row's palette, with columns grouped under header bands.
View provenanceSimulation Bias and Calibration
Compares true and recovered model parameters to assess bias, uncertainty, calibration, and simulation performance.
View provenanceMulti-stage Flow
Trace weighted paths across ordered stages with deterministic node placement, positive-flow validation, optional group filtering, and source-to-target colour gradients.
View provenanceMulti-category Distribution
Compare a numeric measurement across many categories with source-faithful boxes, deterministic quasirandom observations, mean labels, and optional comparison annotations.
View provenanceNon-linear Cox Association
Model non-linear exposure-risk associations with restricted cubic splines, confidence ribbons, overall and non-linearity tests, and optional mortality insets.
View provenancePairwise Correlation
Explore pairwise correlations between numeric variables. Displays scatter plots, histograms, and R²/P-value annotations in a comprehensive matrix layout.
View provenancePearson Matrix + Mantel Links
Relate community profiles to environmental variables with Mantel-test links, alongside an upper-triangle Pearson matrix with significance annotations.
View provenanceOverlay - Facets - Outer Ring - Comparison
Explore five compatible radar modes from one tool: overlaid profiles, polygon facets, circular facets, annotated outer rings, and explicit group differences or ratios.
View provenanceRepeated Measures - LMM - ANOVA
Model repeated observations with a linear mixed-effects analysis, Type-III ANOVA and estimated contrasts, then present the results on an annotated circular radar.
View provenanceViolin - Box - Jitter - Rain Ticks
Explore two compatible distribution modes from one tool: a half violin with box and jitter, or a flexible cloud with box summaries and observation-level rain ticks.
View provenanceHalf-Eye - Quantiles - Grouped Comparisons
Explore three compatible comparison modes from one tool: a differential half-eye cloud, quantile connections for two groups, or grouped treatment comparisons with significance.
View provenanceShowing 86 of 86 methods