# Analysis Functionality

- [Task Menu](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu.md)
- [AI analysis suggestions](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/ai-analysis-suggestions.md): Provides AI-powered recommendations for the next analysis step based on your current data.
- [Task actions](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/task-actions.md)
- [Data summary report](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/data-summary-report.md)
- [QA/QC](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/qa-qc.md)
- [Feature distribution](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/qa-qc/feature-distribution.md)
- [Imported count matrix report](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/qa-qc/feature-distribution-1.md)
- [Single-cell QA/QC](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/qa-qc/single-cell-qa-qc.md)
- [Cell barcode QA/QC](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/qa-qc/cell-barcode-qa-qc.md)
- [5-base Methylation QC](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/qa-qc/5-base-methylation-qc.md)
- [Annotation/Metadata](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/annotation-metadata.md)
- [Annotate cells](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/annotation-metadata/annotate-cells.md)
- [Annotate features](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/annotation-metadata/annotate-cells-1.md)
- [Publish cell attributes to project](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/annotation-metadata/publish-cell-attributes-to-project.md)
- [Attribute report](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/annotation-metadata/annotate-cells-2.md)
- [Pre-analysis tools](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/pre-analysis-tools.md)
- [Pseudobulk](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/pre-analysis-tools/pool-cells.md)
- [Split by feature type](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/pre-analysis-tools/split-matrix.md)
- [Generate group cell counts](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/pre-analysis-tools/generate-group-cell-counts.md)
- [Merge matrices](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/pre-analysis-tools/merge-matrices.md)
- [Spot clean](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/pre-analysis-tools/spot-clean.md)
- [Hashtag demultiplexing](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/pre-analysis-tools/hashtag-demultiplexing.md)
- [Generate beta value](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/pre-analysis-tools/generate-beta-value.md)
- [Generate methylation mvalues](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/pre-analysis-tools/generate-methylation-mvalues.md)
- [Filtering](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/filtering.md)
- [Filter features](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/filtering/filter-features.md)
- [Filter samples/cells](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/filtering/filter-groups-samples-or-cells.md)
- [Filter barcodes](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/filtering/filter-barcodes.md)
- [Split by attribute](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/filtering/split-by-attribute.md)
- [Downsample cells](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/filtering/downsample-cells.md)
- [Normalization and scaling](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/normalization-and-scaling.md)
- [Normalization](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/normalization-and-scaling/normalization.md)
- [Normalize to housekeeping genes](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/normalization-and-scaling/normalize-to-housekeeping-genes.md)
- [Normalize to baseline](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/normalization-and-scaling/normalize-to-baseline.md)
- [Scran deconvolution](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/normalization-and-scaling/scran-deconvolution.md)
- [TF-IDF normalization](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/normalization-and-scaling/tf-idf-normalization.md)
- [Impute missing values](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/normalization-and-scaling/impute-missing-values.md)
- [Impute low expression](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/normalization-and-scaling/impute-low-expression.md)
- [SCTransform](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/normalization-and-scaling/sctransform.md)
- [Batch removal](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/batch-removal.md)
- [General linear model](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/batch-removal/general-linear-model.md)
- [Harmony](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/batch-removal/harmony.md)
- [Seurat3 integration](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/batch-removal/seurat3-integration.md)
- [Statistics](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/statistics.md)
- [Differential Analysis](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/statistics/differential-analysis.md)
- [DESeq2](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/statistics/differential-analysis/deseq2-r-vs-deseq2.md)
- [Hurdle model](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/statistics/differential-analysis/hurdle-model.md)
- [ANOVA/LIMMA-trend/LIMMA-voom](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/statistics/differential-analysis/anova-limma-trend-limma-voom.md)
- [Welch's ANOVA](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/statistics/differential-analysis/kruskal-wallis.md)
- [Kruskal-Wallis / Wilcoxon](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/statistics/differential-analysis/kruskal-wallis-1.md)
- [Detect alt-splicing (ANOVA)](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/statistics/differential-analysis/detect-alt-splicing-anova.md)
- [Poisson/Negative binomial/GSA](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/statistics/differential-analysis/gsa.md)
- [Transcript Expression Analysis - Cuffdiff](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/statistics/differential-analysis/transcript-expression-analysis-cuffdiff.md)
- [Troubleshooting](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/statistics/differential-analysis/troubleshooting.md)
- [Descriptive statistics](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/statistics/correlation-analysis.md)
- [Correlation](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/statistics/correlation-analysis-1.md)
- [Differential methylation](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/statistics/correlation-analysis-2.md)
- [Detect differential methylation](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/statistics/detect-differential-methylation.md)
- [Compute biomarkers](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/statistics/compute-biomarkers.md)
- [Survival Analysis with Cox regression and Kaplan-Meier analysis](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/statistics/survival-analysis-with-cox-regression-and-kaplan-meier-analysis.md)
- [Classification](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/statistics/survival-analysis-with-cox-regression-and-kaplan-meier-analysis-1.md)
- [Spatially Variable Genes](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/statistics/spatially-variable-genes.md)
- [Exploratory analysis](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/exploratory-analysis.md)
- [Graph-based clustering](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/exploratory-analysis/graph-based-clustering.md)
- [K-means clustering](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/exploratory-analysis/k-means-clustering.md)
- [Compare clusters](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/exploratory-analysis/compare-clusters.md)
- [PCA](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/exploratory-analysis/pca.md)
- [t-SNE](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/exploratory-analysis/t-sne.md)
- [UMAP](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/exploratory-analysis/umap.md)
- [Hierarchical clustering / heatmap](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/exploratory-analysis/hierarchical-clustering.md)
- [AUCell](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/exploratory-analysis/aucell.md)
- [Find multimodal neighbors](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/exploratory-analysis/find-multimodal-neighbors.md)
- [SVD](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/exploratory-analysis/svd.md)
- [CellPhoneDB](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/exploratory-analysis/cellphonedb.md)
- [BANKSY - Spatial Domain Identification](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/exploratory-analysis/banksy-spatial-domain-identification.md)
- [Merge differential expression results](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/exploratory-analysis/merge-differential-expression-results.md)
- [Region analysis](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/region-analysis.md)
- [Get Regional Methylation](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/region-analysis/get-regional-methylation.md)
- [Annotate Regions](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/region-analysis/annotate-regions.md)
- [Trajectory analysis](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/trajectory-analysis.md)
- [Monocle 2](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/trajectory-analysis/trajectory-analysis-monocle-2.md)
- [Monocle 3](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/trajectory-analysis/trajectory-analysis-monocle-3.md)
- [Variant Analysis](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/variant-analysis.md)
- [Fusion Gene Detection](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/variant-analysis/fusion-gene-detection.md)
- [Annotate Variants](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/variant-analysis/annotate-variants.md)
- [Annotate Variants (SnpEff)](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/variant-analysis/annotate-variants-snpeff.md)
- [Annotate Variants (VEP)](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/variant-analysis/annotate-variants-vep.md)
- [Filter Variants](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/variant-analysis/filter-variants.md)
- [Summarize Cohort Mutations](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/variant-analysis/summarize-cohort-mutations.md)
- [Combine Variants](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/variant-analysis/combine-variants.md)
- [Remove Background Mutations](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/variant-analysis/remove-background-mutations.md)
- [Combine multiomics data](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/combine-multiomics-data.md)
- [Combine 5-base methylation and variant data](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/combine-multiomics-data/combine-5-base-methylation-and-variant-data.md)
- [Motif Detection](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/motif-detection.md)
- [Biological interpretation](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/biological-interpretation.md)
- [Gene Set Enrichment](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/biological-interpretation/gene-set-enrichment.md)
- [GSEA](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/biological-interpretation/gsea.md)
- [Gene set ANOVA](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/biological-interpretation/gsea-1.md)
- [Correlation Engine Pathway](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/biological-interpretation/correlation-engine-pathway.md)
- [Get targeted mRNA](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/biological-interpretation/get-targeted-mrna.md)
- [Classification](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/classification.md)
- [Classify cell type](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/classification/classify-cell-type.md)
- [Train classifier](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/classification/train-classifier.md)
- [ScType](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/classification/sctype.md)
- [Conversion](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/conversion.md)
- [Region analysis](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/region-analysis-1.md)
- [Annotate regions](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/region-analysis-1/annotate-regions.md)
- [Pipelines](https://help.connected.illumina.com/icm/analyses/analysis-functionality/pipelines.md)
- [Share Analysis](https://help.connected.illumina.com/icm/analyses/analysis-functionality/share-analysis.md)
- [Data Viewer](https://help.connected.illumina.com/icm/analyses/analysis-functionality/data-viewer.md)
- [Chromosome View](https://help.connected.illumina.com/icm/analyses/analysis-functionality/data-viewer/chromosome-view.md)
- [Launching the Chromosome View](https://help.connected.illumina.com/icm/analyses/analysis-functionality/data-viewer/chromosome-view/launching-the-chromosome-view.md)
- [Navigating Through the View](https://help.connected.illumina.com/icm/analyses/analysis-functionality/data-viewer/chromosome-view/navigating-through-the-view.md)
- [Selecting Data Tracks for Visualization](https://help.connected.illumina.com/icm/analyses/analysis-functionality/data-viewer/chromosome-view/selecting-data-tracks-for-visualization.md)
- [Visualizing the Results Using Data Tracks](https://help.connected.illumina.com/icm/analyses/analysis-functionality/data-viewer/chromosome-view/visualizing-the-results-using-data-tracks.md)
- [Annotating the Results](https://help.connected.illumina.com/icm/analyses/analysis-functionality/data-viewer/chromosome-view/annotating-the-results.md)
- [Customizing the View](https://help.connected.illumina.com/icm/analyses/analysis-functionality/data-viewer/chromosome-view/customizing-the-view.md)
- [Dot Plot](https://help.connected.illumina.com/icm/analyses/analysis-functionality/data-viewer/dot-plot.md)
- [Stacked Violin Plot](https://help.connected.illumina.com/icm/analyses/analysis-functionality/data-viewer/stacked-violin-plot.md)
- [Volcano Plot](https://help.connected.illumina.com/icm/analyses/analysis-functionality/data-viewer/volcano-plot.md)
- [Manhattan Plot](https://help.connected.illumina.com/icm/analyses/analysis-functionality/data-viewer/manhattan-plot.md)
- [Venn Diagram](https://help.connected.illumina.com/icm/analyses/analysis-functionality/data-viewer/list-generator-venn-diagram.md)
- [Sources of variation plot](https://help.connected.illumina.com/icm/analyses/analysis-functionality/data-viewer/sources-of-variation-plot.md)
- [Interaction Plots](https://help.connected.illumina.com/icm/analyses/analysis-functionality/data-viewer/interaction-plots.md)
- [Correlation Plot](https://help.connected.illumina.com/icm/analyses/analysis-functionality/data-viewer/correlation-plot.md)
- [Pie Chart](https://help.connected.illumina.com/icm/analyses/analysis-functionality/data-viewer/pie-chart.md)
- [Sankey Plot](https://help.connected.illumina.com/icm/analyses/analysis-functionality/data-viewer/pie-chart-1.md)
- [Histograms](https://help.connected.illumina.com/icm/analyses/analysis-functionality/data-viewer/histograms.md)
- [Settings](https://help.connected.illumina.com/icm/analyses/analysis-functionality/settings.md)
- [Lists](https://help.connected.illumina.com/icm/analyses/analysis-functionality/settings/lists.md)
- [Pipeline management](https://help.connected.illumina.com/icm/analyses/analysis-functionality/settings/pipeline-management.md)
- [Library File Management](https://help.connected.illumina.com/icm/analyses/analysis-functionality/settings/library-file-management.md)
- [Library File Management Page](https://help.connected.illumina.com/icm/analyses/analysis-functionality/settings/library-file-management/library-file-management-page.md)
- [Selecting an Assembly](https://help.connected.illumina.com/icm/analyses/analysis-functionality/settings/library-file-management/selecting-an-assembly.md)
- [Library Files](https://help.connected.illumina.com/icm/analyses/analysis-functionality/settings/library-file-management/library-files.md)
- [Update Library Index](https://help.connected.illumina.com/icm/analyses/analysis-functionality/settings/library-file-management/update-library-index.md)
- [Creating an Assembly on the Library File Management Page](https://help.connected.illumina.com/icm/analyses/analysis-functionality/settings/library-file-management/creating-an-assembly-on-the-library-file-management-page.md)
- [Adding Library Files on the Library File Management Page](https://help.connected.illumina.com/icm/analyses/analysis-functionality/settings/library-file-management/adding-library-files-on-the-library-file-management-page.md)
- [Adding a Reference Sequence](https://help.connected.illumina.com/icm/analyses/analysis-functionality/settings/library-file-management/adding-a-reference-sequence.md)
- [Adding a Cytoband](https://help.connected.illumina.com/icm/analyses/analysis-functionality/settings/library-file-management/adding-a-cytoband.md)
- [Adding a Gene Set](https://help.connected.illumina.com/icm/analyses/analysis-functionality/settings/library-file-management/adding-a-gene-set.md)
- [Adding a Variant Annotation Database](https://help.connected.illumina.com/icm/analyses/analysis-functionality/settings/library-file-management/adding-a-variant-annotation-database.md)
- [Adding a SnpEff Variant Database](https://help.connected.illumina.com/icm/analyses/analysis-functionality/settings/library-file-management/adding-a-snpeff-variant-database.md)
- [Adding a Variant Effect Predictor (VEP) Database](https://help.connected.illumina.com/icm/analyses/analysis-functionality/settings/library-file-management/adding-a-variant-effect-predictor-vep-database.md)
- [Adding an Annotation Model](https://help.connected.illumina.com/icm/analyses/analysis-functionality/settings/library-file-management/adding-an-annotation-model.md)
- [Adding Library Files from Within a Project](https://help.connected.illumina.com/icm/analyses/analysis-functionality/settings/library-file-management/adding-library-files-from-within-a-project.md)
- [Microarray Library Files](https://help.connected.illumina.com/icm/analyses/analysis-functionality/settings/library-file-management/microarray-library-files.md)
- [Removing Library Files](https://help.connected.illumina.com/icm/analyses/analysis-functionality/settings/library-file-management/removing-library-files.md)
- [Option Set Management](https://help.connected.illumina.com/icm/analyses/analysis-functionality/settings/option-set-management.md)
- [Task Management](https://help.connected.illumina.com/icm/analyses/analysis-functionality/settings/task-management.md)
- [Filter Management](https://help.connected.illumina.com/icm/analyses/analysis-functionality/settings/filter-management.md)


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