# Task Menu The Task Menu lists all the tasks that can be performed on a specific node. It can be invoked from either a **Data** or **Task node** and appears on the right hand side of the *Analyses* tab. It is *context-sensitive*, meaning that it will only present tasks that the user can perform on the selected node. For example, selecting an *Aligned reads* data node will not present aligners as options. Clicking a **Data node** presents a variety of tasks: * [Data summary report](/partek/partek-flow/user-manual/task-menu/data-summary-report.md) * [QA/QC](/partek/partek-flow/user-manual/task-menu/qa-qc.md) * [Pre-alignment QA/QC](/partek/partek-flow/user-manual/task-menu/qa-qc/pre-alignment-qa-qc.md) * [ERCC Assessment](/partek/partek-flow/user-manual/task-menu/qa-qc/ercc-assessment.md) * [Post-alignment QA/QC](/partek/partek-flow/user-manual/task-menu/qa-qc/post-alignment-qa-qc.md) * [Coverage Report](/partek/partek-flow/user-manual/task-menu/qa-qc/coverage-report.md) * [Validate Variants](/partek/partek-flow/user-manual/task-menu/qa-qc/validate-variants.md) * [Feature distribution](/partek/partek-flow/user-manual/task-menu/qa-qc/feature-distribution.md) * [Single-cell QA/QC](/partek/partek-flow/user-manual/task-menu/qa-qc/single-cell-qa-qc.md) * [Cell barcode QA/QC](/partek/partek-flow/user-manual/task-menu/qa-qc/cell-barcode-qa-qc.md) * [Pre-alignment tools](/partek/partek-flow/user-manual/task-menu/pre-alignment-tools.md) * [Trim bases](/partek/partek-flow/user-manual/task-menu/pre-alignment-tools/trim-bases.md) * [Trim adapters](/partek/partek-flow/user-manual/task-menu/pre-alignment-tools/trim-adapters.md) * [Filter reads](/partek/partek-flow/user-manual/task-menu/pre-alignment-tools/filter-reads.md) * [Trim tags](/partek/partek-flow/user-manual/task-menu/pre-alignment-tools/trim-tags.md) * [Post-alignment tools](/partek/partek-flow/user-manual/task-menu/post-alignment-tools.md) * [Filter alignments](/partek/partek-flow/user-manual/task-menu/post-alignment-tools/filter-alignments.md) * [Convert alignments to unaligned reads](/partek/partek-flow/user-manual/task-menu/post-alignment-tools/convert-alignments-to-unaligned-reads.md) * [Combine alignments](/partek/partek-flow/user-manual/task-menu/post-alignment-tools/combine-alignments.md) * [Deduplicate UMIs](/partek/partek-flow/user-manual/task-menu/post-alignment-tools/deduplicate-umis.md) * [Downscale alignments](/partek/partek-flow/user-manual/task-menu/post-alignment-tools/downscale-alignments.md) * [Annotation/Metadata](/partek/partek-flow/user-manual/task-menu/annotation-metadata.md) * [Annotate cells](/partek/partek-flow/user-manual/task-menu/annotation-metadata/annotate-cells.md) * [Annotation report](/partek/partek-flow/user-manual/task-menu/annotation-metadata/annotation-report.md) * [Publish cell attributes to project](/partek/partek-flow/user-manual/task-menu/annotation-metadata/publish-cell-attributes-to-project.md) * [Attribute report](/partek/partek-flow/user-manual/task-menu/annotation-metadata/attribute-report.md) * [Annotate Visium image](/partek/partek-flow/user-manual/task-menu/annotation-metadata/annotate-visium-image.md) * [Pre-analysis tools](/partek/partek-flow/user-manual/task-menu/pre-analysis-tools.md) * [Generate group cell counts](/partek/partek-flow/user-manual/task-menu/pre-analysis-tools/generate-group-cell-counts.md) * [Pool cells](/partek/partek-flow/user-manual/task-menu/pre-analysis-tools/pool-cells.md) * [Split matrix](/partek/partek-flow/user-manual/task-menu/pre-analysis-tools/split-matrix.md) * [Hashtag demultiplexing](/partek/partek-flow/user-manual/task-menu/pre-analysis-tools/hashtag-demultiplexing.md) * [Merge matrices](/partek/partek-flow/user-manual/task-menu/pre-analysis-tools/merge-matrices.md) * [Descriptive statistics](/partek/partek-flow/user-manual/task-menu/pre-analysis-tools/descriptive-statistics.md) * [Spot clean](/partek/partek-flow/user-manual/task-menu/pre-analysis-tools/spot-clean.md) * [Aligners](/partek/partek-flow/user-manual/task-menu/aligners.md) * [Quantification](/partek/partek-flow/user-manual/task-menu/quantification.md) * [Quantify to annotation model (Partek E/M)](/partek/partek-flow/user-manual/task-menu/quantification/quantify-to-annotation-model-partek-em.md) * [Quantify to transcriptome (Cufflinks)](/partek/partek-flow/user-manual/task-menu/quantification/quantify-to-transcriptome-cufflinks.md) * [Quantify to reference (Partek E/M)](/partek/partek-flow/user-manual/task-menu/quantification/quantify-to-reference-partek-em.md) * [Quantify regions](/partek/partek-flow/user-manual/task-menu/quantification/quantify-regions.md) * [HTSeq](/partek/partek-flow/user-manual/task-menu/quantification/htseq.md) * [Count feature barcodes](/partek/partek-flow/user-manual/task-menu/quantification/count-feature-barcodes.md) * [Salmon](/partek/partek-flow/user-manual/task-menu/quantification/salmon.md) * [Filtering](/partek/partek-flow/user-manual/task-menu/filtering.md) * [Filter features](/partek/partek-flow/user-manual/task-menu/filtering/filter-features.md) * [Filter groups (samples or cells)](/partek/partek-flow/user-manual/task-menu/filtering/filter-groups-samples-or-cells.md) * [Filter barcodes](/partek/partek-flow/user-manual/task-menu/filtering/filter-barcodes.md) * [Split by attribute](/partek/partek-flow/user-manual/task-menu/filtering/split-by-attribute.md) * [Downsample Cells](/partek/partek-flow/user-manual/task-menu/filtering/downsample-cells.md) * [Normalization and scaling](/partek/partek-flow/user-manual/task-menu/normalization-and-scaling.md) * [Impute low expression](/partek/partek-flow/user-manual/task-menu/normalization-and-scaling/impute-low-expression.md) * [Impute missing values](/partek/partek-flow/user-manual/task-menu/normalization-and-scaling/impute-missing-values.md) * [Normalization](/partek/partek-flow/user-manual/task-menu/normalization-and-scaling/normalization.md) * [Normalize to baseline](/partek/partek-flow/user-manual/task-menu/normalization-and-scaling/normalize-to-baseline.md) * [Normalize to housekeeping genes](/partek/partek-flow/user-manual/task-menu/normalization-and-scaling/normalize-to-housekeeping-genes.md) * [Scran deconvolution](/partek/partek-flow/user-manual/task-menu/normalization-and-scaling/scran-deconvolution.md) * [SCTransform](/partek/partek-flow/user-manual/task-menu/normalization-and-scaling/sctransform.md) * [TF-IDF normalization](/partek/partek-flow/user-manual/task-menu/normalization-and-scaling/tf-idf-normalization.md) * [Batch removal](/partek/partek-flow/user-manual/task-menu/batch-removal.md) * [General linear model](/partek/partek-flow/user-manual/task-menu/batch-removal/general-linear-model.md) * [Harmony](/partek/partek-flow/user-manual/task-menu/batch-removal/harmony.md) * [Seurat3 integration](/partek/partek-flow/user-manual/task-menu/batch-removal/seurat3-integration.md) * [Differential Analysis](/partek/partek-flow/user-manual/task-menu/differential-analysis.md) * [GSA](/partek/partek-flow/user-manual/task-menu/differential-analysis/gsa.md) * [ANOVA/LIMMA-trend/LIMMA-voom](/partek/partek-flow/user-manual/task-menu/differential-analysis/anova-limma-trend-limma-voom.md) * [Kruskal-Wallis](/partek/partek-flow/user-manual/task-menu/differential-analysis/kruskal-wallis.md) * [Detect alt-splicing (ANOVA)](/partek/partek-flow/user-manual/task-menu/differential-analysis/detect-alt-splicing-anova.md) * [DESeq2(R) vs DESeq2](/partek/partek-flow/user-manual/task-menu/differential-analysis/deseq2-r-vs-deseq2.md) * [Hurdle model](/partek/partek-flow/user-manual/task-menu/differential-analysis/hurdle-model.md) * [Compute biomarkers](/partek/partek-flow/user-manual/task-menu/differential-analysis/compute-biomarkers.md) * [Transcript Expression Analysis - Cuffdiff](/partek/partek-flow/user-manual/task-menu/differential-analysis/transcript-expression-analysis-cuffdiff.md) * [Troubleshooting](/partek/partek-flow/user-manual/task-menu/differential-analysis/troubleshooting.md) * [Survival Analysis with Cox regression and Kaplan-Meier analysis - Partek Flow](/partek/partek-flow/user-manual/task-menu/survival-analysis-with-cox-regression-and-kaplan-meier-analysis-partek-flow.md) * [Exploratory Analysis](/partek/partek-flow/user-manual/task-menu/exploratory-analysis.md) * [Graph-based Clustering](/partek/partek-flow/user-manual/task-menu/exploratory-analysis/graph-based-clustering.md) * [K-means Clustering](/partek/partek-flow/user-manual/task-menu/exploratory-analysis/k-means-clustering.md) * [Compare Clusters](/partek/partek-flow/user-manual/task-menu/exploratory-analysis/compare-clusters.md) * [PCA](/partek/partek-flow/user-manual/task-menu/exploratory-analysis/pca.md) * [t-SNE](/partek/partek-flow/user-manual/task-menu/exploratory-analysis/t-sne.md) * [UMAP](/partek/partek-flow/user-manual/task-menu/exploratory-analysis/umap.md) * [Hierarchical Clustering](/partek/partek-flow/user-manual/task-menu/exploratory-analysis/hierarchical-clustering.md) * [AUCell](/partek/partek-flow/user-manual/task-menu/exploratory-analysis/aucell.md) * [Find multimodal neighbors](/partek/partek-flow/user-manual/task-menu/exploratory-analysis/find-multimodal-neighbors.md) * [SVD](/partek/partek-flow/user-manual/task-menu/exploratory-analysis/svd.md) * [CellPhoneDB](/partek/partek-flow/user-manual/task-menu/exploratory-analysis/cellphonedb.md) * [Trajectory Analysis](/partek/partek-flow/user-manual/task-menu/trajectory-analysis.md) * [Trajectory Analysis (Monocle 2)](/partek/partek-flow/user-manual/task-menu/trajectory-analysis/trajectory-analysis-monocle-2.md) * [Trajectory Analysis (Monocle 3)](/partek/partek-flow/user-manual/task-menu/trajectory-analysis/trajectory-analysis-monocle-3.md) * [Variant Callers](/partek/partek-flow/user-manual/task-menu/variant-callers.md) * [SAMtools](/partek/partek-flow/user-manual/task-menu/variant-callers/samtools.md) * [FreeBayes](/partek/partek-flow/user-manual/task-menu/variant-callers/freebayes.md) * [LoFreq](/partek/partek-flow/user-manual/task-menu/variant-callers/lofreq.md) * [Variant Analysis](/partek/partek-flow/user-manual/task-menu/variant-analysis.md) * [Fusion Gene Detection](/partek/partek-flow/user-manual/task-menu/variant-analysis/fusion-gene-detection.md) * [Annotate Variants](/partek/partek-flow/user-manual/task-menu/variant-analysis/annotate-variants.md) * [Annotate Variants (SnpEff)](/partek/partek-flow/user-manual/task-menu/variant-analysis/annotate-variants-snpeff.md) * [Annotate Variants (VEP)](/partek/partek-flow/user-manual/task-menu/variant-analysis/annotate-variants-vep.md) * [Filter Variants](/partek/partek-flow/user-manual/task-menu/variant-analysis/filter-variants.md) * [Summarize Cohort Mutations](/partek/partek-flow/user-manual/task-menu/variant-analysis/summarize-cohort-mutations.md) * [Combine Variants](/partek/partek-flow/user-manual/task-menu/variant-analysis/combine-variants.md) * [Copy Number Analysis (CNVkit)](/partek/partek-flow/user-manual/task-menu/copy-number-analysis-cnvkit.md) * [Peak Callers (MACS2)](/partek/partek-flow/user-manual/task-menu/peak-callers-macs2.md) * [Peak analysis](/partek/partek-flow/user-manual/task-menu/peak-analysis.md) * [Annotate Peaks](/partek/partek-flow/user-manual/task-menu/peak-analysis/annotate-peaks.md) * [Promoter sum matrix](/partek/partek-flow/user-manual/task-menu/peak-analysis/promoter-sum-matrix.md) * [Motif Detection](/partek/partek-flow/user-manual/task-menu/motif-detection.md) * [Metagenomics](/partek/partek-flow/user-manual/task-menu/metagenomics.md) * [Kraken](/partek/partek-flow/user-manual/task-menu/metagenomics/kraken.md) * [Alpha & beta diversity](/partek/partek-flow/user-manual/task-menu/metagenomics/alpha-and-beta-diversity.md) * [Choose taxonomic level](/partek/partek-flow/user-manual/task-menu/metagenomics/choose-taxonomic-level.md) * [10x Genomics](/partek/partek-flow/user-manual/task-menu/10x-genomics.md) * [Cell Ranger - Gene Expression](/partek/partek-flow/user-manual/task-menu/10x-genomics/cell-ranger-gene-expression.md) * [Cell Ranger - ATAC](/partek/partek-flow/user-manual/task-menu/10x-genomics/cell-ranger-atac.md) * [Space Ranger](/partek/partek-flow/user-manual/task-menu/10x-genomics/space-ranger.md) * [STARsolo](/partek/partek-flow/user-manual/task-menu/10x-genomics/starsolo.md) * [V(D)J Analysis](/partek/partek-flow/user-manual/task-menu/vdj-analysis.md) * [Biological Interpretation](/partek/partek-flow/user-manual/task-menu/biological-interpretation.md) * [Gene Set Enrichment](/partek/partek-flow/user-manual/task-menu/biological-interpretation/gene-set-enrichment.md) * [GSEA](/partek/partek-flow/user-manual/task-menu/biological-interpretation/gsea.md) * [Correlation](/partek/partek-flow/user-manual/task-menu/correlation.md) * [Correlation analysis](/partek/partek-flow/user-manual/task-menu/correlation/correlation-analysis.md) * [Sample Correlation](/partek/partek-flow/user-manual/task-menu/correlation/sample-correlation.md) * [Similarity matrix](/partek/partek-flow/user-manual/task-menu/correlation/similarity-matrix.md) * [Export](/partek/partek-flow/user-manual/task-menu/export.md) * [Classification](/partek/partek-flow/user-manual/task-menu/classification.md) * [Task actions](/partek/partek-flow/user-manual/task-menu/task-actions.md) * [Feature linkage analysis](/partek/partek-flow/user-manual/task-menu/feature-linkage-analysis.md) Clicking a **Task node** gives you the option to view the *Task results* or perform *Task actions* such as rerunning the task (Figure 1).

Figure 1. Task menu invoked from a Task node

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