# Pluto Bio Knowledge Base


## Getting Started

- [Accessing Pluto data programmatically](https://help.pluto.bio/articles/8413533605-accessing-pluto-data-programmatically)
- [Welcome to Pluto!](https://help.pluto.bio/articles/3224766639-welcome-to-pluto)
- [Metrics & usage analytics](https://help.pluto.bio/articles/2663718804-metrics-usage-analytics)

### Anatomy of your Lab Space

- [Projects](https://help.pluto.bio/articles/5268271503-projects)
- [Embedded apps in Pluto](https://help.pluto.bio/articles/1485845393-embedded-apps-in-pluto)
- [Experiment Overview](https://help.pluto.bio/articles/9461806862-experiment-overview)
- [Exploring Data Types in Your Lab Space](https://help.pluto.bio/articles/2461592814-exploring-data-types-in-your-lab-space)

### Your Account

- [Change your profile picture](https://help.pluto.bio/articles/5685575152-change-your-profile-picture)
- [Managing your account](https://help.pluto.bio/articles/5461847684-managing-your-account)

### Organization Settings

- [Manage organization-branded color palette](https://help.pluto.bio/articles/2295937108-manage-organization-branded-color-palette)
- [Programs](https://help.pluto.bio/articles/5220211084-programs)
- [Managing favorite colors](https://help.pluto.bio/articles/9189590313-managing-favorite-colors)
- [Organization branding](https://help.pluto.bio/articles/4602051296-organization-branding)
- [Configuring Single Sign-On (SSO) with the Okta Integration for Pluto Bio (updated)](https://help.pluto.bio/articles/7739938194-configuring-single-sign-on-sso-with-the-okta-integration-for-pluto-bio-updated)

### Manage Access

- [Configuring JumpCloud SAML Single Sign-On with Pluto](https://help.pluto.bio/articles/8342815347-configuring-jumpcloud-saml-single-sign-on-with-pluto)
- [Configuring SAML Single Sign-On with Pluto](https://help.pluto.bio/articles/2039841729-configuring-saml-single-sign-on-with-pluto)
- [Inviting users to your organization in Pluto](https://help.pluto.bio/articles/5603916524-inviting-users-to-your-organization-in-pluto)
- [Roles & permissions in Pluto](https://help.pluto.bio/articles/2428910497-roles-permissions-in-pluto)

## Experiments

- [Using Storyboards](https://help.pluto.bio/articles/9159848766-using-storyboards)
- [Selecting strandedness for RNA-seq](https://help.pluto.bio/articles/1287269899-selecting-strandedness-for-rna-seq)
- [Canvas](https://help.pluto.bio/articles/4835632121-canvas)
- [Custom report upload ("Insights" tab)](https://help.pluto.bio/articles/8796180364-custom-report-upload-insights-tab)

### Experiment types in Pluto

- [What kinds of experiment can I analyze with Pluto?](https://help.pluto.bio/articles/9829738012-what-kinds-of-experiment-can-i-analyze-with-pluto)
- [Bulk RNA sequencing - FASTQ upload](https://help.pluto.bio/articles/4810392891-bulk-rna-sequencing-fastq-upload)
- [Bulk RNA sequencing - csv upload](https://help.pluto.bio/articles/1274486994-bulk-rna-sequencing-csv-upload)
- [CUT&RUN - FASTQ upload](https://help.pluto.bio/articles/5353781881-cut-run-fastq-upload)
- [CUT&RUN - csv upload](https://help.pluto.bio/articles/1038932336-cut-run-csv-upload)
- [ATAC-seq - FASTQ upload](https://help.pluto.bio/articles/3575153224-atac-seq-fastq-upload)
- [ATAC-seq - csv upload](https://help.pluto.bio/articles/4153205551-atac-seq-csv-upload)
- [ChIP-seq - csv upload](https://help.pluto.bio/articles/4342448075-chip-seq-csv-upload)
- [ChIP-seq - FASTQ upload](https://help.pluto.bio/articles/4071438268-chip-seq-fastq-upload)
- [Creating a Multi-omics experiment](https://help.pluto.bio/articles/6222362304-creating-a-multi-omics-experiment)

### Data inputs and outputs

- [Data Upload Overview](https://help.pluto.bio/articles/2937074029-data-upload-overview)
- [Importing & editing experiment sample data](https://help.pluto.bio/articles/4467547515-importing-editing-experiment-sample-data)
- [Importing experiment assay data: FASTQ files](https://help.pluto.bio/articles/6737857149-importing-experiment-assay-data-fastq-files)
- [Importing experiment assay data: cloud locations](https://help.pluto.bio/articles/4852542668-importing-experiment-assay-data-cloud-locations)
- [Importing experiment assay data: GEO](https://help.pluto.bio/articles/4795122023-importing-experiment-assay-data-geo)
- [Editing an experiment's FASTQ files](https://help.pluto.bio/articles/8540924452-editing-an-experiment-s-fastq-files)
- [Formatting sample annotations for experiments with multiple antibodies](https://help.pluto.bio/articles/7203260440-formatting-sample-annotations-for-experiments-with-multiple-antibodies)
- [Can I use Pluto to submit my data to GEO?](https://help.pluto.bio/articles/2597807351-can-i-use-pluto-to-submit-my-data-to-geo)

### Single Cell

- [Creating a single cell RNA sequencing experiment](https://help.pluto.bio/articles/8185009579-creating-a-single-cell-rna-sequencing-experiment)
- [Using single cell RNA sequencing preprocessing workflows](https://help.pluto.bio/articles/7324006081-using-single-cell-rna-sequencing-preprocessing-workflows)
- [Single cell RNA-seq preprocessing: Prepare data](https://help.pluto.bio/articles/6437373431-single-cell-rna-seq-preprocessing-prepare-data)
- [Single cell RNA-seq preprocessing: Initialize workflow](https://help.pluto.bio/articles/9973342600-single-cell-rna-seq-preprocessing-initialize-workflow)
- [Single cell RNA-seq preprocessing: Filter](https://help.pluto.bio/articles/1518413215-single-cell-rna-seq-preprocessing-filter)
- [Single cell RNA-seq preprocessing: Normalize](https://help.pluto.bio/articles/4970960904-single-cell-rna-seq-preprocessing-normalize)
- [Single cell RNA-seq preprocessing: Integrate](https://help.pluto.bio/articles/1365591722-single-cell-rna-seq-preprocessing-integrate)
- [Single cell RNA-seq preprocessing: Cluster](https://help.pluto.bio/articles/4075864033-single-cell-rna-seq-preprocessing-cluster)
- [Single cell RNA-seq preprocessing: Refine clusters](https://help.pluto.bio/articles/7308244847-single-cell-rna-seq-preprocessing-refine-clusters)
- [Annotating your single cell RNA-seq data](https://help.pluto.bio/articles/6796163038-annotating-your-single-cell-rna-seq-data)
- [Uploading Seurat objects to Pluto](https://help.pluto.bio/articles/3604602505-uploading-seurat-objects-to-pluto)

### Experiment actions and resources

- [Clone an experiment](https://help.pluto.bio/articles/2598288048-clone-an-experiment)
- [Viewing pipeline methods](https://help.pluto.bio/articles/5124878108-viewing-pipeline-methods)
- [Experiment attachments](https://help.pluto.bio/articles/6646585850-experiment-attachments)
- [Comments and notes](https://help.pluto.bio/articles/5637642497-comments-and-notes)
- [Archiving experiments](https://help.pluto.bio/articles/8338665830-archiving-experiments)
- [Rerunning a pipeline on an experiment](https://help.pluto.bio/articles/8335659198-rerunning-a-pipeline-on-an-experiment)
- [Biological entity annotations in experiments](https://help.pluto.bio/articles/8670508711-biological-entity-annotations-in-experiments)
- [Downloading BAM files](https://help.pluto.bio/articles/8770984026-downloading-bam-files)
- [Experiment change history](https://help.pluto.bio/articles/3202142818-experiment-change-history)
- [Experiment provenance](https://help.pluto.bio/articles/8936866118-experiment-provenance)

## Analyses

- [Adding comparisons for Gene Set Enrichment Analysis](https://help.pluto.bio/articles/2414305995-adding-comparisons-for-gene-set-enrichment-analysis)
- [Choosing between MACS2 and SEACR for peak calling with epigenomics datasets](https://help.pluto.bio/articles/8776924502-choosing-between-macs2-and-seacr-for-peak-calling-with-epigenomics-datasets)
- [Change log: Analyses](https://help.pluto.bio/articles/7670931299-change-log-analyses)
- [Including covariates in differential analyses](https://help.pluto.bio/articles/2914342181-including-covariates-in-differential-analyses)
- [Protein-protein interaction analysis](https://help.pluto.bio/articles/6053389406-protein-protein-interaction-analysis)
- [Marker expression analysis for single cell RNA-seq data](https://help.pluto.bio/articles/6995473090-marker-expression-analysis-for-single-cell-rna-seq-data)
- [Feature filtering for differential expression / binding analyses](https://help.pluto.bio/articles/5546523349-feature-filtering-for-differential-expression-binding-analyses)

### Summary

- [Summary Analysis](https://help.pluto.bio/articles/5579410044-summary-analysis)
- [Summary analysis (CPM-normalized)](https://help.pluto.bio/articles/3882983084-summary-analysis-cpm-normalized)
- [Clustering (differential features)](https://help.pluto.bio/articles/5478206718-clustering-differential-features)
- [Longitudinal analysis](https://help.pluto.bio/articles/3116072061-longitudinal-analysis)

### Pathway

- [Transcription factor enrichment analysis (TFEA)](https://help.pluto.bio/articles/4930142136-transcription-factor-enrichment-analysis-tfea)
- [Gene set enrichment analysis (GSEA)](https://help.pluto.bio/articles/3874260517-gene-set-enrichment-analysis-gsea)
- [Over-representation Analysis](https://help.pluto.bio/articles/9072321836-over-representation-analysis)

### Dimensionality reduction

- [Uniform Manifold Approximation and Projection (UMAP)](https://help.pluto.bio/articles/4469358356-uniform-manifold-approximation-and-projection-umap)
- [t-distributed Stochastic Neighbor Embedding (t-SNE)](https://help.pluto.bio/articles/4164240642-t-distributed-stochastic-neighbor-embedding-t-sne)
- [Principal components analysis (PCA)](https://help.pluto.bio/articles/4751659201-principal-components-analysis-pca)

### Clinical outcomes

- [Survival analysis](https://help.pluto.bio/articles/5776000206-survival-analysis)

### Comparative

- [Differential expression analysis](https://help.pluto.bio/articles/8410190401-differential-expression-analysis)
- [Differential expression analysis for single cell RNA-seq data](https://help.pluto.bio/articles/3008196539-differential-expression-analysis-for-single-cell-rna-seq-data)
- [Sample Correlation](https://help.pluto.bio/articles/7539610996-sample-correlation)
- [Differential Binding Analysis](https://help.pluto.bio/articles/2925289838-differential-binding-analysis)
- [Overlap genes analysis](https://help.pluto.bio/articles/9197970092-overlap-genes-analysis)
- [Why are there so many genes at the top of my volcano plot?](https://help.pluto.bio/articles/2686427829-why-are-there-so-many-genes-at-the-top-of-my-volcano-plot)
- [Motif Analysis](https://help.pluto.bio/articles/4504262687-motif-analysis)

### Content

- [Text](https://help.pluto.bio/articles/2881866855-text)
- [Images](https://help.pluto.bio/articles/5847208604-images)
- [Spreadsheet](https://help.pluto.bio/articles/5901714228-spreadsheet)
- [External Analysis](https://help.pluto.bio/articles/1810805479-external-analysis)

### Genome

- [Peak analysis](https://help.pluto.bio/articles/1183944181-peak-analysis)
- [Coverage Analysis](https://help.pluto.bio/articles/1668099595-coverage-analysis)
- [Functional Annotation Analysis](https://help.pluto.bio/articles/2985182222-functional-annotation-analysis)

### Multi-omics

- [Embedding an analysis from another experiment](https://help.pluto.bio/articles/3884118055-embedding-an-analysis-from-another-experiment)

## Plots

- [Exporting presentation-ready figures](https://help.pluto.bio/articles/1441404631-exporting-presentation-ready-figures)
- [Embedding Pluto plots](https://help.pluto.bio/articles/3799418434-embedding-pluto-plots)
- [Edit plot colors and legends](https://help.pluto.bio/articles/2040068971-edit-plot-colors-and-legends)
- [Plotting gene lists / top genes](https://help.pluto.bio/articles/6758597286-plotting-gene-lists-top-genes)
- [Viewing Analysis Results](https://help.pluto.bio/articles/6135474118-viewing-analysis-results)
- [Reordering plots and widgets](https://help.pluto.bio/articles/2008417793-reordering-plots-and-widgets)
- [Search all plots](https://help.pluto.bio/articles/8032976267-search-all-plots)
- [Customize gene sets on a Score Barplot](https://help.pluto.bio/articles/1535957583-customize-gene-sets-on-a-score-barplot)
- [Label targets on a volcano plot](https://help.pluto.bio/articles/3288874137-label-targets-on-a-volcano-plot)
- [Clone a plot](https://help.pluto.bio/articles/4457791255-clone-a-plot)
- [Reorder plot legends](https://help.pluto.bio/articles/3730744429-reorder-plot-legends)
- [Presentation mode](https://help.pluto.bio/articles/7583484721-presentation-mode)
- [Plot Methods Section](https://help.pluto.bio/articles/9107967718-plot-methods-section)
- [Plot share links](https://help.pluto.bio/articles/2271745086-plot-share-links)

## Data Management

- [Biomarker management](https://help.pluto.bio/articles/3753655436-biomarker-management)
- [Evidence](https://help.pluto.bio/articles/6434593340-evidence)
- [Target management](https://help.pluto.bio/articles/8170089379-target-management)
- [Downloading data from Pluto](https://help.pluto.bio/articles/4860170995-downloading-data-from-pluto)

## Literature

- [Searching in literature collections](https://help.pluto.bio/articles/7281858743-searching-in-literature-collections)
- [Literature Search](https://help.pluto.bio/articles/3522890696-literature-search)

## Integrations

- [Import from S3 to Pluto](https://help.pluto.bio/articles/4895924581-import-from-s3-to-pluto)
- [Benchling + Pluto](https://help.pluto.bio/articles/5361950297-benchling-pluto)
- [Sequencing vendors + Pluto](https://help.pluto.bio/articles/3799161656-sequencing-vendors-pluto)
- [Colabra + Pluto](https://help.pluto.bio/articles/3090134149-colabra-pluto)
- [PowerPoint + Pluto - Embedding dynamic plots in your slides](https://help.pluto.bio/articles/1603571533-powerpoint-pluto-embedding-dynamic-plots-in-your-slides)
- [Airtable + Pluto](https://help.pluto.bio/articles/7552108300-airtable-pluto)
- [Notion + Pluto](https://help.pluto.bio/articles/1898207778-notion-pluto)
- [BaseSpace + Pluto](https://help.pluto.bio/articles/7102597437-basespace-pluto)
- [Graphpad Prism + Pluto](https://help.pluto.bio/articles/4612523570-graphpad-prism-pluto)
- [Confluence + Pluto](https://help.pluto.bio/articles/4400191975-confluence-pluto)
- [Squarespace + Pluto](https://help.pluto.bio/articles/9474643761-squarespace-pluto)
- [CellKb: Cell type annotation suggestions](https://help.pluto.bio/articles/8529601000-cellkb-cell-type-annotation-suggestions)
- [Linking your Synapse account to Pluto](https://help.pluto.bio/articles/2262678851-linking-your-synapse-account-to-pluto)

## Sharing and Security

- [Sharing projects & experiments](https://help.pluto.bio/articles/1058820509-sharing-projects-experiments)
- [Preparing to publish!](https://help.pluto.bio/articles/9064956549-preparing-to-publish)
- [Change tracking and analysis reproducibility](https://help.pluto.bio/articles/7156243897-change-tracking-and-analysis-reproducibility)
- [Is Pluto SOC2 Type II compliant?](https://help.pluto.bio/articles/5244121090-is-pluto-soc2-type-ii-compliant)
- [Creating your API token](https://help.pluto.bio/articles/6700389148-creating-your-api-token)
- [Does Pluto meet the NIH GDS requirements?](https://help.pluto.bio/articles/8900361244-does-pluto-meet-the-nih-gds-requirements)
- [Configuring SAML Single Sign-On (SSO) with Okta for Pluto](https://help.pluto.bio/articles/7080872787-configuring-saml-single-sign-on-sso-with-okta-for-pluto)

## Explore

- [Querying published data sets](https://help.pluto.bio/articles/2613309583-querying-published-data-sets)
- [Requesting new GEO experiments in Pluto](https://help.pluto.bio/articles/4315231511-requesting-new-geo-experiments-in-pluto)
- [Citing Pluto](https://help.pluto.bio/articles/1225061090-citing-pluto)
- [Performing exploratory analysis in Pluto](https://help.pluto.bio/articles/3836280993-performing-exploratory-analysis-in-pluto)
- [Performing exploratory analysis](https://help.pluto.bio/articles/7651323634-performing-exploratory-analysis)
- [What's Pluto all about?](https://help.pluto.bio/articles/4387463280-what-s-pluto-all-about)

## Pipelines

- [What is a pipeline?](https://help.pluto.bio/articles/7118026629-what-is-a-pipeline)
- [RNA-seq pipeline parameters](https://help.pluto.bio/articles/6179752613-rna-seq-pipeline-parameters)
- [CUT&RUN pipeline parameters](https://help.pluto.bio/articles/7938410265-cut-run-pipeline-parameters)
- [Standard ChIP-seq parameters in Pluto](https://help.pluto.bio/articles/8232700057-standard-chip-seq-parameters-in-pluto)
- [Standard PRO-seq parameters in Pluto](https://help.pluto.bio/articles/5464795268-standard-pro-seq-parameters-in-pluto)
- [Merging lanes in NGS pipelines](https://help.pluto.bio/articles/5979644497-merging-lanes-in-ngs-pipelines)
- [Concatenating FASTQ files](https://help.pluto.bio/articles/8097913558-concatenating-fastq-files)
- [Broad vs narrow peak mode for peak calling in epigenomics experiments](https://help.pluto.bio/articles/8441204245-broad-vs-narrow-peak-mode-for-peak-calling-in-epigenomics-experiments)

## Billing

- [Purchasing Pluto with a Purchase Order (PO)](https://help.pluto.bio/articles/5213459323-purchasing-pluto-with-a-purchase-order-po)
- [Registering Pluto as a vendor with your company / institution](https://help.pluto.bio/articles/3781715912-registering-pluto-as-a-vendor-with-your-company-institution)
- [EIN & W-9](https://help.pluto.bio/articles/2402079914-ein-w-9)

## Reference: Analysis Terms & Methods

- [Introduction to Proteomics](https://help.pluto.bio/articles/5201454987-introduction-to-proteomics)

### Software Packages

- [What is EdgeR?](https://help.pluto.bio/articles/2041331350-what-is-edger)
- [What is DESeq2?](https://help.pluto.bio/articles/3687216850-what-is-deseq2)
- [What is RSEM? | Pluto Help Center](https://help.pluto.bio/articles/2653047670-what-is-rsem-pluto-help-center)
- [What is Glimma?](https://help.pluto.bio/articles/8241347146-what-is-glimma)
- [What is Trim Galore?](https://help.pluto.bio/articles/4063621123-what-is-trim-galore)
- [What is SAMtools?](https://help.pluto.bio/articles/3929721810-what-is-samtools)
- [What is FASTQC?](https://help.pluto.bio/articles/3525467479-what-is-fastqc)
- [What is Kallisto?](https://help.pluto.bio/articles/1311761554-what-is-kallisto)
- [What is RSeQC?](https://help.pluto.bio/articles/9800615224-what-is-rseqc)
- [What is SortMeRNA?](https://help.pluto.bio/articles/4450605713-what-is-sortmerna)
- [What is STAR?](https://help.pluto.bio/articles/2190260030-what-is-star)

### Sequencing

- [Introduction to RNA-seq](https://help.pluto.bio/articles/5967681127-introduction-to-rna-seq)
- [What is paired-end sequencing?](https://help.pluto.bio/articles/1696801220-what-is-paired-end-sequencing)
- [Where does variance come from in RNA-seq data?](https://help.pluto.bio/articles/9713565202-where-does-variance-come-from-in-rna-seq-data)
- [What are adapters?](https://help.pluto.bio/articles/4105915113-what-are-adapters)
- [What is fold change?](https://help.pluto.bio/articles/3840998589-what-is-fold-change)
- [What is a reference genome?](https://help.pluto.bio/articles/8908791680-what-is-a-reference-genome)
- [What is multiplexing?](https://help.pluto.bio/articles/7734969213-what-is-multiplexing)
- [What QC information does Pluto provide for RNA-seq analysis?](https://help.pluto.bio/articles/1149729980-what-qc-information-does-pluto-provide-for-rna-seq-analysis)
- [What is depth of sequencing?](https://help.pluto.bio/articles/2507429340-what-is-depth-of-sequencing)
- [What is a FASTQ file?](https://help.pluto.bio/articles/8221939043-what-is-a-fastq-file)
- [What is FPKM?](https://help.pluto.bio/articles/7646814074-what-is-fpkm)
- [What is TPM?](https://help.pluto.bio/articles/5330431591-what-is-tpm)
- [What is RPKM?](https://help.pluto.bio/articles/3528892948-what-is-rpkm)
- [What is the read-count?](https://help.pluto.bio/articles/9008758049-what-is-the-read-count)

### Statistics

- [SD versus SEM](https://help.pluto.bio/articles/6203995347-sd-versus-sem)
- [Statistical tests for comparing groups of samples](https://help.pluto.bio/articles/7013200437-statistical-tests-for-comparing-groups-of-samples)
- [What is voom?](https://help.pluto.bio/articles/3556335563-what-is-voom)

## Solutions

- [Pluto for lab incubators, non-profits, and other multi-lab groups](https://help.pluto.bio/articles/3809088595-pluto-for-lab-incubators-non-profits-and-other-multi-lab-groups)
- [Pluto for biotech](https://help.pluto.bio/articles/5938878403-pluto-for-biotech)
- [About Pluto's collaborative life sciences platform](https://help.pluto.bio/articles/2829812149-about-pluto-s-collaborative-life-sciences-platform)
- [Pluto for academic labs](https://help.pluto.bio/articles/3744091758-pluto-for-academic-labs)
- [Pluto for service providers](https://help.pluto.bio/articles/6012227794-pluto-for-service-providers)

## Program Management

- [Program Types & Stages](https://help.pluto.bio/articles/5346263700-program-types-stages)
- [Programs](https://help.pluto.bio/articles/9355314724-programs)


- [Test import - direct from KB help.pluto.bio](https://help.pluto.bio/articles/9402914245-test-import-direct-from-kb-help-pluto-bio)
- [Entity databases](https://help.pluto.bio/articles/8655647150-entity-databases)
- [Importing data from sequencing vendors (FTP)](https://help.pluto.bio/articles/6804843714-importing-data-from-sequencing-vendors-ftp)
- [Spatial transcriptomics](https://help.pluto.bio/articles/2538593453-spatial-transcriptomics)
- [Preparing and exploring spatial data in Spatial Studio](https://help.pluto.bio/articles/5599751044-preparing-and-exploring-spatial-data-in-spatial-studio)