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Experiments

Experiments

The "Experiment" model in Pluto is a container for storing raw data and running analyses

Using Storyboards

Selecting strandedness for RNA-seq

Canvas

Experiment types in Pluto

What kinds of experiment can I analyze with Pluto?

Bulk RNA sequencing - FASTQ upload

Bulk RNA sequencing - csv upload

CUT&RUN - FASTQ upload

CUT&RUN - csv upload

ATAC-seq - FASTQ upload

ATAC-seq - csv upload

ChIP-seq - csv upload

ChIP-seq - FASTQ upload

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Data inputs and outputs

Importing & editing experiment sample data

Importing experiment assay data: FASTQ files

Importing experiment assay data: cloud locations

Importing experiment assay data: GEO

Editing an experiment's FASTQ files

Formatting sample annotations for experiments with multiple antibodies

Can Pluto submit my data to GEO?

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Single cell

Creating a single cell RNA sequencing experiment

Using single cell RNA sequencing preprocessing workflows

Annotating your single cell RNA-seq data

Single cell RNA-seq preprocessing: Prepare data

Single cell RNA-seq preprocessing: Initialize workflow

Single cell RNA-seq preprocessing: Filter

Single cell RNA-seq preprocessing: Normalize

Single cell RNA-seq preprocessing: Integrate

Single cell RNA-seq preprocessing: Cluster

Single cell RNA-seq preprocessing: Refine clusters

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Experiment actions and resources

Clone an experiment

Viewing pipeline methods

Experiment attachments

Comments and notes

Archiving experiments

Rerunning a pipeline on an experiment

Biological entity annotations in experiments

Downloading BAM files

Experiment change history

Experiment provenance

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