SC1: scRNA-Seq Analysis Pipeline

Colors

Select color palette:

Load local .scDat file.

Choose a public dataset .scDat file.

Load local .scDat File

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Select example data set:

Dataset Name/ID:

Dataset Description:

Quick View
Counts Matrix

t-SNE PCA UMAP

Download Libraries

Data QC Features:

Outliers:

Show Libraries

Show Clusters

Min Number of Genes per Cell:

Max Total UMIs/Counts per Cell:

Min Total UMIs/Counts per Cell:

Max Number of Genes per Cell:

Max ERCC % per Cell:

Max Mitochondrial % per Cell:

Min Ribosomal % per Cell:

Max Ribosomal % per Cell:

Download new .scDat

View in log-scale

Clustering scRNA-Seq data:

Select Number of Clusters:

Select Clustering Method:

Select Similarity Metric:

Lineage/Pseudotime Analysis (Slingshot)

Select clusters to download:

Download Clusters' scDat Download Clusters' Labels

Group by cluster Group by Library

Percentage

Legend

Plot Type:

Number of Genes MT-Percent

Select Cluster/Library:

By Cluster By Library

Differential Expression Analysis:

Cluster IDs

Library IDs

Select DE Analysis Method:

Fold Change Cutoff:

P-Value Cutoff:

Detection Rate Cutoff:

Download DE Analysis

Differential Analysis - One vs. Rest
DE Analysis - Select Clusters

Select cluster(s) Group 1: (Up-regulated in Red)

Select cluster(s) Group 2:

Download

Gene Enrichment Analysis:

Select DE genes of cluster/library:

Cluster Label

Selection criteria

Up-regulated

Down-regulated

Based on p-Value

Download Genes

Download GE Analysis

DE Genes per Cluster - Enrichment Analysis
DE Genes Enrichment Scores

Genes Group View:

Select Genes:

Genes from list (.csv)

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Combine Genes:

Show Libraries

Show Clusters

Show Lineage

Point Size

Show Axes

Gradient One Gene View (Log-scale)

Download selected cells

Exclude selected cells

Download cells (.csv)

Download gene list

t-SNE UMAP

Genes Pair View:

Select Gene 1:

Gene 1 Threshold:

Select Gene 2:

Gene 2 Threshold:

Show Libraries

Point Size

Show Axes

t-SNE UMAP

Violin/Bar Plots:

Select Gene:

Clusters LibraryIDs

Scale:

Trim Violins

Fixed Violins y-Range

Violins
Bars

Legend

TCR Analysis:

Combined

Single Library

Select TCR-Seq Library:

TCR-Seq output files expected in 10x format:

-clonotypes.csv

-filtered_contig_annotations.csv

TCR-Seq Data (10x-style .csv files)

Browse...

TCR Analysis

Save Analysis Files

TF-IDF Plots

Cluster/Library Composition Plot

Heatmap

Summary Heatmap

Violin Heatmap

Cell Cycle Heatmap

Generate PDF Docs

Save Analysis scDat

Global Settings:

Data Upload & Pre-Processing

Preprocessing options:

Imputation options:

Upload 10x data file (Three files: matrix.mtx, barcodes.tsv and genes.tsv/features.tsv files are expected):

Upload raw data file (One file: .csv file with genes as rows and cells as columns is expected):

Data QC Features:

Top Genes:

Clustering scRNA-Seq data:

Plot Type:

Select Cluster/Library:

Differential Expression Analysis:

Gene Enrichment Analysis:

Genes Group View:

Genes Pair View:

Violin/Bar Plots:

Heatmap ft. top Genes

Cell Cycle Analysis:

Cell Cycle Phases/Clusters Mean-Scores

Cell Cycle Phases/Clusters Smoothness-Scores

TCR Analysis:

TCR-Seq output files expected in 10x format:

-clonotypes.csv

-filtered_contig_annotations.csv

Analysis Documents:

Documents (.pdf) are generated based on current analysis status.