SC1: scRNA-Seq Analysis Pipeline

Colors

Select color palette:

Quick View
Counts Matrix

t-SNE PCA UMAP

Download Libraries

Data QC Features:

Outliers: 00.0500000.010.020.030.040.05

Show Libraries

Show Clusters

Min Number of Genes per Cell: 1010,0000010101,0102,0103,0104,0105,0106,0107,0108,0109,01010,000

Max Total UMIs/Counts per Cell: 1,0001,000,00000100,0001,000101,000201,000301,000401,000501,000601,000701,000801,000901,0001,000,000

Min Total UMIs/Counts per Cell: 01,000,000005000100,000200,000300,000400,000500,000600,000700,000800,000900,0001,000,000

Max Number of Genes per Cell: 1,00015,0000010,0001,0002,5004,0005,5007,0008,50010,00011,50013,00014,50015,000

Max ERCC % per Cell: 0.005100001000.00510.00520.00530.00540.00550.00560.00570.00580.00590.005100

Max Mitochondrial % per Cell: 1100001001112131415161718191100

Min Ribosomal % per Cell: 0.5500010.55.510.515.520.525.530.535.540.545.550

Max Ribosomal % per Cell: 101000010010192837465564738291100

Download new .scDat

View in log-scale

Group by cluster Group by Library

Percentage

Legend

Plot Type:

Number of Genes MT-Percent

Select Cluster/Library:

By Cluster By Library

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

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

Select cluster(s) Group 2:

Download

DE Genes per Cluster - Enrichment Analysis
DE Genes Enrichment Scores

t-SNE UMAP

Violins
Bars

Legend

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.