GAnnoViz

Parameters

Download Version, Parameter, MD5

GFF/GTF file

Browse...

Format

Gene ID

Promoter upstream

Promoter downstream

Feature alpha

Intron width

X breaks

Arrow length

Arrow count

Arrow unit

Promoter color

5'UTR color

3'UTR color

Exon color

Intron color

Width (in)

Height (in)

DPI

Format

Plot

Plot gene structure

1. App Name:
plot_gene_structure

2. Function Description

Plot gene structure (Promoter, 3'UTR, Exon, Intron, 5'UTR).

3. Demo Output

Example Datasets

1. Genomic Annotation (GFF3/GTF)
Mus musculus: GRCm39.115 Download GFF3

2. Differentially expressed genes (DESeq2)
Download DEG

3. Differentially methylated regions (MethylKit)
Download DMR

4. SNP mutation site (VCFtools)
Download SNP

Parameters

Download Version, Parameter, MD5

DEG table

Browse...

GFF/GTF file

Browse...

Format

ID column

FC column

Use strand

Drop unmapped

Data

Annotate DEGs on chromosomes

1. App Name:
anno_deg_chrom

2. Function Description

Annotate and plot differentially expressed genes (DEGs) on chromosomes.

3. Demo Output

Example Datasets

Parameters

Download Version, Parameter, MD5

Gene name

Species

Transcript ID

Transcript choice

Palette

Legend columns

Width (in)

Height (in)

DPI

Format

Plot

Plot protein domains

1. App Name:
plot_gene_domains

2. Function Description

Plot protein domains from Ensembl.

3. Demo Output

Example Datasets

Parameters

Download Version, Parameter, MD5

DMR table

Browse...

Chrom ID

Smooth span

Hyper color

Hypo color

Point size

Point alpha

Width (in)

Height (in)

DPI

Format

Plot

Plot chromosomal DMGs trend

1. App Name:
plot_dmg_trend

2. Function Description

Plot chromosomal DMGs trend.

3. Demo Output

Example Datasets

Parameters

Download Version, Parameter, MD5

GFF/GTF file

Browse...

Format

Chrom ID

Start

End

X breaks

Promoter upstream

Promoter downstream

Feature alpha

Intron width

Arrow length

Arrow count

Arrow unit

Promoter color

5'UTR color

3'UTR color

Exon color

Intron color

Width (in)

Height (in)

DPI

Format

Plot

Plot gene structures for interval

1. App Name:
plot_interval_structure

2. Function Description

Plot gene structures for a genomic interval.

3. Demo Output

Example Datasets

Parameters

Download Version, Parameter, MD5

GFF/GTF file

Browse...

Format

Gene ID

Flank upstream

Flank downstream

Show promoters

Promoter upstream

Promoter downstream

Arrow length

Arrow unit

Gene color

Promoter color

Label size

Width (in)

Height (in)

DPI

Format

Plot

Gene neighborhood architecture

1. App Name:
plot_interval_flank

2. Function Description

Plot gene neighborhood around a focal gene.

3. Demo Output

Example Datasets

Parameters

Download Version, Parameter, MD5

GFF/GTF file

Browse...

Format

Orientation

Bar width

Chrom alpha

Gene width

Chrom color

Gene color

Telomere color

Label size

Width (in)

Height (in)

DPI

Format

Plot

Plot chromosome structures and gene stats

1. App Name:
plot_chrom_structure

2. Function Description

Plot chromosome structures and gene stats.

3. Demo Output

Example Datasets

Parameters

Download Version, Parameter, MD5

GFF/GTF file

Browse...

Format

Gene table (2 cols: id,name)

Browse...

Annotate

Orientation

Min gap frac

Bar width

Chrom alpha

Gene width

Chrom color

Gene color

Telomere color

Label size

Connector dx1

Connector dx2

Width (in)

Height (in)

DPI

Format

Plot

Plot chromosome structures and gene annotation

1. App Name:
plot_chrom_genes

2. Function Description

Plot chromosome structures and gene annotation.

3. Demo Output

Example Datasets

Parameters

Download Version, Parameter, MD5

GFF/GTF file

Browse...

Format

Feature

Bin size

Orientation

Palette start

Palette end

Alpha

Width (in)

Height (in)

DPI

Format

Plot

Plot genomic feature density heatmap

1. App Name:
plot_chrom_heatmap

2. Function Description

Plot genomic feature density heatmap.

3. Demo Output

Example Datasets

Parameters

Download Version, Parameter, MD5

DEG table

Browse...

GFF/GTF file

Browse...

Format

ID column

FC column

Violin scale

Violin border

Point shape

Point size

Jitter width

Hyper color

Hypo color

Width (in)

Height (in)

DPI

Format

Plot

Plot DEGs hyper/hypo distributions

1. App Name:
plot_deg_chrom

2. Function Description

Plot differentially expressed genes (DEGs) hyper/hypo distributions by chromosomes.

3. Demo Output

Example Datasets

Parameters

Download Version, Parameter, MD5

DEG table

Browse...

GFF/GTF file

Browse...

Format

ID column

FC column

Orientation

Chrom alpha

Bar height

Chrom color

Point size

Point alpha

Up color

Down color

Mark style

Line width

Line height

Width (in)

Height (in)

DPI

Format

Plot

Plot DEGs up/down along chromosomes

1. App Name:
plot_deg_exp

2. Function Description

Plot DEGs up/down along chromosomes.

3. Demo Output

Example Datasets

Parameters

Download Version, Parameter, MD5

DEG table

Browse...

ID column

FC column

Sig column

FC threshold

Sig threshold

Point size

Point alpha

Up color

Down color

NS color

Width (in)

Height (in)

DPI

Format

Plot

Plot DEGs volcano

1. App Name:
plot_deg_volcano

2. Function Description

Plot differentially expressed genes (DEGs) volcano.

3. Demo Output

Example Datasets

Parameters

Download Version, Parameter, MD5

FST table

Browse...

Bin size

Metric

Orientation

Palette start

Palette end

Alpha

Width (in)

Height (in)

DPI

Format

Plot

Plot genomic weighted FST heatmap

1. App Name:
plot_snp_fst

2. Function Description

Plot genomic weighted FST heatmap.

3. Demo Output

Example Datasets

Parameters

Download Version, Parameter, MD5

FST table

Browse...

GFF/GTF file

Browse...

Format

Chrom ID

Top N

Orientation

Smooth span

Point size

Point alpha

Label size

Connector dx1

Connector dx2

Gap frac

FST color

Width (in)

Height (in)

DPI

Format

Plot

Plot genomic FST with annotations

1. App Name:
plot_snp_anno

2. Function Description

Plot genomic FST with Top-N gene annotations.

3. Demo Output

Example Datasets

Parameters

Download Version, Parameter, MD5

DMR table

Browse...

Violin scale

Violin border

Point shape

Point size

Jitter width

Hyper color

Hypo color

Width (in)

Height (in)

DPI

Format

Plot

Plot DMRs hyper/hypo distributions

1. App Name:
plot_dmg_chrom

2. Function Description

Plot differentially methylated regions (DMRs) hyper/hypo distributions by chromosome.

3. Demo Output

Example Datasets

Parameters

Download Version, Parameter, MD5

DMR table

Browse...

Orientation

Chrom alpha

Bar height

Chrom color

Point size

Point alpha

Hyper color

Hypo color

Mark style

Line width

Line height

Width (in)

Height (in)

DPI

Format

Plot

Plot DMGs hyper/hypo along chromosomes

1. App Name:
plot_dmg_exp

2. Function Description

Plot DMGs hyper/hypo along chromosomes.

3. Demo Output

Example Datasets

Parameters

Download Version, Parameter, MD5

GFF/GTF file

Browse...

Format

Bar width

Bar color

Label size

Width (in)

Height (in)

DPI

Format

Plot

Plot gene stats

1. App Name:
plot_gene_stats

2. Function Description

Plot gene stats for chromosomes.

3. Demo Output

Example Datasets

Parameters

Download Version, Parameter, MD5

FST table

Browse...

LOG10

Bin size

Density color 1

Density color 2

Density color 3

Width (in)

Height (in)

DPI

Format

Plot

Plot SNP density

1. App Name:
plot_snp_density

2. Function Description

Plot SNP density at chromosome level.

3. Demo Output

Example Datasets

Parameters

Download Version, Parameter, MD5

GFF/GTF file

Browse...

Format

Genomic ranges (FST/DMR)

Browse...

Chrom column

Start column

End column

Promoter upstream

Promoter downstream

Ignore strand

Features

Data

Annotate FST/DMR

1. App Name:
anno_fst_dmr

2. Function Description

Annotate FST/DMR windows with genomic features.

3. Demo Output

Example Datasets

Parameters

Download Version, Parameter, MD5

Parameters

Download Version, Parameter, MD5

GFF/GTF file

Browse...

Format

Info

Data

Extract 3'UTR ranges

1. App Name:
extract_utr3

2. Function Description

Extract 3'UTR ranges from GFF or GTF.

3. Demo Output