README.md

Oviz-Bio-demo

Documents of Oviz-Bio, a Platform for Bioinformatics Visualization

Intergrated

LandScape

The 'LandScape' visualization is frequently utilized to provide a systematic illustration of integrative data from multiple layers of batch samples, which are always compared to each other on certain attributes, such as genes and biological pathways mutated in cancers. To visualize data, a CSV file in the required format is needed.

demo_csv

Several demo CSV files are provided.

• landscape_demo.csv is the official demo CSV file.
• PMIDxxx.Figx.landscape.csv files to present LandScape instances in published papers (see Reference).

markdown

Markdown files of LandScape analysis page on Oviz-Bio Platform.

• Manual
• References
• About

Circos

Small Mutation

Mut: On Genes

SNV: Context

The 'Context' visualization, otherwise known as the 'Lego plot' of mutational frequencies, describes the distribution of mutations across batch samples on a given region. To visualize data, To visualize data, a BGZ file in the required format is needed.

demo_data

Several demo TSV files are provided.

• SNV_Context_demo_MutList.tsv.bgz is the official demo BGZ file for the visualization.
• SNV_Context_demo_Region-1.bed and SNV_Context_demo_Region-2.bed are the official demo TSV file for the optional custom region data.

markdown

Markdown files of Context analysis page on Oviz-Bio Platform.

• Manual
• References
• About

SNV: Signature

The 'Signature' visualization is wildly used in mutational signature analysis. It shows the signature profile with the conventional 96 mutation type classification. We also compare each signature with all recorded signature references in the COSMIC database by the cosine similarity test. The top three similar signature references are listed with their percentage of similarity. To visualize data, a CSV file in the required format is needed.

demo_data

Check the official demo input here.

markdown

Markdown files of Signature analysis page on Oviz-Bio Platform.

• Manual
• References
• About

SNV: Signature Dist

The 'Signature Dist' visualization shows the fraction of signatures within individual samples. It can also be used to show the fraction of signatures within several cancer types. To visualize data, a CSV file in the required format is needed.

demo_data

Check the official demo input here.

markdown

Markdown files of Signature Dist analysis page on Oviz-Bio Platform.

• Manual
• References
• About

Copy Number Variation

CNV: Single Sample

The 'Single Sample' visualization is an interactive version of the output plot from 'Patchwork', a bioinformatics tool for analyzing allele-specific copy numbers and loss-of-heterozygosity in cancer genomes. This visualization summarizes all 24 chromosomal plots generated by 'Patchwork' and provides user with the choice to highlight information of one particular chromosome. To visualize data, a CSV file in the required format is needed.

demo_data

Check the official demo input here. User can directly use the output from the 'Patchwork' tool as our input file.

markdown

Markdown files of Single Sample analysis page on Oviz-Bio Platform.

• Manual
• References
• About

CNV: Group Samples

The 'Group Sample' visualization is an interactive and extended version of the output plot from 'GISTIC', a bioinformatics tool for identifying regions of the genome that are significantly amplified or deleted across a set of samples. To visualize data, three TSV files in the required format are needed.

demo_data

Several demo TSV files are provided.

• scores: Group_Sample_scores.tsv. User can directly use the score output from the 'GISTIC' tool as our input file.
• amp_genes.conf_90: Group_Sample_amp_genes.conf_90.tsv. User can directly use the amp_genes.conf_90 output from the 'GISTIC' tool as our input file.
• del_genes.conf_90: Group_Sample_del_genes.conf_90.tsv. User can directly use the del_genes.conf_90 output from the 'GISTIC' tool as our input file.

markdown

Markdown files of Group Samples analysis page on Oviz-Bio Platform.

• Manual
• References
• About

Structure Variation

SV:Heatmap

Linkage heatmap is an useful method to visualize read linkage patterns on SV event, especially in studies with long-range sequencing data, such as 10x linked-reads. We apply the "SV: Heatmap" visualization to display the heatmap matrix based on sequencing reads linkage between two local windowlized regions of SV case. The color depth of each cross-linked window pair is proportional to the number of linkages. Along the chromosome coordinate axis of the heatmap matrix, annotation information is added, such as Ensembl genes. To visualize data, upload a TXT file in the required format, and then use sidebar options to adjust heatmap color scheme and choose other SVs to display if uploaded data contains multiple cases.

demo_data

Two demo TXT files are provided.

• 10x.txt stores the shared 10x barcodes linkage matrix.
• pair_end.txt stores the shared pair end reads linkage matrix.

markdown

Markdown files of SV:Heatmap analysis page on Oviz-Bio Platform.

• Manual
• References
• About

SV:Reads Support

The "SV:Reads Support" visualization is frequently utilized to provide the detail illustration of supporting split reads for given SV events. To visualize data, a TXT file in the required format is needed.

demo_data

Two demo TXT files are provided, simu.junc.reads.txt and junc.reads.txt store information of supporting split reads for given SV events.

markdown

Markdown files of SV:Reads Support analysis page on Oviz-Bio Platform.

• Manual
• References
• About

Gene Fusion

Onco Virus