Pages tagged "schemas"

Services: Schemas

Examples

2020-10-20: more ...

Publication DB Criteria

Progenetix publication collection: Which scientific publications are included?

The Progenetix Publication DB contains articles describing whole genome screening (WGS, WES, aCGH, cCGH1) experiments in cancer. Genomic information about the analyzed cancer samples is extracted from these publications to generate cancer mutation data, with a focus on copy number abnormalities (CNV / CNA).

  1. Whole-genome screening techniques: 

2021-06-17: more ...

Progenetix Image Formats

The standard format for (plot-)images generated on Progenetix is Scalable Vector Graphics (SVG). As the name implies, SVG is scalable, i.e. images can be scaled up without loosing quality or expanding in storage size. However, some of teh generated images use also embedded rastered components which will deteriorate during scaling - this is e.g. the case for array probe plots.

According to Wikipedia

All major modern web browsers—including Mozilla Firefox, Internet Explorer, Google Chrome, Opera, Safari, and Microsoft Edge—have SVG rendering support

On most pages where plots are being displayed there is a download option for the images - (please alert us where those are missing). Browsers also have the option to export SVGs themselves e.g. as PDF.

@mbaudis 2021-02-12: more ...

Progenetix File Formats

Contents


Progenetix Segment Files .pgxseg

Progenetix uses a variation of a standard tab-separated columnar text file such as produced by array or sequencing CNV software, with an optional metadata header for e.g. plot or grouping instructions.

Wile the first edition only was geared towards sample-linked segment annotations, a variation is now being provided for CNV frequencies.

@mbaudis 2021-04-16: more ...