Welcome

Welcome to Lipid Reporter

Lipid Reporter modifies csv files with a range of user defined filters.

The filters describe rules that relate to the columns.

The output of a filter can be either additional columns that contain new infomation or the deletion of a row.

The output of the application is a new csv file with extra information and/or some rows removed.

With this scheme you can create markers that you can use to filter the whole data set in the application you use to visualise the data.

It is intended to be used to process Nonlinear Dynamics' Progenesis QI identification exports. These have a specific csv format.
However, it can also be used in a more general sense of processing any csv file where you know a relationship between an entry in a column and some sort of validation rule.

Using Lipid Reporter

You have to choose what you expect to read in and what you want to write out. That bit is up to you.

With a csv file happily loaded the filters that appear in the UI are applied to each of the rows. The filters that are supplied each have a different function. You combine them as you want.
Some add new columns based on the row content, some delete rows if cells don't match specific criteria.

There are some filters supplied, but you can write your own, although you have to create a .Net class library so make sure you have some idea what you are doing before you start.

This is a link to the Updates page [Updates/]https://sourceforge.net/p/lipid-reporter/wiki/Updates/)

Input Data

Lipid Reporter reads text files, typically csv files.
Files must have a header row that describes the columns. All the filters use the header row to navigate through the data.
The data is expected to line up with the headers. If it doesn't you get unpredictable results.
Read more about what data you can bring in and what format it must have here [Input Data]

Output Data

Lipid Reporter creates a new file that is the result of the processing filters.
It saves it in the same place as the input and adds a user defined prefix and suffix so you can tell which one is which.
Read more about the output files here [Output Data]

Filters

The filters that are supplied with the installation all contain rules that are relevent to Lipids. If you study or work with Lipids then these will mean something to you.
You can write your own, but a note of caution that this is a programatic exercise not a scripting exercise.
Writing your own means that this application can be used as a general purpose tool rather than a lipid specfic tool.

You can read more about filters here [Filters]. Meanwhile here is a brief example of one of the installed filters.

If your input data has a column that contains the LipidMaps ID then the filter "Add Class Descriptions" will add 4 new columns to the data for LM Category, LM Class,LM Subclass and LM Level4. Let's say that the input colum contained "TG(16:0/16:0/18:1(11E))" then the output (the processed file) would contain this in the 4 new columns "Glycerolipids[GL], Triradylglycerols[GL03], Triacylglycerols[GL0301], {blank}"
From here you could read the output in another application and directly filter for those containing "Triradylglycerols"