Timeline for How can I read FCS files using open source libraries?
Current License: CC BY-SA 3.0
15 events
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| Feb 3, 2019 at 2:49 | answer | added | Fiver | timeline score: 4 | |
| Jul 4, 2017 at 16:11 | comment | added | Peter | Why do you say .fcs is a patented format? The disclaimer in the linked documentation just states "Attention is called to the possibility that implementation of this standard may require use of subject matter covered by patent rights". It may not even be possible to patent it, see: patents.stackexchange.com/questions/11968/… | |
| Jul 2, 2017 at 11:20 | comment | added | WYSIWYG | @KonradRudolph What I want is an instruction on how these files are to be read. The documentation describes the format but I could not figure out the general procedure to read the format which is what I meant by pseudocode. Just assume that I do not want to use bioconductor; lets say that I want to read these files in C. How should I go about that? Do the FACS machines use a standard mechanism/io library for reading/writing FCS files or they use their own codes? I assumed that if a format is defined by a consortium, they would have provided a standard interface for rw operation. | |
| Jul 1, 2017 at 13:54 | comment | added | llrs | @WYSIWYG In addition to what Konrad said, the flowCore in Bioconductor is available for Windows, iOS and Linux. | |
| Jul 1, 2017 at 12:13 | comment | added | Konrad Rudolph | I’m still not really sure what you want: the documentation you link to is as close to a general pseudocode as you will get: it contains a detailed, concise specification of the format. That’s the same information that a pseudocode would convey, and it’s the conventional way in which data formats are described (pseudocode is virtually never used for this). That, in addition to the existence of libraries for common analysis languages (R, Python, Matlab), should be sufficient to work with the format. | |
| Jul 1, 2017 at 6:28 | comment | added | WYSIWYG | @Llopis By standard, I mean is there an OS/language independent interface that allows reading of these files. More importantly, I want to know how FCS files can be read by any general language. I am expecting something like a pseudocode, for this purpose. | |
| Jun 30, 2017 at 14:32 | comment | added | llrs | @terdon I am not sure how standard libraries are decided but a R/Bioconductor package or a MATLAB one seems to me quite standard (Except if the FCS consortium provides one of course). | |
| Jun 30, 2017 at 14:28 | comment | added | terdon♦ | @Llopis the OP isn't rejecting standard tools, on the contrary, he is looking for standard libraries. | |
| Jun 30, 2017 at 14:19 | comment | added | llrs | I find strange you ask for standard libraries but you exclude the existing standard tools. | |
| Jun 30, 2017 at 12:51 | answer | added | bli | timeline score: 5 | |
| Jun 30, 2017 at 11:56 | answer | added | gringer♦ | timeline score: 3 | |
| Jun 30, 2017 at 10:41 | history | edited | WYSIWYG | CC BY-SA 3.0 |
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| Jun 30, 2017 at 10:40 | history | edited | terdon♦ | CC BY-SA 3.0 |
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| Jun 30, 2017 at 10:38 | review | First posts | |||
| Jul 2, 2017 at 6:54 | |||||
| Jun 30, 2017 at 10:37 | history | asked | WYSIWYG | CC BY-SA 3.0 |