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Algorithms for the selection of fluorescent reporters.

Home Page: http://fpselection.org/

License: BSD 3-Clause "New" or "Revised" License

Java 87.98% HTML 9.02% JavaScript 0.98% CSS 0.86% PHP 0.08% Dockerfile 0.07% Dockerfile 0.16% R 0.85%
fluorescence cytometry workflow scientific-computing scientific-workflows webapp selection-algorithms

fpselection's Introduction

FPselection

Install and Run FPselection

Instructions to install FPselection can be found in INSTALL.md.

Case Studies

The Case Study folder contains the files required to recreate the case studies of the FPselection manuscript. To learn more about the input files, please refer to the README file.

The Flow Cytometry Standard (fcs) data files containing measurements from the 3 cytometers can be found in the following folders:

Compensation matrix creation

We have also included our scripts to help create compensation matrices from raw cytometry data using R Bioconductor packages. The scripts and the README can be found in this folder.

Contributing to this project

Anyone and everyone is welcome to contribute. Please take a moment to review the guidelines for contributing.

Contact Us

If you would like to receive updates from the FPselection team regarding bug fixes, patches, feature updates or if you would like to contact the FPselection team, please check the links in CONTACT.md

fpselection's People

Contributors

alexvahid avatar dependabot[bot] avatar djtran avatar eappleton avatar prashantvaidyanathan avatar

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fpselection's Issues

Update DataAnalytics for Bleed-through

To more accurately portray bleedthrough information I updated the method in ProteinSelector that generates the noise treemap. I noticed there was a lot of references to a noiseKey in DataAnalytics, so you should double check those calculations if you need to.

Bleedthrough for a given FP & Detector is now represented as the sum of expressions of all other FPs using the given FP's selected laser. (Before it was of all FPs intended to be used with other lasers, not all other FPs)

Algorithms

Remove all options for algorithms and make the default algorithm: Simulated Annealing.

Settings/Inputs

Have the following input fields:

Cytometer Settings - Required

Fluorophore Spectra List - Required

Brightness - Required

Autofluoresence - Optional

N - Required

Plots Info

Plots Info should have the following format:
FP ; Laser ; Filter ; Signal ; Bleedthrough

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