Software

1. Color Selection Tools for Quantifying Histological Data

Description

Current methods for selecting target color of interest often utilize thresholds in the RGB color space. However, this can be imprecise and prone to wide variation. We have found that color separation using the HSV color space is highly consistent with visual recognition of color and much more reliable that the conventional RGB color selection method. We have published the results (*1) and have provided the software tools we reference.

*1. A Hue Saturation Value Method for Quantifying Histological Data.
Katsumi Yabusaki, Tyler Faits, Eri McMullen, Jose-Luiz Figueiredo, Masanori Aikawa and Elena Aikawa., Plos One (2014).

Software tools are available online.

2. mIMT-visHTS

Description

mIMT-visHTS is a software for multiplexing time-resolved protein abundance profiles, typically collected by, but not limited to, isobaric mass tagging methods. Please contact sasingh@partners.org if you have any comments or questions.

The downloadable package includes:

  1. A brief tutorial (PDF)
  2. The application file (RebuildSuperDataSet)
  3. Three .dll files to run the application file
  4. 3 TMT-6plex sample datasets (all proteins quantified with 2 or more unique peptides)
  5. The mIMT.r for standalone clustering
  6. The mIMT-visHTS_packages.r script

3. XPI (The extracted PRM peak intensity)

Description

The XPI program was developed to quantify parallel reaction monitoring (PRM) data of stable isotope labeled peptides. As a result, this software is currently optimized for Thermo instrument .RAW file data. The XPI program extracts the centroided peak intensity of each PRM target ion scan.

The downloadable package includes:

  1. Manual_v1.0.pdf: The user guide for XPI
  2. Testset: it has mzML files, an inclusion list and configuration files for an user’s quick test.(for Mac or for Windows)
  3. XPILib.pyc: XPI library compiled code (for Mac or for Windows)
  4. XPIPeak.py: XPI peak detection script (for Mac or for Windows)
  5. XPIQuant.py: XPI quantification script (for Mac or for Windows)
  6. XPIViz.py: XPI visualization script (for Mac or for Windows)

Download full package for Mac or for Windows.