smoothseg 0.0.4 – Robust smooth segmentation approach for array CGH data analysis

smoothseg 0.0.4

:: DESCRIPTION

smoothseg is an R package to compute smooth-segmentation of array CGH data, including the estimation of FDR for comparative studies.

::DEVELOPER

Huang Jian <j.huang@ucc.ie>, Prof. Yudi Pawitan ,Arief Gusnanto <Arief.Gusnanto@mrc-bsu.cam.ac.uk>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux /MacOsX
R package

:: DOWNLOAD

smoothseg

:: MORE INFORMATION

Citation

Bioinformatics. 2007 Sep 15;23(18):2463-9. Epub 2007 Jul 27.
Robust smooth segmentation approach for array CGH data analysis.
Huang J1, Gusnanto A, O’Sullivan K, Staaf J, Borg A, Pawitan Y.

MPSS 1.2 – Multi-platform Segmentation

MPSS 1.2

:: DESCRIPTION

MPSS is a method based on a correlated random-effect model for the unobserved patterns and extend the robust smooth segmentation approach to the multiple-platform scenario.

::DEVELOPER

Prof. Yudi Pawitan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux /MacOsX
R package

:: DOWNLOAD

MPSS

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jun 1;27(11):1555-61. doi: 10.1093/bioinformatics/btr162. Epub 2011 Apr 5.
Multi-platform segmentation for joint detection of copy number variants.
Teo SM1, Pawitan Y, Kumar V, Thalamuthu A, Seielstad M, Chia KS, Salim A.

CONSERTING – Copy Number Segmentation by Regression Tree in Next Generation Sequencing

CONSERTING

:: DESCRIPTION

CONSERTING (Copy Number Segmentation by Regression Tree in Next Generation Sequencing) is an accurate method for detecting somatic DNA copy number variation in whole genome sequencing data.

::DEVELOPER

Zhang (Jinghui Zhang) Lab,St. Jude Children’s Research Hospital

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX
R package

:: DOWNLOAD

CONSERTING

:: MORE INFORMATION

sephaCe v3 – Segmentation of Adherent Biological Cell Boundaries

sephaCe v3

:: DESCRIPTION

sephaCe ( stands for “see phase of cells”,) is an open-source tool for automatic segmentation of adherent biological cell boundaries from brightfield microscopy images.

::DEVELOPER

Rehan Ali

:: SCREENSHOTS

:: REQUIREMENTS

Windows / MacOSX /Linux
Matlab

:: DOWNLOAD

sephaCe

:: MORE INFORMATION

snapCGH 1.62.0- Segmentation, Normalisation And Processing of Array CGH data

snapCGH 1.62.0

:: DESCRIPTION

snapCGH is a softwaer for the analysis of array CGH data. It has been written to be compatible with limma so that the user can apply all of the preprocessing functions available within limma to array CGH data.

::DEVELOPER

snapCGH team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOsX
R package
Bioconductor

:: DOWNLOAD

snapCGH

:: MORE INFORMATION

MCF – Image Segmentation Algorithms for automated Single Cell Analysis

MCF

:: DESCRIPTION

The MCF (Model Controlled Flooding) image segmentation algorithms and example code for automated single cell analysis.

::DEVELOPER

Mike West

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux/MacOsX
Matlab

:: DOWNLOAD

MCF

:: MORE INFORMATION

Citation

Model-controlled flooding with applications to image reconstruction and segmentation.
Wang Q, West M.
J Electron Imaging. 2012 Jun 22;21(2). doi:pii: 023020.

CellX 2.12 – MATLAB Image Segmentation Package

CellX 2.12

:: DESCRIPTION

CellX is a tool for segmentation, fluorescence quantification, and tracking of cells on microscopy images.

::DEVELOPER

CSB – Computational Systems Biology Group

:: SCREENSHOTS

N/A

::REQUIREMENTS

Windows/Linux/MacOsX
MatLab

:: DOWNLOAD

CellX

:: MORE INFORMATION

Citation

Using CellX to quantify intracellular events.
Mayer C, Dimopoulos S, Rudolf F, Stelling J.
Curr Protoc Mol Biol. 2013;Chapter 14:Unit 14.22.. doi: 10.1002/0471142727.mb1422s101.

Bioinformatics. 2014 Sep 15;30(18):2644-51. doi: 10.1093/bioinformatics/btu302. Epub 2014 May 21.
Accurate cell segmentation in microscopy images using membrane patterns.
Dimopoulos S, Mayer CE, Rudolf F, Stelling J.

copynumber 1.32.0 – Segmentation of Single- and multi-track Copy Number data by penalized least Squares Regression

copynumber 1.32.0

:: DESCRIPTION
The R package copynumber is a software suite for segmentation of single- and multi-track copy number data using algorithms based on coherent least squares principles.

::DEVELOPER

Research Group for Biomedical Informatics (BMI)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows
R / BioCOnductor

:: DOWNLOAD

copynumber

:: MORE INFORMATION

Citation:

BMC Genomics. 2012 Nov 4;13:591. doi: 10.1186/1471-2164-13-591.
Copynumber: Efficient algorithms for single- and multi-track copy number segmentation.
Nilsen G1, Liestøl K, Van Loo P, Moen Vollan HK, Eide MB, Rueda OM, Chin SF, Russell R, Baumbusch LO, Caldas C, Børresen-Dale AL, Lingjaerde OC.

LEVER – Stem Cell Segmentation, Tracking and Lineaging

LEVER

:: DESCRIPTION

LEVER (Lineage Editing and Validation) is a collection of software tools for analyzing the development of proliferating (dividing) cells in time-lapse microscopy image sequences. LEVER includes algorithms for segmentation, tracking and lineaging. LEVER also includes a user interface that allows the segmentation, tracking and lineaging results to be validated, with any errors in the automated processing easily identified and quickly corrected

CloneView is an incredibly useful tool for visualizing the results from the LEVER program together with the image data.

::DEVELOPER

computational image sequence analysis

:: SCREENSHOTS

:: REQUIREMENTS

Windows
MatLab

:: DOWNLOAD

LEVER

:: MORE INFORMATION

Citation

LEVER: software tools for segmentation, tracking and lineaging of proliferating cells.
Winter M, Mankowski W, Wait E, Temple S, Cohen AR.
Bioinformatics. 2016 Jul 16. pii: btw406.

DP2 – Distributed 3D Image Segmentation using Micro-labor workforce

DP2

:: DESCRIPTION

DP2 (Dual Point Decision Process) is a software for segmentation of 3D structures contained in 3D microscopy.

::DEVELOPER

Rick Giuly

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

:: MORE INFORMATION

Citation

Bioinformatics. 2013 May 15;29(10):1359-60. doi: 10.1093/bioinformatics/btt154. Epub 2013 Apr 10.
DP2: Distributed 3D image segmentation using micro-labor workforce.
Giuly RJ1, Kim KY, Ellisman MH.