ssNPA 1.0 – subtyping samples based on Deregulation of their Gene Networks

ssNPA 1.0

:: DESCRIPTION

ssNPA is a new approach for subtyping samples based on deregulation of their gene networks.

:: DEVELOPER

Benos Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

ssNPA

:: MORE INFORMATION

Citation:

Bioinformatics 2019 Dec 24[Online ahead of print]
Causal Network Perturbations for Instance-Specific Analysis of Single Cell and Disease Samples
Kristina L Buschur , Maria Chikina , Panayiotis V Benos

DANCE 0.99.0 – Deregulation of Copy-number and Expression

DANCE 0.99.0

:: DESCRIPTION

DANCE quantifies the impact of copy-number alterations on gene expression and compares it between tumour sub-types.

::DEVELOPER

the Markowetz lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • R

:: DOWNLOAD

 DANCE

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Oct 1;27(19):2679-85. doi: 10.1093/bioinformatics/btr450. Epub 2011 Jul 30.
Penalized regression elucidates aberration hotspots mediating subtype-specific transcriptional responses in breast cancer.
Yuan Y1, Rueda OM, Curtis C, Markowetz F.

JODA 1.33.0 – Quantifying Gene Deregulation using Knowledge

JODA 1.33.0

:: DESCRIPTION

JODA (Joint deregulation analysis) proves advantageous over separate analysis of the cell populations and analysis without incorporation of knowledge.

:: DEVELOPER

JODA team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 JODA

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2011 Jun 21;12:249. doi: 10.1186/1471-2105-12-249.
Deregulation upon DNA damage revealed by joint analysis of context-specific perturbation data.
Szczurek E1, Markowetz F, Gat-Viks I, Biecek P, Tiuryn J, Vingron M.