Comb-p 0.43 – Combining, Analyzing, Grouping and Correcting Spatially Correlated P-values

Comb-p 0.43

:: DESCRIPTION

comb-p is a command-line tool and a python library that manipulates BED files of possibly irregularly spaced P-values and (1) calculates auto-correlation, (2) combines adjacent P-values, (3) performs false discovery adjustment, (4) finds regions of enrichment (i.e. series of adjacent low P-values) and (5) assigns significance to those regions.

::DEVELOPER

Katerina Kechris , Brent Pedersen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • Python

:: DOWNLOAD

 Comb-p

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Nov 15;28(22):2986-8. doi: 10.1093/bioinformatics/bts545. Epub 2012 Sep 5.
Comb-p: software for combining, analyzing, grouping and correcting spatially correlated P-values.
Pedersen BS1, Schwartz DA, Yang IV, Kechris KJ.

SCG 20110716 – Self Consistency Grouping

SCG 20110716

:: DESCRIPTION

SCG clusters whose members are closer in rank to each other than to any member outside the cluster. SCG does not take any additional parameters and consequently does not impose any restriction on the size or the number of the clusters that it finds, since the natural boundaries of clusters are determined by the inconsistencies in the ranks.

::DEVELOPER

Grishin Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 SCG 

:: MORE INFORMATION

Citation:

Bong-Hyun Kim, Bhadrachalam Chitturi and Nick V Grishin.
Self consistency grouping: a stringent clustering method
BMC Bioinformatics 2012, 13(Suppl 13):S3.

GRUNT – Grouping Ungrouping Naming Tool

GRUNT

:: DESCRIPTION

 GRUNTwill facilitate researchers requiring comprehensive hierarchical grouping of large tree topologies in, for example, database curation, microarray design and pangenome assignments.

::DEVELOPER

Daniel Dalevi (daniel.dalevi@gmail.com)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 GRUNT

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2007 Oct 18;8:402.
Automated group assignment in large phylogenetic trees using GRUNT: GRouping, Ungrouping, Naming Tool.
Dalevi D, Desantis TZ, Fredslund J, Andersen GL, Markowitz VM, Hugenholtz P.