ProbCD statistics

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Popular tool citations

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Associated diseases

Associated diseases

ProbCD specifications

Information


Unique identifier OMICS_18769
Name ProbCD
Alternative name Probabilistic Categorical Data analysis
Interface Web user interface
Restrictions to use None
Input data A microarray data.
Input format TSV
Programming languages R
Computer skills Basic
Stability Stable
Source code URL http://xerad.systemsbiology.net/ProbCD/ProbCD.zip
Maintained Yes

Maintainers


  • person_outline Ilya Shmulevich <>
  • person_outline Ricardo Vencio <>

Information


Unique identifier OMICS_18769
Name ProbCD
Alternative name Probabilistic Categorical Data analysis
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainers


  • person_outline Ilya Shmulevich <>
  • person_outline Ricardo Vencio <>

Publication for Probabilistic Categorical Data analysis

ProbCD in publications

 (5)
PMCID: 4413041
PMID: 25961029
DOI: 10.1155/2015/610595

[…] and weak coexpression classes, called the disease-specific cutoff point (c). the cutoff point represented a coexpression level, at which f d and f n were extremely deviated: (2)d=max⁡cfdc−fnc,fdc=probcd≥c,fnc=probcn≥c, where f d and f n refer to the cumulative distribution functions of c d and c n, respectively; d represents the maximum deviation; c is the cutoff point., the specifically […]

PMCID: 4363532
PMID: 25821802
DOI: 10.1155/2015/459840

[…] was identified, the gene pairs can be bisected into two coexpression classes. chi-square test was also used to verify the association between the coexpression class and the disease. consider (3)fdc=probcd≥c,fnc=probcn≥c. , for clearer illustration of gene network, the identified gene pairs were classified into common, normal-specific, and disease-specific connections. the common connections […]

PMCID: 4058919
PMID: 24574114
DOI: 10.1093/bioinformatics/btu110

[…] in this scenario include the ability to use optimization proportions, rather than filtered annotations based on a threshold, directly with enrichment methods that support annotation weights [e.g. probcd ()], and flexibility regarding the algorithm used to cluster genes., using emvc to refine gene set collections. the emvc method can also be used for the general refinement of gene set […]

PMCID: 3644270
PMID: 23627640
DOI: 10.1186/1471-2105-14-143

[…] and permutation test to identify significantly enriched gene sets []. in addition, other statistical methods including significance analysis of function and expression (safe) [], baygo [], probcd [], easygo [], profcom [], globalancova [], goeast [] and lrpath [] were also developed for enrichment analysis., based on the methods mentioned above, researchers can subsequently reveal […]

PMCID: 3329418
PMID: 22300537
DOI: 10.1186/1471-2105-13-23

[…] quantitative instance scores to compute class enrichment values using an analytical approximation of the statistical distribution and is asymptotically equivalent to the lrpath technique; and probcd [], which supports probabilistic instance and annotation weights and computes statistical significance using goodman-kruskal gamma and comparison against a null distribution estimated via […]


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ProbCD institution(s)
Institute for Systems Biology, Seattle, WA, USA
ProbCD funding source(s)
Supported by NIH grants U54-AI54253, U19- AI057266 and P50-GMO-76547.

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