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PMM specifications

Information


Unique identifier OMICS_15997
Name PMM
Alternative name Parallel Mixed Model
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.12.0
Stability Stable
Requirements
splines, R(>=2.10), lme4
Maintained Yes

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Documentation


Maintainer


  • person_outline Anna Drewek

PMM citations

 (4)
library_books

Simultaneous analysis of large scale RNAi screens for pathogen entry

2014
BMC Genomics
PMCID: 4326433
PMID: 25534632
DOI: 10.1186/1471-2164-15-1162

[…] athogen screens. In addition to obtain a list of hits for individual pathogens, our aim was to discover shared mechanisms between pathogens. To this purpose, we propose a new statistical method – the Parallel Mixed Model (PMM). Our approach simultaneously takes into account the knock-down effects of several non-identical screens performed in parallel with the same RNAi libraries. Additionally, the […]

library_books

Association between Inflammatory Infiltrates and Isolated Monosomy 22/del(22q) in Meningiomas

2013
PLoS One
PMCID: 3788099
PMID: 24098347
DOI: 10.1371/journal.pone.0074798

[…] LN, HLA-DMA, HOXC4, ITGAM, LTBP2, MYO1F, PIK3CD, PLCB1 and TLR2 genes (). Conversely, diploid tumors were mainly characterized by overexpression of a group of genes, (e.g. ABCB1, ADSL, CHKB, PACSIN2, PMM1 and TCN2 genes) which are mainly involved in small molecule metabolism and cellular biochemistry, including also the NF2 gene. Finally, tumors with complex karyotypes were characterized by a grea […]

library_books

Systems infection biology: a compartmentalized immune network of pig spleen challenged with Haemophilus parasuis

2013
BMC Genomics
PMCID: 3610166
PMID: 23339624
DOI: 10.1186/1471-2164-14-46

[…] covariate classifier or genomic signature that could distinguish the samples. In the first 20 genes with the largest positive loadings on the second axis (see Additional file : Table S2), except for PMM2, all members were also identified to be differentially expressed (see Figure B and C and section 2 of the Results and Discussion). This result indicates that the PCA analysis might provide an alt […]

library_books

Computational prediction of Pho regulons in cyanobacteria

2007
BMC Genomics
PMCID: 1906773
PMID: 17559671
DOI: 10.1186/1471-2164-8-156

[…] ators. Alternatively, these genes could be regulated by SphR through different binding motifs. In addition, it has been shown that the expression of the urtA gene in PCC6803 (slr0447) [] and in MED4 (PMM0970) [] is strongly repressed during phosphorus starvation. However, no sphR binding site has been experimentally identified in PCC6803 [] or by our computational study. Thus the inhibition of urt […]

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