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MMDiff specifications

Information


Unique identifier OMICS_00474
Name MMDiff
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 1.8.0
Stability Stable
Requirements
parallel, Biobase, IRanges, GenomicRanges, Rsamtools, R(>=2.14.0), DiffBind, GMD, MMDiffBamSubset
Maintained Yes

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Maintainers


  • person_outline Guido Sanguinetti <>
  • person_outline Gabriele Schweikert <>

Publication for MMDiff

MMDiff in publications

 (12)
PMCID: 5891941
PMID: 29636086
DOI: 10.1186/s13059-018-1422-4

[…] samples clearly clustered by the histone mark, but they did not further cluster by treatment (fig. ), suggesting dex treatment does not have a general affect on histone methylation., we used mmdiff to identify specific loci with where dex treatment altered the histone methylation profile using all peaks called in at least two samples. mmdiff inspects the difference between chip-seq […]

PMCID: 5554779
PMID: 28768205
DOI: 10.1016/j.celrep.2017.07.025

[…] which considers transcripts as whole units, to facilitate the integration with the proteomic dataset. we first estimated transcript expression levels with mmseq () and then used its companion tool mmdiff () to identify both differentially expressed genes and differentially used transcripts. genes with differential transcript usage (dtu) are defined as cases where there is a change […]

PMCID: 5511350
PMID: 28703137
DOI: 10.1038/ncomms16058

[…] --strata -s -m 100 -x 500 --chunkmbs 256 --nofw -fr’. mmseq 1.0.8a (refs , ), and was used with default parameters to quantify gene expression. genes with posterior probability>0.5 (calculated by mmdiff), absolute fold change >2 and fragments per kilobase of transcript per million mapped reads (fpkm) >1 in at least one of the two cell types were considered differentially expressed., […]

PMCID: 5146288
PMID: 27910854
DOI: 10.1038/ncomms13652

[…] pman_1.0 reference (gca_000500345.1). we estimated expression using star alignments in transcriptomic coordinates and the mmseq package v1.0.8, and calculated differential expression using mmdiff., to validate the prkar1a mrna estimates from rnaseq, we conducted quantitative pcr on testis of p. maniculatus and p. polionotus. first, we extracted mrna from whole testis using an rneasy […]

PMCID: 5927328
PMID: 27863248
DOI: 10.1016/j.cell.2016.09.034

[…] levels, rna-seq reads were aligned to the ensembl v68 human transcriptome using bowtie. quantification of gene expression was performed using mmseq. differential expression was determined using mmdiff. a two model comparison was used to identify differentially expressed genes that confer cellular identity mo/mf. the null-model is that the mean expression levels are the same in both cell […]


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MMDiff institution(s)
School of Informatics, University of Edinburgh, Edinburgh, UK; Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
MMDiff funding source(s)
Supported by the Wellcome Trust, from the University of Edinburgh through its iDEA lab program and from the EU FP7 Marie Curie Actions, European Research Council through grant MLCS306999 and BBSRC under the Sysmo SUMO2 project.

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