diffReps protocols

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diffReps specifications

Information


Unique identifier OMICS_00472
Name diffReps
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Programming languages Perl
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.55.6
Stability Stable
Requirements
CPAN modules: Statistics::TTest, Math::CDF, Parallel::ForkManager
Maintained Yes

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Documentation


Maintainer


  • person_outline Li Shen <>

Additional information


https://github.com/shenlab-sinai/diffreps/wiki

Publication for diffReps

diffReps in pipelines

 (11)
2018
PMCID: 5763571
PMID: 29321036
DOI: 10.1186/s12989-017-0239-8

[…] through trimmomatic [] (fig. ). reads were then mapped to the rat genome (rn6) using the default parameters in bowtie2. to perform differential binding analysis on reads while distinguishing peaks, diffreps was used []. bedtools functions were used to delineate upstream promoter regions of genes (bedtools slop) and evaluate the promoter/gene overlay (bedtools intersect). genes were defined […]

2018
PMCID: 5906078
PMID: 29675472
DOI: 10.1126/sciadv.aar8187

[…] for go term enrichment analysis using david with default settings ()., genome-wide regions that were differentially marked by histone modifications were identified and annotated to refseq genes by diffreps () with default settings., enhancers were defined as h3k4me3low + h3k27achigh and predicted using csi-ann () with normalized h3k4me3 and h3k27ac signals as inputs. the predicted enhancers […]

2017
PMCID: 5501531
PMID: 28683804
DOI: 10.1186/s13059-017-1261-8

[…] cascades and responses to hormone stimuli, both in control conditions and after flg22 treatment (additional file : figure s24f)., we next compared the two chip-seq datasets using seqminer and diffreps, which allows qualitative and quantitative comparisons to be made between a reference set of genomic positions and multiple chip-seq datasets []. using this approach, we observed three […]

2017
PMCID: 5506428
PMID: 28597562
DOI: 10.1111/acel.12621

[…] were downloaded from ensembl 74 to determine gene ensembl identifiers, symbols, gene start, gene end strand, and gene biotype. analysis was limited to genes on standard chromosomes (1‐23,x,y)., diffreps (shen et al., ) was used to identify genomic regions differentially enriched for h3k27me3 and h3k4me3. chip‐seq bam files reads were converted to bed files. fragment lengths used for input […]

2017
PMCID: 5570105
PMID: 28472346
DOI: 10.1093/nar/gkx364

[…] 4) (). peaks were visualized using the ucsc genome browser. bed formatted files were generated from the aligned bam files using bedtools (version 2.17.0) (). differential peaks were identified using diffreps (version 1.55.6) (), using the negative binomial model with p-value cut-off 0.0001 and sliding window of 1 kb and a step size of 100 bp. significantly differential peaks (α < 0.05) […]


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diffReps in publications

 (30)
PMCID: 5906078
PMID: 29675472
DOI: 10.1126/sciadv.aar8187

[…] examined locations of the signal that was variable between the two brain regions (pneun+ and cneun+; pneun− and cneun−) (). a large fraction of these differentially marked regions (identified by diffreps, p < 0.0001) for h3k27me3 were located in intergenic regions (70% for pneun+/cneun+ and 70% for pneun−/cneun−), whereas a substantial fraction of the differentially marked h3k4me3/h3k27ac […]

PMCID: 5909434
PMID: 29425303
DOI: 10.1093/nar/gky080

[…] coverage among the gene bodies in each resulted cluster. regions that were differentially enriched for plzf, h3k27me3 or h3k4me3 upon shplzf or shezh2 were identified using macs2 bdgdiff module and diffreps with slight modifications (p-values re-adjusted in r using bonferroni correction) () depending on their localization to distinguish promoter and gene body regions and converted into official […]

PMCID: 5763571
PMID: 29321036
DOI: 10.1186/s12989-017-0239-8

[…] through trimmomatic [] (fig. ). reads were then mapped to the rat genome (rn6) using the default parameters in bowtie2. to perform differential binding analysis on reads while distinguishing peaks, diffreps was used []. bedtools functions were used to delineate upstream promoter regions of genes (bedtools slop) and evaluate the promoter/gene overlay (bedtools intersect). genes were defined […]

PMCID: 5662632
PMID: 29084993
DOI: 10.1038/s41598-017-14366-0

[…] occupies broad regions of dna, such as histone modifications, can be challenging because most peak calling algorithms are designed to identify narrow peaks of factor occupancy. we therefore used diffreps, an algorithm specifically designed to identify differential histone occupancy between two conditions, to identify significant regions of differential h3k4me2 occupancy between the epo […]

PMCID: 5560095
PMID: 28671686
DOI: 10.1038/ng.3906

[…] retained and the alignments were subsequently filtered using the samtools package (v0.1.19) to remove duplicate reads. differential analysis between mutant and control samples was performed using diffreps with window size 1000 bp and moving step size 500 bp, and fdr<5% as significance cutoff and data visualized on the genome using the integrative genomics viewer (igv) program. for h3k27ac […]


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diffReps institution(s)
Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
diffReps funding source(s)
Supported by the seed grant from Friedman Brain Institute, National Institutes of Health (NIH) grants P01 DA008227 and P50 MH096890.

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