DFilter protocols

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DFilter specifications


Unique identifier OMICS_08442
Name DFilter
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages MATLAB
Computer skills Advanced
Stability Stable
Maintained Yes


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  • person_outline Vibhor Kumar <>
  • person_outline Shyam Prabhakar <>

Publication for DFilter

DFilter in pipelines

PMCID: 5225521
PMID: 28077088
DOI: 10.1186/s12864-016-3428-1

[…] sample, while 97.40% was the analogous value for vehicle-treated samples. the equivalent numbers for t-47d cell line were 97.45% and 97.75%. dnase hypersensitive sites (dhss) were detected using dfilter []. the standard deviation was set to 2, bin size 100 bp and kernel size 50. in addition, the refine parameter was used. to mitigate the effects of mappability and coverage bias samples […]

PMCID: 5083138
PMID: 27428650
DOI: 10.1038/nn.4347

[…] data were mapped to mouse mm9 reference genome using bwa aligner. after filtering out duplicate reads (pcr artifact), the reads from biological replicates were concatenated for peak calling using dfilter software (threshold p value = 1×10−5, bin size = 25 bp, kernel size = 50 bp). enrichment of hdac3 binding peaks at different genomic regions were compared for wt and mecp2 ko mice., human […]

PMCID: 5085127
PMID: 27129152
DOI: 10.18632/oncotarget.8983

[…] create a meta-pool of control input material. this meta-pool material was used as a reference sample for further analysis., to identify enriched genomic regions we used two peak callers, macs [] and dfilter []. we ran macs using the default parameters with the exception of a more significant p-value threshold at 1.00e-7. dfilter settings were default for transcription factor detection. […]

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DFilter in publications

PMCID: 5797120
PMID: 29396493
DOI: 10.1038/s41467-018-02856-2

[…] sequenced samples were aligned to the reference human genome (ensembl 37) using burrows-wheeler aligner (bwa, v0.7.5a) with a mapping quality >20. peak calling was performed using macs (v1.4) and dfilter (v1.5), where only peaks were considered that were shared by the two peak callers. genome browser snapshots were generated using igv (v2.3.67), heatmaps were compiled using seqminer (v1.3.3) […]

PMCID: 5738507
PMID: 29279824
DOI: 10.5624/isd.2017.47.4.247

[…] a constant k, which is proportional to the atomic number of the tube's target material. the simulation assumed that the radiation first passed the aluminum filter of the x-ray unit with thickness dfilter. the simulated attenuation coefficient then contained a polymethyl methacrylate (pmma) layer of thickness ddisc, which was introduced to simulate a layer of soft tissue. for a given sample […]

PMCID: 5640250
PMID: 29028826
DOI: 10.1371/journal.pone.0186435

[…] through a macs algorithm with a cut-off p-value threshold of 10−8. since there are no previously determined cis-regulatory sequence datasets in this species, peak detection was also carried out by dfilter [] to confirm the robustness of our data. applying a cut-off p-value threshold of 1x10-8, this algorithm identified 38 305 open chromatin, cis-regulatory sites. the comparison of the sites […]

PMCID: 5344973
PMID: 28272467
DOI: 10.1038/ncomms14694

[…] peaks of histone 3 lysine 27 acetylation (h3k27ac). a total of 140 h3k27ac data sets were downloaded from the roadmap epigenomics project (http://www.roadmapepigenomics.org), and reprocessed using dfilter. only peaks with p<10−10 (dfilter) were retained. four in house data sets from a human balding and a non-balding dermal papilla cell line with and without 10 nm of dht treatment […]

PMCID: 5083138
PMID: 27428650
DOI: 10.1038/nn.4347

[…] of transcribed genes genome-wide we performed chromatin immunoprecipitation (chip) against hdac3 in the hippocampus of 3-month wild-type mice, followed by next-generation sequencing (chip-seq). the dfilter peak-finding algorithm was utilized to define hdac3 binding sites and identified 6149 regions. downstream analysis revealed that hdac3 binding is enriched at the promoter and 5’ utr of genes, […]

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DFilter institution(s)
Computational and Systems Biology, Genome Institute of Singapore, Singapore; Gene Regulation Laboratory, Genome Institute of Singapore, Singapore.; Stem Cell and Developmental Biology, Genome Institute of Singapore, Singapore; Department of Biology, Clarkson University, Potsdam, New York, NY, USA
DFilter funding source(s)
Supported by the Agency for Science, Technology and Research (A*STAR), Singapore including grant JCOAG03_FG02_2009 from Joint Council Office of A*STAR.

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