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fluff specifications

Information


Unique identifier OMICS_11395
Name fluff
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Simon van Heeringen

Publication for fluff

fluff citations

 (5)
call_split

Chromatin Accessibility Based Characterization of the Gene Regulatory Network Underlying Plasmodium falciparum Blood Stage Development

2018
PMCID: 5899830
PMID: 29649445
DOI: 10.1016/j.chom.2018.03.007
call_split See protocol

[…] re uploaded in the UCSC genome browser. Bedtools intersect (version 2.20.1; ) was used to define the overlap between the ATAC-seq peaks with the trimmed AP2-I peaks (in 3D7 coordinates) reported in . Fluff was used to generate the heatmap of accessibility over the AP2-I peaks that overlap with ATAC-seq peaks (). We used the build-in Gene Ontology tool of PlasmoDB with default settings to identify […]

library_books

Functional convergence of histone methyltransferases EHMT1 and KMT2C involved in intellectual disability and autism spectrum disorder

2017
PLoS Genet
PMCID: 5656305
PMID: 29069077
DOI: 10.1371/journal.pgen.1006864

[…] rther analysis. Remaining putative trr binding regions were visualized in a heatmap that was sorted based on k-means clustering of read intensity around the centre of the peak using the python script fluff_heatmap.py (https://github.com/simonvh/fluff) (). Individual clusters were examined visually in the genome browser to assess the quality of the peaks within the clusters. Two clusters (8 and 15) […]

library_books

Regulatory remodeling in the allo tetraploid frog Xenopus laevis

2017
Genome Biol
PMCID: 5655803
PMID: 29065907
DOI: 10.1186/s13059-017-1335-7

[…] ck using the options --broad -g 2.3e9 -q 0.001. --buffer-size 1000. Peaks were combined for replicates using bedtools intersect (version v.2.20.1) []. Figures of genomic profiles were generated using fluff v1.62 [].In addition to the RNA-seq triplicate produced in this study, we used the eight stage 10.5 samples from NCBI GEO series GSE56586 (GSM1430926, GSM1430927, GSM1430928, GSM1430929, GSM1430 […]

library_books

Histone Modifications in a Mouse Model of Early Adversities and Panic Disorder: Role for Asic1 and Neurodevelopmental Genes

2016
Sci Rep
PMCID: 4848503
PMID: 27121911
DOI: 10.1038/srep25131

[…] olor Space format via Life Technologies Lifescope 2.5.1 analysis software. After removal of duplicated reads, we identified ChIP enrichments using MACS2. Enrichment profiles at TSS were obtained with Fluff package (http://github.com/simonvh/fluff). Correlation among enrichment profiles was calculated with the wigCorrelate tool, which is part of UCSC genome browser utilities. We then applied an Irr […]

library_books

Embryonic transcription is controlled by maternally defined chromatin state

2015
Nat Commun
PMCID: 4703837
PMID: 26679111
DOI: 10.1038/ncomms10148

[…] All heatmaps were generated using fluff ( http://simonvh.github.com/fluff) or gplots ( http://cran.r-project.org/web/packages/gplots/index.html). For all heatmap clustering, the Euclidean distance metric was used. Other plots were gen […]

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fluff institution(s)
Radboud University, Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Nijmegen, Netherlands
fluff funding source(s)
The Netherlands Organisation for Scientific Research (NWO­ALW) [863.12.002]; the US National Institutes of Health (NICHD) [R01HD069344].

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