ChiLin protocols

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ChiLin specifications

Information


Unique identifier OMICS_15292
Name ChiLin
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Mac OS
Programming languages Python, R, Shell (Bash)
License BSD 3-clause “New” or “Revised” License
Computer skills Advanced
Stability Stable
Requirements
BWA, seqtk, fastqc, samtools, macs2, bedGraphToBigWig, wigCorrelate, bx-Python, mdseqpos
Source code URL https://codeload.github.com/cfce/chilin/zip/master
Maintained Yes

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Maintainer


  • person_outline Liu Shirley <>

Publication for ChiLin

ChiLin in pipelines

 (2)
2017
PMCID: 5629025
PMID: 28826504
DOI: 10.7554/eLife.27159.041

[…] kit (rubicon genomics, ann arbor, mi) and were sequenced on the illumina nextseq 500 platform at the molecular biology core facility (dana-farber cancer institute). chip-seq data was processed using chilin2 (). all chip-seq data have been deposited at the geo depository under accession number gse89939., total rna was extracted from cells using innuprep rna mini (analytic jena ag, jena, germany), […]

2017
PMCID: 5796974
PMID: 29435103
DOI: 10.18632/oncotarget.21378

[…] the spectral index [], based on the formula: (average pulldown in pra - average pulldown in prb) / (average pulldown in pra + average pulldown in prb)., the chip-seq analyses were performed using chilin, a chip-seq pipeline developed at center for functional cancer epigenomics (cfce), dana-farber cancer institute (dfci). briefly, short reads were aligned to the hg19 human genome using bowtie2 […]


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ChiLin in publications

 (15)
PMCID: 5796974
PMID: 29435103
DOI: 10.18632/oncotarget.21378

[…] the spectral index [], based on the formula: (average pulldown in pra - average pulldown in prb) / (average pulldown in pra + average pulldown in prb)., the chip-seq analyses were performed using chilin, a chip-seq pipeline developed at center for functional cancer epigenomics (cfce), dana-farber cancer institute (dfci). briefly, short reads were aligned to the hg19 human genome using bowtie2 […]

PMCID: 5635289
PMID: 29089668
DOI: 10.1155/2017/2389487

[…] anti-inflammatory effects on different cells orchestrating the innate immune response in the lung., this study was supported by ffc (fondazione ricerca fibrosi cistica) projects ffc#1/2016 (adriana chilin) and ffc#3/2016 (roberto gambari) and cib (consorzio interuniversitario di biotecnologie)., the authors declare that there is no conflict of interest regarding the publication of this paper., […]

PMCID: 5577741
PMID: 28854894
DOI: 10.1186/s12884-017-1462-x

[…] we thank all of the participants who responded to the qace. we thank delphine courvoisier for serving as the methodological expert for the questionnaires as well as ophélie boucher and antonina chilin (clinical midwives), and anne gendre and barbara kaiser (academic midwives). their comments helped refine the questionnaire for the pre-test. we also thank corine oberson for the data […]

PMCID: 5587812
PMID: 28911122
DOI: 10.1093/nar/gkx594

[…] (version 0.11.5) and htseqtools (version 1.16.0) () for assessing the overall quality of the chip-exo/nexus sequences. collectively, these encompass all the metrics available for read-level data in chilin (), which is another qc tool for chip-seq and dnase-seq, and q-nexus (), which is a chip-nexus analysis pipeline with qc features that are similar to that of fastqc. the remaining metrics […]

PMCID: 5334454
PMID: 28275716
DOI: 10.1523/ENEURO.0286-16.2017

[…] unclear which possibility is correct, these studies suggest that histamine signaling plays similar roles in regulating zebrafish and mammalian sleep/wake states., acknowledgements: we thank daisy chilin and axel dominguez for animal husbandry assistance and laura glass, viveca sapin, and uyen pham for technical assistance., reviewing editor: rae silver, columbia university, decisions […]


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ChiLin institution(s)
Shanghai Key laboratory of tuberculosis, Shanghai Pulmonary Hospital, Shanghai, China; Department of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai, China; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA, USA; Department of Biochemistry, University at Buffalo, Buffalo, NY, USA; Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute and Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
ChiLin funding source(s)
The project was funded by National Science Foundation of China (31329003), the National Institute of Health (U01 CA180980 and R01 HG4069), by the Dana-Farber Cancer Institute, by National Natural Science Foundation of China (31329003) and National Institutes of Health (CA180980).

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