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@Manual{chron,
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@Manual{TxDb_Hsapiens_UCSC_hg19_knownGene,
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@Article{clusterProfiler,
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@Article{wavClusteR,
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@Article{ChIPseeker,
    title = {ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization},
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    journal = {Bioinformatics},
    year = {2015},
    volume = {31},
    number = {14},
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@Article{DiffBind,
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@article{Bowtie1,
  title = {Ultrafast and memory-efficient alignment of short {DNA} sequences to the human genome},
	volume = {10},
	issn = {1465-6914},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/19261174},
	doi = {10.1186/gb-2009-10-3-r25},
	abstract = {Bowtie is an ultrafast, memory-efficient alignment program for aligning short {DNA} sequence reads to large genomes. For the human genome, Burrows-Wheeler indexing allows Bowtie to align more than 25 million reads per {CPU} hour with a memory footprint of approximately 1.3 gigabytes. Bowtie extends previous Burrows-Wheeler techniques with a novel quality-aware backtracking algorithm that permits mismatches. Multiple processor cores can be used simultaneously to achieve even greater alignment speeds. Bowtie is open source (http://bowtie.cbcb.umd.edu).},
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	urldate = {2011-03-03},
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	year = {2009},
	note = {{PMID:} 19261174},
	keywords = {Algorithms, Base Sequence, Genome, Human, Humans, Sequence Alignment},
	pages = {R25},
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}
,
@article{Bowtie2,
  title = {Aligning short sequencing reads with Bowtie},
  volume = {Chapter 11},
	issn = {1934-{340X}},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/21154709},
	doi = {10.1002/0471250953.bi1107s32},
	abstract = {This unit shows how to use the Bowtie package to align short sequencing reads, such as those output by second-generation sequencing instruments. It also includes protocols for building a genome index and calling consensus sequences from Bowtie alignments using {SAMtools.}},
	urldate = {2011-03-03},
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	author = {Langmead, Ben},
	month = dec,
	year = {2010},
	note = {{PMID:} 21154709},
	pages = {Unit 11.7},
	file = {Langmead 2010.pdf:/home/anderspd/.mozilla/firefox/uehvves0.default/zotero/storage/2TCI9DID/Langmead 2010.pdf:application/pdf}
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	year = {2010},
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@article{MACS,
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	doi = {10.1002/0471250953.bi0214s34},
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	year = {2012},
	note = {http://liulab.dfci.harvard.edu/MACS/},

}
,
@article{GenomicTools,
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@article{ROSE,
  title = {Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes},
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@article{MapArg,
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@electronic{novoalign,
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}
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@electronic{CIMS,
author = {Chaolin Zhang},
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author = {Chaolin Zhang},
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	url = {https://sourceforge.net/projects/czplib/},
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	year = {2014},
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@article{meme,
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year = {2009},
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@article{memechip,
  title = {MEME-ChIP: motif analysis of large DNA datasets},
	url = {http://meme-suite.org/index.html},
	journal = {Bioinformatics},
	author = {Philip Machanick and Timothy L. Bailey},
year = {2011},
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@misc{FASTX,
  title = {FASTX Toolkit},
	url = {http://hannonlab.cshl.edu/fastx_toolkit/index.html},
}
@article{MultiQC,
  title = {MultiQC: Summarize analysis results for multiple tools and samples in a single report},
	journal = {Bioinformatics},
	author = {Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller},
	year = {2016},
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},
@article{GATKToolkit,
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author = {Andrews S.},
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@article{NameHere,
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	url = {},
	journal = {},
	author = {},
	year = {},
    volume = {},
    number = {},
    pages = {},
    doi = {},
}