ChIP-seq data analysis using iSeq package

The folder below contains the slides, R scripts and data files.  If you are interested in the course materials, you may read QMoBioc2012.pdf first, which will show you how to analyze ChIP-seq data through demonstration using the R scripts and data files.

QMoBioc2012.pdf --- A guide for ChIP-seq data analysis using iSeq package.

iSeqDemo.R --- R scripts used to generate the results shown in QMoBioc2012.pdf.   

iSeq.R --- R script that can be used as a command line program in Unix/Linux environment.

iSeqPar.txt --- A plain text file specifying the parameters used by iSeq.R.

nrsfFiles.txt --- A plain text file specifying the full path of the ChIP-seq data files.  Note the users need to modify this file to reflect their own path to the data files.

chipFC*.txt and mockFC*.txt --- the NRSF chromosomes 7 and 8 data  (Johnson et al., 2007;  Science 316, 1497-1502).  There are three treatments (chipFC*.txt) and three controls (mockFC*.txt). 

Human_hg17UCSCRefSeqTSS.bed  --- A BED file of UCSC Human hg17 RefSeq Transcription Start Sites. 

chr1.noisy.RData --- A noisy ChIP-seq data used as an example of handing noisy data.  Please see QMoBioc2012.pdf for details.

reg.txt, er.txt and erhg18.txt --- the enriched regions used for demonstration of annotation of enriched regions.  reg.txt and er.txt are based on hg17 coordinate, and erhg18.txt is based on hg18 coordinate.  Please see QMoBioc2012.pdf for details.

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Human_hg17UCSCRefSeqTSS.bed
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Quincy Mo,
Sep 23, 2012, 11:50 AM
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Quincy Mo,
Sep 22, 2012, 9:13 PM
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chipFC1592_uniq_hg17.txt
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Quincy Mo,
Sep 22, 2012, 9:15 PM
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chipFC1862_uniq_hg17.txt
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Quincy Mo,
Sep 23, 2012, 11:42 AM
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chipFC2002_uniq_hg17.txt
(3619k)
Quincy Mo,
Sep 23, 2012, 11:42 AM
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chr1.noisy.RData
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Quincy Mo,
Sep 23, 2012, 11:44 AM
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er.txt
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Quincy Mo,
Sep 23, 2012, 2:02 PM
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erhg18.txt
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Quincy Mo,
Sep 23, 2012, 11:49 AM
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iSeq.R
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Quincy Mo,
Sep 22, 2012, 9:14 PM
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iSeqDemo.R
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Quincy Mo,
Sep 22, 2012, 9:14 PM
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iSeqPar.txt
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Quincy Mo,
Sep 23, 2012, 1:45 PM
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mockFC1592_uniq_hg17.txt
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Quincy Mo,
Sep 23, 2012, 11:43 AM
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mockFC1862_uniq_hg17.txt
(3823k)
Quincy Mo,
Sep 23, 2012, 11:43 AM
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mockFC2002_uniq_hg17.txt
(4618k)
Quincy Mo,
Sep 23, 2012, 11:43 AM
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nrsfFiles.txt
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Quincy Mo,
Sep 23, 2012, 11:50 AM
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reg.txt
(192k)
Quincy Mo,
Sep 23, 2012, 2:04 PM
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