BIOS6660 Day1 Slides

Tzu L. Phang
October 20, 2015

BioC Libraries

Please install these libraries for Thursday class


source(“http://bioconductor.org/biocLite.R”)
biocLite(‘GenomicAlignments’); biocLite(‘DBChIP’); biocLite(‘ShortRead’)
biocLite(‘rtracklayer’); biocLite(‘GenomicRanges’); biocLite(‘GenomicFeatures’)
biocLite(‘Rsamtools’); biocLite(‘chipseq’); biocLite(‘annaffy’)
biocLite(‘annotate’); biocLite(‘ChIPseeker’); biocLite(‘TxDb.Hsapiens.UCSC.hg19.knownGene’)
biocLite(‘BSgenome.Hsapiens.UCSC.hg19’); biocLite(‘org.Hs.eg.db’); biocLite(‘BayesPeak’)

Intetrated Genome Viewer (IGV)

We will be using a stand-alone genome viewing software; Integrated Genome Viewer (IGV), from Broad Institue to visualize our result. Goto the bottom of the page; register, download the install the software.

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A working copy of Microsoft Excel

We will be using Microsoft Excel to open the final result file. So, make sure your copy on your computer is in working order

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ChIPseq Practice Dataset


Gerber_chr22.zip

Dex_GR_7A_chr22.bam,
Dex_GR_7C_chr22.bam,
Veh_GR_2B_chr22.bam,
Veh_GR_2D_chr22.bam
Background_2A_Input_chr22.bed
Dex_GR_7A_ori_peaks.bed,
Dex_GR_7C_ori_peaks.bed,
Veh_GR_2B_ori_peaks.bed,
Veh_GR_2D_ori_peaks.bed
Gerber_QC.Rdata