QuEST is a statistical software for analysis of ChIP-Seq data with data and analysis results visualization through UCSC Genome Browser.  http://www-hsc.usc.edu/~valouev/QuEST/QuEST.html

peak calling 阈值的选择： http://www.nature.com/nprot/journal/v7/n1/fig_tab/nprot.2011.420_F2.html

MeDIP-seq and histone modification ChIP-seq analysis  http://crazyhottommy.blogspot.com/2014/01/medip-seq-and-histone-modification-chip.html

2011-review-CHIP-seq-high-quaility-data: http://www.nature.com/ni/journal/v12/n10/full/ni.2117.html?message-global=remove

不同处理条件的CHIP-seq的差异peaks分析： http://www.slideshare.net/thefacultyl/diffreps-automated-chipseq-differential-analysis-package

一个实际的CHIP-seq数据分析例子： http://www.biologie.ens.fr/~mthomas/other/chip-seq-training/

## ppt : http://159.149.160.51/epigen_milano/epigen_barozzi.pdf

## best practise: http://bioinformatics-core-shared-training.github.io/cruk-bioinf-sschool/

## pipeline : https://github.com/shenlab-sinai/chip-seq_preprocess

## https://sites.google.com/site/anshul...e/projects/idr  ## samtools view -b -F 1548 -q 30 chipSampleRep1.bam

## pipeline : http://daudin.icmb.utexas.edu/wiki/index.php/ChIPseq_prep_and_map

## pipeline : https://github.com/BradyLab/ChipSeq/blob/master/chipseq.sh

## https://github.com/crukci-bioinformatics/chipseq-pipeline

## https://github.com/ENCODE-DCC/chip-seq-pipeline

## Hands-on introduction to ChIP-seq analysis - VIB Training   http://www.biologie.ens.fr/~mthomas/other/chip-seq-training/

## video(A Step-by-Step Guide to ChIP-Seq Data Analysis Webinar) : http://www.abcam.com/webinars/a-step-by-step-guide-to-chip-seq-data-analysis-webinar

## Using ChIP-Seq to identify and/or quantify bound regions (peaks)  http://barcwiki.wi.mit.edu/wiki/SOPs/chip_seq_peaks

## http://jura.wi.mit.edu/bio/education/hot_topics/ChIPseq/ChIPSeq_HotTopics.pdf

## http://pedagogix-tagc.univ-mrs.fr/courses/ASG1/practicals/chip-seq/mapping_tutorial.html

## 公开课： https://www.coursera.org/learn/galaxy-project/lecture/FUzcg/chip-sequence-analysis-with-macs

##ＥＢＩ的教程：https://www.ebi.ac.uk/training/online/course/ebi-next-generation-sequencing-practical-course/chip-seq-analysis/chip-seq-practical

## 日语教程：http://genomejack.net/download/GenomeJackBrowserAppendix/browser_appendix_j/tutorials/chipSeq.html

## 台湾教程：http://lsl.sinica.edu.tw/Services/Class/files/20151118475_2.pdf 徐唯哲 Paul Wei-Che HSU

中央研究院 分子生物研究所

研究助技師

## peak finder软件大全： http://wodaklab.org/nextgen/data/peakfinders.html

## https://www.encodeproject.org/documents/049704a4-5c58-4631-acf1-4ef152bdb3ef/@@download/attachment/Learning_Chromatin_States_from_ChIP-seq_data.pdf

## https://bioshare.bioinformatics.ucdavis.edu/bioshare/download/47aq5pp5mzza5vb/PDFs/Tuesday_MB_ChIP-Seq_Intro.pdf

## paper： Large-Scale Quality Analysis of Published ChIP-seq Data http://www.g3journal.org/content/4/2/209.full

## paper： Chip-seq data analysis: from quality check to motif discovery and more http://ccg.vital-it.ch/var/sib_april15/cases/landt12/strand_correlation.html

## Workshop hands on session(RNA-Seq / ChIP-Seq  ) :  https://hpc.oit.uci.edu/biolinux/handson.docx

## http://www.gqinnovationcenter.com/documents/bioinformatics/ChIPseq.pptx

## paper supplement : http://genome.cshlp.org/content/suppl/2015/10/02/gr.192005.115.DC1/Supplemental_Information.docx

http://www.ncbi.nlm.nih.gov/pubmed/22130887 "Analyzing ChIP-seq data: preprocessing, normalization, differential identification, and binding pattern characterization."

http://www.ncbi.nlm.nih.gov/pubmed/22499706 "Normalization, bias correction, and peak calling for ChIP-seq." (stat heavy)

http://www.ncbi.nlm.nih.gov/pubmed/24244136 "Practical guidelines for the comprehensive analysis of ChIP-seq data."

http://www.ncbi.nlm.nih.gov/pubmed/25223782 "Identifying and mitigating bias in next-generation sequencing methods for chromatin biology."

A quick search also turned up this recent paper (which I haven't read) that might be of interest to you

http://www.ncbi.nlm.nih.gov/pubmed/24598259 "Impact of sequencing depth in ChIP-seq experiments."

## figures: https://github.com/shenlab-sinai/ngsplot

还有两个ｗｅｂ－ｔｏｏｌｓ也是可视化

bioconductor系列工具和教程 :

http://faculty.ucr.edu/~tgirke/HTML_Presentations/Manuals/Workshop_Dec_6_10_2012/Rchipseq/Rchipseq.pdf

## 公司教程： http://www.partek.com/Tutorials/microarray/Tiling/ChipSeqTutorial.pdf