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|a 572.8/7
|2 23
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| 100 |
1 |
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|a Mifsud, Borbala.
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| 245 |
1 |
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|a Practical Guide to ChIP-Seq Data Analysis.
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| 264 |
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1 |
|a Milton :
|b Chapman and Hall/CRC,
|c 2018.
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| 300 |
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|a 1 online resource.
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| 336 |
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|a text
|b txt
|2 rdacontent
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| 337 |
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|a computer
|b c
|2 rdamedia
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| 338 |
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|a online resource
|b cr
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1 |
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|a Focus Computational Biology Ser
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| 588 |
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|a Print version record.
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|a Cover; Half Title; Title Page; Copyright Page; Preface; Authors; Table of Contents; CHAPTER 1: Introduction to ChIP-seq; 1.1 CHIP-SEQ EXPERIMENT; 1.2 IMPROVED DETECTION PROTOCOLS; 1.2.1 ChIP-exo; 1.2.2 ChIP-nexus; 1.2.3 CUT 1.2.4 DamID; 1.3 CHIP-SEQ DATA ANALYSIS WORKFLOW; 1.4 DESIGNING A CHIP-SEQ EXPERIMENT; 1.4.1 ChIP-seq controls; 1.4.2 Sources of bias; 1.4.3 Antibody quality; 1.4.4 Read depth; 1.4.5 Read properties; 1.4.6 Replicates; CHAPTER 2: Getting Started; 2.1 CHIP-SEQ DATASETS; 2.2 COMPUTATIONAL REQUIREMENTS; 2.2.1 Computing environment; 2.2.2 Data; 2.2.3 Software.
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| 505 |
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|a 2.2.4 File formats2.3 DATA RETRIEVAL FROM GEO; 2.4 CODING TIPS; 2.5 GRAPHICAL USER INTERFACE TOOLS; CHAPTER 3: General Quality Control; 3.1 INTRODUCTION; 3.1.1 FASTQ files; 3.1.2 Available tools; 3.2 MEASURES OF HTS DATA QUALITY; 3.2.1 Selected quality metrics; 3.2.2 FastQC; 3.3 TRIMMING AND FILTERING; 3.3.1 Adapter removal; 3.3.2 Low-quality trimming; 3.3.3 Trim Galore!; CHAPTER 4: Genomic Alignment; 4.1 INTRODUCTION; 4.1.1 Alignment concepts; 4.1.2 Available tools; 4.2 PARAMETERS AND CONSIDERATIONS; 4.2.1 Mismatches; 4.2.2 Multi-mapping; 4.2.3 Other parameters; 4.2.4 Output format.
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| 505 |
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|a 4.3 GENOMIC ALIGNMENT WITH BOWTIE 2CHAPTER 5: ChIP-seq-specific Quality Control; 5.1 CHIP-SEQ-SPECIFIC QUALITY METRICS; 5.1.1 Signal enrichment; 5.1.2 Forward and reverse read distribution; 5.1.3 Duplicate reads; 5.2 CHIPQC; CHAPTER 6: Peak Calling; 6.1 CHIP-SEQ SIGNAL TYPES; 6.1.1 Sharp signal for transcription factors; 6.1.2 Broad signal for histone marks; 6.1.3 Mixed signal for RNA polymerase II; 6.2 GENERAL PEAK CALLING STRATEGY; 6.2.1 Estimation of fragment size; 6.2.2 Enrichment of reads; 6.2.3 Significance score; 6.2.4 Multiple testing correction; 6.2.5 Choice of thresholds.
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| 505 |
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|a 6.3 EXISTING TOOLS AND CONSIDERATIONS6.3.1 Single-end versus paired-end libraries; 6.3.2 Sequencing depth and library complexity; 6.3.3 Experimental resolution; 6.3.4 New generation of peak callers; 6.3.5 Post-processing; 6.4 PEAKZILLA FOR TRANSCRIPTION FACTOR DATA; 6.5 MACS2 FOR HISTONE MARK DATA; 6.6 SATURATION ANALYSIS; CHAPTER 7: Data Visualisation; 7.1 READ DENSITIES; 7.2 PEAK REGIONS; 7.3 GENOME BROWSER; CHAPTER 8: Comparative Analysis; 8.1 OVERLAP OF PEAK REGIONS; 8.2 IRREPRODUCIBLE DISCOVERY RATE (IDR); 8.2.1 Peak calling for IDR; 8.2.2 Calculating IDR.
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|a 8.3 COMPARISON OF READ DENSITIES8.3.1 Merging peak regions; 8.3.2 Counting reads for each sample; 8.3.3 Normalising read counts; 8.3.4 Comparing read counts; 8.4 DIFFERENTIAL BINDING ANALYSIS; 8.4.1 Using DESeq2; 8.4.2 DiffBind; CHAPTER 9: Downstream Analyses; 9.1 GENOMIC CONTEXT; 9.1.1 Genomic location; 9.1.2 Distance to genes; 9.2 FUNCTIONAL ANALYSES; 9.2.1 Assignment to target genes; 9.2.2 Gene ontology analysis; 9.2.3 Other gene-set enrichment analyses; 9.3 SEQUENCE ANALYSIS; 9.3.1 Motif analysis; 9.3.2 Sequence conservation; 9.4 INTEGRATION WITH OTHER DATASETS.
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| 500 |
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|a 9.4.1 Additional ChIP-seq datasets.
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| 500 |
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|a Electronic resource.
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| 655 |
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7 |
|a Electronic books.
|2 local
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| 700 |
1 |
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|a Zarnack, Kathi.
|0 http://id.loc.gov/authorities/names/n2018061424
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| 700 |
1 |
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|a Bardet, Anaïs F.
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| 710 |
2 |
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|a ProQuest (Firm)
|0 http://id.loc.gov/authorities/names/n2007068018
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| 776 |
1 |
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|i Print version:
|a Mifsud, Borbala.
|t Practical Guide to ChIP-Seq Data Analysis.
|d Milton : Chapman and Hall/CRC, ©2018
|z 9781138596528
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| 830 |
|
0 |
|a Focus Computational Biology Ser.
|
| 856 |
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|u https://ebookcentral.proquest.com/lib/tamucs/detail.action?docID=5568360
|z Connect to the full text of this electronic book
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|a Texas A&M University
|b College Station
|c Electronic Resources
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|d Available Online
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|e QH599 .M547 2019
|h Library of Congress classification
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| 998 |
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|a QH599 .M547 2019
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|l Available Online
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