It's DE-licious : a recipe for differential expression analyses of RNA-seq experiments using quasi-likelihood methods in edgeR / Aaron T.L. Lun, Yunshun Chen, and Gordon K. Smyth. Integrative exploratory analysis of two or more genomic datasets / Chen Meng and Aedin Culhane -- Study design for sequencing studies / Loren A. Honaas, Naomi S. Altman, and Martin Krzywinski -- Genomic annotation resources in R/Bioconductor / Marc R.J. Carlson, Hervé Pagès, Sonali Arora, Valerie Obenchain, and Martin Morgan -- The gene expression omnibus database / Emily Clough and Tanya Barrett -- A practical guide to The Cancer Genome Atlas (TCGA) / Zhining Wang, Mark A. Jensen, and Jean Claude Zenklusen -- Working with oligonucleotide arrays / Benilton S. Carvalho -- Meta-analysis in gene expression studies / Levi Waldron and Markus Riester -- Practical analysis of genome contact interaction experiments / Mark A Carty and Olivier Elemento -- Quantitative comparison of large-scale DNA enrichment sequencing data / Matthias Lienhard and Lukas Chavez -- Variant calling from next generation sequence data / Nancy F. Hansen -- Genome-scale analysis of cell-specific regulatory codes using nuclear enzymes / Songjoon Baek and Myong-Hee Sung -- NGS-QC generator : a quality control system for ChIP-seq and related deep sequencing-generated datasets / Marco Antonio Mendoza-Parra, Mohamed-Ashick M. Saleem, Matthias Blum, Pierre-Etienne Cholley, and Hinrich Gronemeyer -- Operating on genomic ranges using BEDOPS / Shane Neph, Alex P. Reynolds, M. Scott Kuehn, and John A. Stamatoyannopoulos -- GMAP and GSNAP for genomic sequence alignment : enhancements to speed, accuracy, and functionality / Thomas D. Wu, Jens Reeder, Michael Lawrence, Gabe Becker, and Matthew J. Brauer -- Visualizing genomic data using Gviz and Bioconductor / Florian Hahne and Robert Ivanek -- Introducing machine learning concepts with WEKA / Tony C. Smith and Eibe Frank -- Experimental design and power calculation for RNA-seq experiments / Zhijin Wu and Hao Wu -- It's DE-licious : a recipe for differential expression analyses of RNA-seq experiments using quasi-likelihood methods in edgeR / Aaron T.L. Lun, Yunshun Chen, and Gordon K. Smyth.
Summary:
This volume expands on statistical analysis of genomic data by discussing cross-cutting groundwork material, public data repositories, common applications, and representative tools for operating on genomic data.
Series:
Methods in molecular biology, 1064-3745 ; 1418 Springer protocols, 1949-2448
This resource is supported by the Institute of Museum and Library Services under the provisions of the Library Services and Technology Act as administered by State Library of Iowa.