RNA

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RNA-Skim: a rapid method for RNA-Seq quantification at transcript level http://bioinformatics.oxfordjournals.org/content/30/12/i283.full.pdf+html

Li HD, Menon R, Omenn GS, Guan Y. (2014) The emerging era of genomic data integration for analyzing splice isoform function. http://www.rna-seqblog.com/emerging-computational-approaches-that-integrate-rna-seq-data-for-predicting-the-functions-of-alternatively-spliced-isoforms/?utm_source=RNA-Seq+Blog+Subscribers&utm_campaign=f78f05e80b-RSS_EMAIL_CAMPAIGN&utm_medium=email&utm_term=0_e9607034ee-f78f05e80b-85918069

Kalari KR et al. (2014) MAP-RSeq: Mayo Analysis Pipeline for RNA sequencing. BMC Bioinformatics http://www.biomedcentral.com/content/pdf/1471-2105-15-224.pdf

Meng J, Lu Z, Liu H, Zhang L, Zhang S, Chen Y, Rao MK, Huang Y. (2014) A protocol for RNA methylation differential analysis with MeRIP-Seq data and exomePeak R/Bioconductor package. http://www.rna-seqblog.com/a-protocol-for-rna-methylation-differential-analysis-with-merip-seq-data/

Zhao H, Cao F, Gong Y, Xu H, Fei Y, Wu L, Ye X, Yang D, Liu X, Li X, Zhou J. (2014) Stratification of Gene Coexpression Patterns and GO Function Mining for a RNA-Seq Data Series. Biomed Res Int http://www.rna-seqblog.com/stratification-of-gene-coexpression-patterns-and-go-function-mining-for-a-rna-seq-data-series/?utm_source=RNA-Seq+Blog+Subscribers&utm_campaign=f78f05e80b-RSS_EMAIL_CAMPAIGN&utm_medium=email&utm_term=0_e9607034ee-f78f05e80b-85918069

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BITS Wiki – RNA-Seq analysis for differential expression

http://www.rna-seqblog.com/bits-wiki-rna-seq-analysis-for-differential-expression/