cole-trapnell-lab/cufflinks
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RNAseq analysis notes from Ming Tang
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The Leek group guide to genomics papers
ChIP-seq analysis notes from Ming Tang
Bayesian haplotype-based genetic polymorphism discovery and genotyping.
RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly