Thesis/abbrevs.tex

\newabbreviation{RNA-seq}{RNA-seq}{high-throughput RNA sequencing}
\newabbreviation{ChIP-seq}{ChIP-seq}{chromatin immunoprecipitation followed by high-throughput DNA sequencing}
\newabbreviation{GLM}{GLM}{generalized linear model}
\newabbreviation{NB}{NB}{negative binomial}
\newabbreviation{BCV}{BCV}{biological coefficient of variation}
\newabbreviation{FDR}{FDR}{false discovery rate}
\newabbreviation{IDR}{IDR}{irreproducible discovery rate}
\newabbreviation{SVD}{SVD}{singular value decomposition}
\newabbreviation{SVA}{SVA}{surrogate variable analysis}

% TODO
\newabbreviation{PCA}{PCA}{principal component analysis}
\newabbreviation{PCoA}{PCoA}{principal coordinate analysis} % AKA MDS?
\newabbreviation{MOFA}{MOFA}{multi-omics factor analysis}
\newabbreviation{LF}{LF}{latent factor}
\newabbreviation{TSS}{TSS}{transcription start site}
\newabbreviation{CPM}{CPM}{counts per million}
\newabbreviation{logCPM}{logCPM}{logarithm of counts per million}
\newabbreviation{logFC}{logFC}{logarithm of fold change}
\newabbreviation{RMA}{RMA}{robust multichip average}
\newabbreviation{fRMA}{fRMA}{frozen robust multichip average}
\newabbreviation{GRSN}{GRSN}{global rank-invariant set normalization}
\newabbreviation{SCAN}{SCAN}{single-channel array normalization}
\newabbreviation{MSC}{MSC}{mesenchymal stem cell}
% Figure out the exactly correct way to write interferon gamma
\newabbreviation{IFNg}{IFN-g}{interferon gamma}
\newabbreviation{SRA}{SRA}{Sequence Read Archive}
\newabbreviation{GEO}{GEO}{Gene Expression Omnibus}
\newabbreviation{TMM}{TMM}{trimmed mean of M-values}
\newabbreviation{FPKM}{FPKM}{fragments per kilobase per million fragments}
\newabbreviation{CpGi}{CpGi}{CpG island}
\newabbreviation{AUC}{AUC}{area under ROC curve}
% ROC
% differential expression
% differential modification?
% effective promoter radius?
% DNA? RNA?
\newabbreviation{TX}{TX}{healthy transplant}
\newabbreviation{AR}{AR}{acute rejection}
\newabbreviation{ADNR}{ADNR}{acute dysfunction with no rejection}
\newabbreviation{CAN}{CAN}{chronic allograft nephropathy}
\newabbreviation{T1D}{T1D}{Type 1 disbetes}
\newabbreviation{T2D}{T2D}{Type 2 disbetes}
\newabbreviation{SWAN}{SWAN}{subset-quantile within array normalization}
\newabbreviation{BH}{BH}{Benjamini-Hochberg}
% MA plot
\newabbreviation{mRNA}{mRNA}{messenger RNA}
% oligo?
% HBA/B?
% cDNA
\newabbreviation{GB}{GB}{globin blocking}
% oligos

% These are just here as examples
\newabbreviation{XML}{XML}{eXtensible Markup Language}
\newabbreviation{HTML}{HTML}{Hyper-Text Markup Language}