\usepackage{textgreek}

%% Wet-lab methods
\newabbreviation{RNA-seq}{RNA-seq}{high-throughput RNA sequencing}
\newabbreviation{ChIP-seq}{ChIP-seq}{chromatin immunoprecipitation followed by high-throughput DNA sequencing}
\newabbreviation{ChIP}{ChIP}{chromatin immunoprecipitation}
\newabbreviation{oligo}{oligo}{oligonucleotide}
\newabbreviation{GB}{GB}{globin blocking}
\newabbreviation{PCR}{PCR}{polymerase chain reaction}
\newabbreviation{HTS}{HTS}{high-throughput sequencing}

%% TODO
%% PolyA
%% RT = reverse transcription/transcriptase
%% DTT
%% dNTP? dUTP? dCTP?
%% cDNA?
%% TE?
%% bp & kbp?
%% CD4, CD8, etc.
%% Check Sarah's list of abbreviations for more

%% Computational methods
\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}
\newabbreviation{PCA}{PCA}{principal component analysis}
\newabbreviation{PC}{PC}{principal component}
\newabbreviation{LF}{LF}{latent factor}
%% Note: Can't start with math or else capitalization fails
\newabbreviation{logCPM}{logCPM}{log$_2$ counts per million}
\newabbreviation{CPM}{CPM}{counts per million}
\newabbreviation{logFC}{logFC}{log$_2$ fold change}
\newabbreviation{M-value}{M-value}{log$_2$ ratio}
\newabbreviation{FPKM}{FPKM}{fragments per kilobase per million fragments}
\newabbreviation{ID}{ID}{identifier}

\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{MACS}{MACS}{Model-based Analysis of ChIP-seq}
\newabbreviation{SICER}{SICER}{Spatial Clustering for Identification of ChIP-Enriched Regions}
\newabbreviation{TMM}{TMM}{trimmed mean of M-values}
\newabbreviation{PCoA}{PCoA}{principal coordinate analysis} % AKA MDS?
\newabbreviation{MOFA}{MOFA}{Multi-Omics Factor Analysis}
\newabbreviation{SWAN}{SWAN}{subset-quantile within array normalization}
\newabbreviation{BH}{BH}{Benjamini-Hochberg}
\newabbreviation{PAM}{PAM}{Prediction Analysis for Microarrays}

\newabbreviation{ROC}{ROC}{receiver operating characteristic}
\newabbreviation{AUC}{AUC}{area under ROC curve}

%% Data sources
\newabbreviation{GEO}{GEO}{Gene Expression Omnibus}
\newabbreviation{SRA}{SRA}{Sequence Read Archive}
\newabbreviation{ENCODE}{ENCODE}{Encyclopedia Of DNA Elements}
\newabbreviation{GRCh38}{GRCh38}{Genome Reference Consortium Human Build 38}

%% Biology
\newabbreviation{TSS}{TSS}{transcription start site}
\newabbreviation{CpGi}{CpGi}{CpG island} % TODO: Switch to CGI
\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 diabetes}
\newabbreviation{T2D}{T2D}{Type 2 diabetes}
\newabbreviation{mRNA}{mRNA}{messenger RNA}
\newabbreviation{ncRNA}{ncRNA}{non-coding RNA}
\newabbreviation{APC}{APC}{antigen-presenting cell}
\newabbreviation{TCR}{TCR}{T-cell receptor}
\newabbreviation{MHC}{MHC}{major histocompatability complex}

%% TODO
%% Do these after writing a section on MSC
\newabbreviation{MSC}{MSC}{mesenchymal stem cell}
\newabbreviation{IFNg}{IFN\textgamma}{interferon gamma}
%% cyno?

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

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