mapping method qtlreaper
definition: Rapidly scan microarray expression data for QTLs

mapping method Rqtl
definition: R/qtl is an extension library for the R statistics system. It is used to analyze experimental crosses for identifying genes contributing to variation in quantitative traits (so-called quantitative trait loci, QTLs). Using a hidden Markov model, R/qtl estimates genetic maps, to identify genotyping errors, and to perform single-QTL and two-QTL, two-dimensional genome scans.

mapping method HappyR
definition: Haplotype-based QTL mapping method, often used for multiparent populations.

mapping method PLINK
definition: Genome-wide association and population-based linkage analysis tool.

mapping method FastMap
definition: Efficient mapping algorithm optimized for large datasets.

avg method MAS5
definition: Affymetrix Microarray Suite 5 normalization method.

avg method PDNN
definition: Probe-level normalization method that models sequence-dependent hybridization effects in microarray data.

avg method RMA
definition: Robust Multi-array Average normalization for microarray data.

avg method dChip
definition: Model-based normalization and expression summarization method for microarray data using probe-level intensity modeling.

avg method GCRMA
definition: GC-content adjusted RMA normalization method.

avg method Herit
definition: Method that estimates heritability by partitioning phenotypic variance into genetic and environmental components.

avg method Rank
definition: Normalization method that transforms values based on their rank order within a dataset.

avg method RankInv
definition: Normalization method that applies an inverse rank transformation to enforce a uniform distribution of values.

avg method LOESS
definition: Locally estimated scatterplot smoothing normalization.

avg method LOESS NB
definition: LOESS-based normalization method that corrects systematic biases without assuming a parametric noise model.

avg method QUANT
definition: Quantile normalization method that forces all samples to share the same empirical distribution.

avg method QUANT NB
definition: Quantile normalization method applied without background correction or parametric noise assumptions.

avg method RSN
definition: Robust spline normalization method that adjusts microarray data to remove systematic technical variation.

avg method RSN NB
definition: Robust spline normalization method applied without background correction or parametric noise assumptions.

avg method Sscore
definition: Statistical scoring method for identifying significant gene expression changes in microarray data.

avg method mlratio
definition: Method calculating the log-ratio of expression values between two conditions for microarray analysis.

avg method VST
definition: Variance stabilizing transformation for RNA-seq count data to reduce heteroscedasticity.

avg method RPN
definition: Robust Probe Normalization method for microarray data to adjust probe-level intensities.

TPM Log2
definition: Transcripts Per Million normalized expression values, log2 transformed.

avg method RPKM
definition: Reads Per Kilobase Million normalization for RNA-seq data.

avg method RNA seq
definition: Normalization pipeline applied to RNA sequencing datasets.

avg method SRM
definition: Normalization method for targeted proteomics using Selected Reaction Monitoring.

avg method SWATH
definition: Normalization and quantification method for SWATH-MS proteomics data.

avg method RPKM log2
definition: Log2-transformed Reads Per Kilobase per Million mapped reads for RNA-seq data.

avg method Sesame
definition: Normalization method for Illumina methylation arrays using the Sesame pipeline.

avg method TPM Log2
definition: Log2-transformed Transcripts Per Million for RNA-seq expression quantification.

avg method rlog
definition: Regularized log transformation for RNA-seq count data to stabilize variance.

avg method edgeR
definition: Normalization and differential expression analysis method for RNA-seq using edgeR.

avg method minfi
definition: Normalization pipeline for Illumina methylation arrays using the minfi Bioconductor package.

avg method 2Z 8
definition: Microarray normalization method that applies a 2Z+8 transformation to expression values.

avg method Log2
definition: Simple log2 transformation applied to expression values to reduce skew and stabilize variance.

avg method DESeq2 rlog2
definition: Regularized log transformation from the DESeq2 RNA-seq workflow.

avg method N A
definition: Indicates that no normalization or averaging method applies.