# Analysis Tools and Methods
ColocBoost      # Multiple trait colocalization algorithm we propsed
Colocalization  # Method to identify shared genetic signals
COLOC           # A pairwise colocalization method name
FineBoost       # Single trait fine-mapping algorithm we proposed
HyPrColoc       # Hypothesis Prioritization in multi-trait Colocalization method name
SuSiE           # Sum of Single Effects regression model

# Statistical and Genetic Terms
bim             # PLINK BIM variant information file
eQTL            # Expression Quantitative Trait Loci
GWAS            # Genome-Wide Association Study
INDELs          # Insertions and Deletions
LD              # Linkage Disequilibrium
ld              # Linkage Disequilibrium
MAF             # Minor Allele Frequency
maf             # Minor Allele Frequency
pvalue          # Statistical p-value
sQTL            # Splicing Quantitative Trait Loci
Sumstat         # Summary Statistics
sumstat         # Summary Statistics
sumstats        # Summary Statistics
xQTL            # Any molecular Quantitative Trait Loci

# Software, Platforms and Tools
Biobank         # Refer to UK Biobank, a large-scale biomedical database and research resource
Bioinformatics  # Computational biology field
bioinformatics  # Computational biology field
Codecov         # Code coverage testing tool
Conda           # Package and environment management system
GTEx            # Genotype-Tissue Expression project
Micromamba      # Lightweight Conda implementation
Nealelab        # Lab developing genetics GWAS summary statistics
PLINK           # Whole genome association analysis toolset
RAISS           # Summary-statistics imputation method
tabix           # Tool for indexing genomic data
UKBB            # UK Biobank dataset
YAML            # Human-readable configuration file format
medRxiv         # A preprint resource
pixi            # An environment manager
conda           # Package and environment management system
xz              # Compression format

# Researcher Names
Jager           # Philip L. de Jager
KK              # Kushal K. Dey
Mazumder        # Rahul Mazumder
Najar           # Cristian F. B. Najar
CFB             # Cristian F. B. Najar
YI              # Yang I. Li
et              # and more
al              # and more

# Technical Terms
changelog       # Release change log
cis             # Referring to nearby location of a regulatory element
chrom           # Chromosome
decayrate       # Decay rate, an input parameter in our package
doi             # Digital Object Identifier
func            # Function abbreviation used in parameter names
grey            # One color name in R
iteratively     # Performed through iterations
loglik          # Log-likelihood abbreviation used in parameter names
lfsr            # Local False Sign Rate
lth             # Lower threshold
modularity      # Property of network structure
omics           # Collective biological data fields
phenotypes      # Observable traits
pos             # Position in genome
precomputed     # Computed in advance
precomputes     # Computes in advance
probabilistically # Based on probability theory
qc              # Quality Control
rcond           # Reciprocal condition number
reconciliate    # Process of resolving discrepancies
repo            # Repository
rss             # Residual Sum of Squares
subsampled      # Analyzed using data subsets
uncolocalized   # Not showing colocalization
uCoS            # Trait-specific (uncolocalization) confidence set
ucos            # Trait-specific (uncolocalization) confidence set
VCP             # Variant colocalization probability
VPA             # Variant probability of association
vcp             # Variant colocalization probability
Xcorr           # Cross-correlation matrix
Recalibrate     # Process of adjusting statistical calibration
recalibrate     # Process of adjusting statistical calibration
recalibrated    # Process of adjusting statistical calibration
Colocalized     # Having undergone colocalization analysis
colocalize      # Having undergone colocalization analysis
colocalized     # Having undergone colocalization analysis
CoS             # Colocalization confidence set in our proposed ColocBoost method
NPC             # Normalization probability of colocalization in our proposed ColocBoost method
PIPs            # Posterior Inclusion Probabilities
SEL             # Single-effect learner in our proposed ColocBoost method
uS              # The number of uCoS
npc             # Normalization probability of colocalization in our proposed ColocBoost method
Pre             # Before
pre             # Before
jk              # Index used in ColocBoost
nd              # Second
