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Add a couple packages for statistical genetics #221

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30f4f69
add packages under the openmendel org
biona001 Dec 7, 2023
0a0fd8f
add a few of my own packages
biona001 Dec 7, 2023
12b9664
committing db.csv (and reorder 2 entries)
biona001 Dec 7, 2023
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1 change: 1 addition & 0 deletions AI.md
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+ [SimpleML.jl](https://github.com/aviks/SimpleML.jl) :: Textbook implementations of some Machine Learning Algorithms in Julia.
+ [SFA.jl](https://github.com/makokal/SFA.jl) :: Implementation of the standard SFA (Slow Feature Analysis) algorithm (both linear and non-linear signal expansion) in Julia.
+ [SoftConfidenceWeighted.jl](https://github.com/IshitaTakeshi/SoftConfidenceWeighted.jl) :: Exact Soft Confidence-Weighted Learning.
+ [SparseKmeansFeatureRanking.jl](https://github.com/kose-y/SparseKmeansFeatureRanking.jl) :: An efficient multi-threaded implementation of sparse K-means via feature ranking.
+ [Strada.jl](https://github.com/pcmoritz/Strada.jl) :: A deep learning library for Julia based on Caffe.
+ [SVMLightLoader.jl](https://github.com/IshitaTakeshi/SVMLightLoader.jl) :: Loader of svmlight / liblinear format files.
+ [JuliaTakingFittingAPIsSeriously](https://github.com/JuliaTakingFittingAPIsSeriously) :: proof of concept taking the APIs for statistics, machine learning and other infomatics.
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33 changes: 30 additions & 3 deletions Biology.md
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+ [BioMedQuery.jl](https://github.com/bcbi/BioMedQuery.jl) :: Utilities for interacting with different BioMedical Databases and APIs provided by the National Library of Medicine (NLM).
+ Link to Clinical research data management: https://github.com/svaksha/Julia.jl/blob/master/DataManagement.md
+ [OrbitTomography.jl](https://github.com/lstagner/OrbitTomography.jl).

+ [Thyrosim.jl](https://github.com/biona001/Thyrosim.jl) :: A thyroid hormone mechanistic model for predicting T4/T3/TSH dynamics.

----

# BIOSTATISTICS
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----

# GENOMICS
+ [ADMIXTURE.jl](https://github.com/OpenMendel/ADMIXTURE.jl) :: Julia wrapper of the popular ADMIXTURE program for estimating ancestry in a model-based manner from large autosomal SNP genotype data sets.
+ [BGEN.jl](https://github.com/OpenMendel/BGEN.jl) :: Routines for reading genotypes stored in Oxford BGEN format.
+ [BioAlignments.jl](https://github.com/BioJulia/BioAlignments.jl) :: Sequence alignment tools in BioJulia
+ [BioArgParse.jl](https://github.com/Ward9250/BioArgParse.jl) :: Extension to 'ArgParse.jl', enabling parsing of command line parameters to types in 'Bio.jl'.
+ [BioFeatures.jl](https://github.com/nw11/BioFeatures.jl).
+ [BioSeq.jl](https://github.com/BioJulia/BioSeq.jl) :: Julia's package for working on Bioinformatics with DNA, RNA and Protein Sequences.
+ [BismarkSummary.jl](https://github.com/nw11/BismarkSummary.jl) :: Basic summary of multiple Bismark runs.
+ [COSMIC.jl](https://github.com/haploxer/COSMIC.jl) :: Data analysis engine for [COSMIC](http://cancer.sanger.ac.uk/cosmic) written in Julia.
+ [EasyLD.jl](https://github.com/biona001/EasyLD.jl) :: Downloading and parsing Hail's LD (linkage disequilibrium) matrices.
+ [Ensemble.jl](https://github.com/farr/Ensemble.jl) :: Ensemble Samplers for Julia.
+ [FastaIO.jl](https://github.com/carlobaldassi/FastaIO.jl) :: Utilities to read/write FASTA format files in Julia.
+ [fastPHASE.jl](https://github.com/biona001/fastPHASE.jl) :: Julia wrapper of the popular fastPHASE genetics program, designed for haplotype reconstruction and estimating missing genotypes from population data.
+ [FusionDirect.jl](https://github.com/OpenGene/FusionDirect.jl) :: Detect gene fusion directly from raw fastq files.
+ [GeneticsMakie.jl](https://github.com/mmkim1210/GeneticsMakie.jl) :: High-performance genetics- and genomics- related data visualization using Makie.jl
+ [GenomeAnnotations.jl](https://github.com/nw11/GenomeAnnotations.jl) :: Manage Local Genome Annotation files.
+ [GenomeGraphs.jl](https://github.com/BioJulia/GenomeGraphs.jl) :: A modern genomics framework for julia
+ [GenomicTiles.jl](https://github.com/nw11/GenomicTiles.jl)
+ [Gillespie.jl](https://github.com/sdwfrost/Gillespie.jl) :: Stochastic Gillespie-type simulations using Julia.
+ [gtf-parse-off](https://github.com/dcjones/gtf-parse-off) :: Experiments with parsing gene transfer format (GTF).
+ [HaploADMIXTURE.jl](https://github.com/OpenMendel/HaploADMIXTURE.jl) :: Global ancestry inference by modeling haplotypes, supporting multithreading and GPUs.
+ [HTSLIB.jl](https://github.com/OpenGene/HTSLIB.jl) :: A julia wrapper of htslib for accessing common high-throughput sequencing data file formats such as BAM/SAM files.
+ [HyperNEAT.jl](https://github.com/kzahedi/HyperNEAT.jl) :: A generative encoding for evolving ANN based on the NeuroEvolution of Augmented Topologies (NEAT) algorithm for evolutionary computation.
+ [IntervalTrees.jl](https://github.com/BioJulia/IntervalTrees.jl) :: A data structure for efficient manipulation of sets of intervals.
+ [MendelAimSelection.jl](https://github.com/OpenMendel/MendelAimSelection.jl) :: Selecting SNPs that are most informative at predicting ancestry - the best Ancestry Informative Markers (AIMs).
+ [MendelBase.jl](https://github.com/OpenMendel/MendelBase.jl) :: contains the base functions of OpenMendel.
+ [MendelEstimateFrequencies.jl](https://github.com/OpenMendel/MendelEstimateFrequencies.jl) :: Likelihood-based estimation of allele frequencies.
+ [MendelGameteCompetition.jl](https://github.com/OpenMendel/MendelGameteCompetition.jl) :: Implements a gamete competition analysis, which is a generalization of the TDT analysis.
+ [MendelGeneDropping.jl](https://github.com/OpenMendel/MendelGeneDropping.jl) :: Julia package for performing gene dropping with several useful options for the output.
+ [MendelGeneticCounseling.jl](https://github.com/OpenMendel/MendelGeneticCounseling.jl) :: Risk calculations for genetic counseling problems.
+ [MendelKinship.jl](https://github.com/OpenMendel/MendelKinship.jl) :: Computes genetic kinship and other identity coefficients.
+ [MendelLocationScores.jl](https://github.com/OpenMendel/MendelLocationScores.jl) :: Mapping a trait via the method of Location Scores, i.e. multipoint linkage analysis.
+ [MendelSearch.jl](https://github.com/OpenMendel/MendelSearch.jl) :: Performs function optimizations permitting bounds and linear constraints to be imposed on parameters and computes asymptotic standard errors and correlations of parameter estimates.
+ [MendelTwoPointLinkage.jl](https://github.com/OpenMendel/MendelTwoPointLinkage.jl) :: Julia package for two-point linkage analysis.
+ [MerCounting.jl](https://github.com/BioJulia/MerCounting.jl) :: Kmer counting algorithms and count-data utilities for the BioJulia framework
+ [LCS.jl](https://github.com/WestleyArgentum/LCS.jl) :: A package for finding longest common and longest contiguous subsequences.
+ [OBC.jl](https://github.com/binarybana/OBC.jl) :: Optimal Bayesian classification for RNA-Seq data.
+ [OpenADMIXTURE.jl](https://github.com/OpenMendel/OpenADMIXTURE.jl) :: A faster, open-source reimplementation of the ADMIXTURE program for estimating global ancestry proportions.
+ [OpenGene.jl](https://github.com/OpenGene/OpenGene.jl) :: OpenGene core library in Julia.
+ [Pagel.jl](https://github.com/porterjamesj/Pagel.jl) :: Detect correlated evolution on phylogenies.
+ [Pathogen.jl](https://github.com/jangevaa/Pathogen.jl) :: Utilities to simulate and perform inference of disease dynamics.
+ [PedModule.jl](https://github.com/QTL-rocks/PedModule.jl) :: Geno-type pedigree module.
+ [PGENFiles.jl](https://github.com/OpenMendel/PGENFiles.jl) :: Routines for reading genotypes stored in PGEN (PLINK 2) format.
+ [Phylogenetics.jl](https://github.com/BioJulia/Phylogenetics.jl) :: The Julia package for analysis of evolution and phylogeny.
+ [PhyloNetworks.jl](https://github.com/crsl4/PhyloNetworks.jl) :: A Julia package for statistical inference, data manipulation and visualization of phylogenetic networks.
+ [PhyloTrees.jl](https://github.com/jangevaare/PhyloTrees.jl) :: Phylogenetic tree simulation.
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+ [PureSeq.jl](https://github.com/slundberg/PureSeq.jl) :: Code for the Pure-seq project.
+ [seqhax.jl](https://github.com/kdmurray91/seqhax.jl) :: yet another NGS command.
+ [SpeedDate.jl](https://github.com/Ward9250/SpeedDate.jl) :: A simple tool for the estimation of coalescence times between sequences.
+ [SnpArrays.jl](https://github.com/OpenMendel/SnpArrays.jl) :: provides utilities for handling compressed storage of binary PLINK formatted data.
+ [TimeTrees.jl](https://github.com/tgvaughan/TimeTrees.jl) :: Phylogenetic tree type for julia.
+ [VariantCall.jl](https://github.com/mgvel/VariantCall.jl).
+ [VariantCallFormat.jl](https://github.com/rasmushenningsson/VariantCallFormat.jl) :: Provides read/write functionality for VCF files as well as for its binary sister format BCF.
+ [VCFTools.jl](https://github.com/OpenMendel/VCFTools.jl) :: High level utility functions for working with VCF (.vcf or .vcf.gz) formatted files.
+ [XSim.jl](https://github.com/reworkhow/XSim.jl) :: A fast and user-friendly tool to simulate sequence data and complicated pedigree structures.
+ [YARS.jl](https://github.com/kzahedi/YARS.jl) :: YARS communication for RNA/proteins.


## GWAS
__Genome Wide Association Study (GWAS)__
+ [AlignmentStatistics.jl](https://github.com/DanielHoffmann32/AlignmentStatistics.jl) :: A package for statistical analyses of sequence alignments.
+ [GhostKnockoffGWAS.jl](https://github.com/biona001/GhostKnockoffGWAS) :: Performs a knockoff-based analysis of GWAS summary statistics data.
+ [JWAS.jl](https://github.com/reworkhow/JWAS.jl) :: An open-source software tool written in Julia for Bayesian multiple regression methods applied to genome-wide association studies and genomic prediction.
+ [MendelBase.jl](https://github.com/OpenMendel/MendelBase.jl) :: contains the base functions of OpenMendel.
+ [SnpArrays.jl](https://github.com/OpenMendel/SnpArrays.jl) :: provides utilities for handling compressed storage of biallelic SNP (Single-Nucleotide Polymorphism) data.
+ [MendelImpute.jl](https://github.com/OpenMendel/MendelImpute.jl) :: A fast data-driven method for genotype imputation, phasing, and local ancestry inference.
+ [MendelIHT.jl](https://github.com/OpenMendel/MendelIHT.jl) :: Implements the iterative hard thresholding (IHT) algorithm as a multiple regression approach for GWAS.
+ [MendelPlots.jl](https://github.com/OpenMendel/MendelPlots.jl) :: Generate Manhattan and QQ plots from GWAS.
+ [OrdinalGWAS.jl](https://github.com/OpenMendel/OrdinalGWAS.jl) :: GWAS for ordered categorial phenotypes.
+ [StatGenData.jl](https://github.com/dmbates/StatGenData.jl) :: Statistical analysis of genomic data.
+ [TrajGWAS.jl](https://github.com/OpenMendel/TrajGWAS.jl): GWAS for continuous longitudinal phenotypes using a modified linear mixed effects model.
+ [TraitSimulation.jl](https://github.com/OpenMendel/TraitSimulation.jl) :: A convenient tool for simulating phenotypes for unrelateds or families under a variety of supported models.
+ [VarianceComponentTest.jl](https://github.com/Tao-Hu/VarianceComponentTest.jl) :: A Julia package for performing exact variance component tests in genome-wide association study (GWAS).


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7 changes: 7 additions & 0 deletions Probability-Statistics.md
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Expand Up @@ -69,16 +69,22 @@ The [Markov Logic Network](https://en.wikipedia.org/wiki/Markov_logic_network)
+ [Lasso.jl](https://github.com/JuliaStats/Lasso.jl) :: Lasso solvers for linear and generalized linear models.
+ [Metida.jl](https://github.com/PharmCat/Metida.jl) :: Julia package for fitting mixed-effects models with flexible random/repeated covariance structure.
+ [MixedModels.jl](https://github.com/dmbates/MixedModels.jl) :: A Julia package for fitting (statistical) mixed-effects models.
+ [MultiResponseVarianceComponentModels.jl](https://github.com/Hua-Zhou/MultiResponseVarianceComponentModels.jl) :: Fitting and testing multivariate response variance components linear mixed models.
+ [NonNegLeastSquares.jl](https://github.com/ahwillia/NonNegLeastSquares.jl) :: Some nonnegative least squares solvers in Julia.
+ [OrdinalMultinomialModels.jl](https://github.com/OpenMendel/OrdinalMultinomialModels.jl) :: Fit ordered multinomial models, including proportional odds model and ordered Probit model as special cases.
+ [ParallelSparseRegression.jl](https://github.com/madeleineudell/ParallelSparseRegression.jl) :: A Julia library for parallel sparse regression, that implements solvers for regression problems including least squares, ridge regression, LASSO, non-negative least squares, and elastic net; and proposes to add fast methods to obtain regularization paths.
+ [QuantileRegression.jl](https://github.com/pkofod/QuantileRegressions.jl) :: Quantile regression in Julia.
+ [Regression.jl](https://github.com/lindahua/Regression.jl) :: Algorithms for regression analysis (e.g. linear regression and logistic regression).
+ [SparseRegression.jl](https://github.com/joshday/SparseRegression.jl) :: Statistical Models with Regularization in Pure Julia.
+ [VarianceComponentModels.jl](https://github.com/OpenMendel/VarianceComponentModels.jl) :: Utilities for fitting and testing variance component models.
+ [VCSEL.jl](https://github.com/juhkim111/VCSEL.jl) :: Variance components selection via Lasso, adaptive lasso, or MCP penalization.
+ [WiSER.jl](https://github.com/OpenMendel/WiSER.jl) :: A regression aproach for estimating the effects of predictors on the within-subject variation in a longitudinal setting

## [DENSITIES](https://en.wikipedia.org/wiki/Density_estimation)
+ [AverageShiftedHistograms.jl](https://github.com/joshday/AverageShiftedHistograms.jl) :: David Scott's Average Shifted Histogram density estimation.
+ [KernelDensity.jl](https://github.com/JuliaStats/KernelDensity.jl) :: Kernel density estimators for continuous variables.
+ [KernelEstimator.jl](https://github.com/panlanfeng/KernelEstimator.jl) :: A Julia package for nonparametric density estimation.
+ [QuasiCopula.jl](https://github.com/OpenMendel/QuasiCopula.jl): A Flexible Quasi-Copula Distribution for Statistical Modeling.

## [MULTIVARIATE](https://en.wikipedia.org/wiki/Category:Multivariate_statistics)
+ [LowRankModels.jl](https://github.com/madeleineudell/LowRankModels.jl) :: A Julia package for modeling and fitting generalized low rank models.
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+ [GaussDCA.jl](https://github.com/carlobaldassi/GaussDCA.jl) :: Multivariate Gaussian Direct Coupling Analysis for residue contact prediction in protein families.
+ [JointMoments.jl](https://github.com/tensorjack/JointMoments.jl) :: Tensors and statistics for joint central moments.
+ [KernSmooth.jl](https://github.com/lendle/KernSmooth.jl) :: A direct port of the R package KernSmooth, (v2.23-10.), carrying an unlimited license.
+ [Knockoffs.jl](https://github.com/biona001/Knockoffs.jl) :: Variable selection via the knockoff filter.
+ [PowerLaws.jl](https://github.com/johnybx/PowerLaws.jl) :: A Julia package for power laws distributions.
+ [PValueAdjust.jl](https://github.com/dirkschumacher/PValueAdjust.jl) :: P-value adjustment methods for multiple testing correction.
+ [Rmath.jl](https://github.com/JuliaStats/Rmath.jl) :: Archive of functions that emulate R's d-p-q-r functions for probability distributions.
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