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r-gmmat
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public |
Perform association tests using generalized linear mixed models (GLMMs) in genome-wide association studies (GWAS) and sequencing association studies. First, GMMAT fits a GLMM with covariate adjustment and random effects to account for population structure and familial or cryptic relatedness. For GWAS, GMMAT performs score tests for each genetic variant as proposed in Chen et al. (2016) <doi:10.1016/j.ajhg.2016.02.012>. For candidate gene studies, GMMAT can also perform Wald tests to get the effect size estimate for each genetic variant. For rare variant analysis from sequencing association studies, GMMAT performs the variant Set Mixed Model Association Tests (SMMAT) as proposed in Chen et al. (2019) <doi:10.1016/j.ajhg.2018.12.012>, including the burden test, the sequence kernel association test (SKAT), SKAT-O and an efficient hybrid test of the burden test and SKAT, based on user-defined variant sets.
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2025-04-08 |
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bioconductor-genesis
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public |
GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness
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2025-04-08 |
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bioconductor-seqarray
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public |
Data Management of Large-Scale Whole-Genome Sequence Variant Calls
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2025-04-08 |
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bioconductor-snprelate
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public |
Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data
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2025-04-08 |
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bioconductor-gdsfmt
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public |
R Interface to CoreArray Genomic Data Structure (GDS) Files
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2025-04-08 |
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bioconductor-cytolib
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public |
C++ infrastructure for representing and interacting with the gated cytometry data
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2025-04-08 |
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quantas
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public |
Tools for inference of gene transcript structure and quantification of gene expression and alternate splicing
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2025-04-08 |
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torch-spline-conv-gpu
|
public |
Implementation of the Spline-Based Convolution Operator of SplineCNN in PyTorch
|
2025-04-04 |
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torch-spline-conv
|
public |
Implementation of the Spline-Based Convolution Operator of SplineCNN in PyTorch
|
2025-04-04 |
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torch-sparse-gpu
|
public |
PyTorch Extension Library of Optimized Autograd Sparse Matrix Operations
|
2025-04-04 |
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torch-scatter-gpu
|
public |
PyTorch Extension Library of Optimized Scatter Operations
|
2025-04-04 |
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torch-cluster-gpu
|
public |
PyTorch Extension Library of Optimized Graph Cluster Algorithms
|
2025-04-03 |
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r-minque
|
public |
'This package offers three important components: (1) to construct a use-defined linear::
mixed model, (2) to employ one of linear mixed model approaches: minimum norm quadratic
- unbiased estimation (MINQUE) (Rao, 1971) for variance component estimation and random
- effect prediction; and (3) to employ a jackknife resampling technique to conduct
- various statistical tests. In addition, this package provides the function for model
- or data evaluations.This R package offers fast computations for large data sets
- "analyses for various irregular data structures.'"
|
2025-04-03 |
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r-fsusier
|
public |
Draft package for "Sum of Single Functions" method.
|
2025-04-03 |
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r-smashr
|
public |
An R package for smoothing & signal denoising using adaptive shrinkage.
|
2025-04-03 |
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torch-sparse
|
public |
PyTorch Extension Library of Optimized Autograd Sparse Matrix Operations
|
2025-04-03 |
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pegasusio
|
public |
PegasusIO is the IO package for Pegasus.
|
2025-04-03 |
|
pegasuspy
|
public |
An efficient Python analysis tool which scales to transcriptomes of millions of single cells.
|
2025-04-03 |
|
torch-scatter
|
public |
PyTorch Extension Library of Optimized Scatter Operations
|
2025-04-03 |
|
torch-cluster
|
public |
PyTorch Extension Library of Optimized Graph Cluster Algorithms
|
2025-04-03 |
|
poppler-utils
|
public |
Precompiled command-line utilities (based on Poppler) for manipulating PDF files and converting them to other formats.
|
2025-04-03 |
|
torchviz
|
public |
A small package to create visualizations of PyTorch execution graphs
|
2025-04-03 |
|
pywfa
|
public |
A python wrapper for wavefront alignment using WFA2-lib
|
2025-03-28 |
|
watershed-sv
|
public |
Watershed-SV extends Watershed to model the impact of rare SVs
|
2025-03-26 |
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r-pecotmr
|
public |
pecotmr implements pair-wise enrichment, colocalization, TWAS and Mendelian Randomization to integrate QTL and GWAS analysis based on a fine-mapped single effects model.
|
2025-03-26 |
|
scikit-misc
|
public |
Miscellaneous tools for scientific computing.
|
2025-03-25 |
|
pyfit-sne
|
public |
Python wrapper for FFT-accelerated Interpolation-based t-SNE (FIt-SNE) package.
|
2025-03-25 |
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r-plinkqc
|
public |
Genotyping arrays enable the direct measurement of an individuals genotype at thousands
of markers. 'plinkQC' facilitates genotype quality control for genetic association
studies as described by Anderson and colleagues (2010) <doi:10.1038/nprot.2010.116>.
It makes 'PLINK' basic statistics (e.g. missing genotyping rates per individual,
allele frequencies per genetic marker) and relationship functions accessible from
'R' and generates a per-individual and per-marker quality control report. Individuals
and markers that fail the quality control can subsequently be removed to generate
a new, clean dataset. Removal of individuals based on relationship status is optimised
to retain as many individuals as possible in the study.
|
2025-03-25 |
|
quantas_cu
|
public |
Tools for inference of gene transcript structure and quantification of gene expression and alternate splicing
|
2025-03-25 |
|
onepassword-cli
|
public |
CLI for 1Password password manager
|
2025-03-25 |
|
keepassxc
|
public |
KeePassXC is a cross-platform community-driven port of the Windows application “Keepass Password Safe”.
|
2025-03-25 |
|
botan
|
public |
Crypto library written in C++
|
2025-03-25 |
|
argon
|
public |
The password hash Argon2, winner of PHC
|
2025-03-25 |
|
password-store
|
public |
Stores, retrieves, generates, and synchronizes passwords securely
|
2025-03-25 |
|
dashlane-cli
|
public |
Dashlane CLI - Access your secrets in your terminal, servers and CI/CD
|
2025-03-25 |
|
bitwarden-cli
|
public |
A secure and free password manager for all of your devices.
|
2025-03-25 |
|
keepercommander
|
public |
Keeper Commander for Python 3
|
2025-03-25 |
|
aiortc
|
public |
An implementation of WebRTC and ORTC
|
2025-03-25 |
|
pylibsrtp
|
public |
Python wrapper around the libsrtp library
|
2025-03-25 |
|
libsrtp
|
public |
Library for SRTP (Secure Realtime Transport Protocol)
|
2025-03-25 |
|
splicetransformer
|
public |
SpliceTransformer(SpTransformer) is a deep learning tool to predict tissue specific splicing site from pre-mRNA sequence
|
2025-03-25 |
|
splicebert
|
public |
Primary RNA sequence model
|
2025-03-25 |
|
absplice
|
public |
Invoke py.test as distutils command with dependency resolution
|
2025-03-25 |
|
cyvcf2
|
public |
A cython wrapper around htslib built for fast parsing of Variant Call Format (VCF) files
|
2025-03-25 |
|
splicemap
|
public |
Invoke py.test as distutils command with dependency resolution
|
2025-03-25 |
|
fastbetabino3
|
public |
Superfast betabinomial fit implemented in Cython
|
2025-03-25 |
|
r-blipr
|
public |
A Bayesian Linear Program for resolution-adaptive signal detection
|
2025-03-25 |
|
r-rcbc
|
public |
An R interface to the CBC solver for mixed-integer linear programs.
|
2025-03-25 |
|
r-scalespikeslab
|
public |
A scalable Gibbs sampling implementation for high dimensional Bayesian regression
with the continuous spike-and-slab prior. Niloy Biswas, Lester Mackey and Xiao-Li
Meng, "Scalable Spike-and-Slab" (2022) <arXiv:2204.01668>.
|
2025-03-25 |
|
r-truncatednormal
|
public |
A collection of functions to deal with the truncated univariate and multivariate normal
and Student distributions, described in Botev (2017) <doi:10.1111/rssb.12162> and
Botev and L'Ecuyer (2015) <doi:10.1109/WSC.2015.7408180>.
|
2025-03-25 |
