Showing 4 of total 4 results (show query)
hturner
BradleyTerry2:Bradley-Terry Models
Specify and fit the Bradley-Terry model, including structured versions in which the parameters are related to explanatory variables through a linear predictor and versions with contest-specific effects, such as a home advantage.
Maintained by Heather Turner. Last updated 6 years ago.
bradley-terry-modelspaired-comparisonsstatistical-models
21 stars 8.10 score 172 scripts 1 dependents
bioc
DRIMSeq:Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq
The package provides two frameworks. One for the differential transcript usage analysis between different conditions and one for the tuQTL analysis. Both are based on modeling the counts of genomic features (i.e., transcripts) with the Dirichlet-multinomial distribution. The package also makes available functions for visualization and exploration of the data and results.
Maintained by Malgorzata Nowicka. Last updated 5 months ago.
immunooncologysnpalternativesplicingdifferentialsplicinggeneticsrnaseqsequencingworkflowstepmultiplecomparisongeneexpressiondifferentialexpression
6.91 score 136 scripts 2 dependents
deploid-dev
DEploid:Deconvolute Mixed Genomes with Unknown Proportions
Traditional phasing programs are limited to diploid organisms. Our method modifies Li and Stephens algorithm with Markov chain Monte Carlo (MCMC) approaches, and builds a generic framework that allows haplotype searches in a multiple infection setting. This package is primarily developed as part of the Pf3k project, which is a global collaboration using the latest sequencing technologies to provide a high-resolution view of natural variation in the malaria parasite Plasmodium falciparum. Parasite DNA are extracted from patient blood sample, which often contains more than one parasite strain, with unknown proportions. This package is used for deconvoluting mixed haplotypes, and reporting the mixture proportions from each sample.
Maintained by Joe Zhu. Last updated 2 months ago.
deconvoluting-mixed-genomeshmmmalariamcmcparasitesphasingunknown-proportionszlibcpp
1 stars 4.99 score 39 scripts
shajoezhu
DEploid.utils:'DEploid' Data Analysis and Results Interpretation
'DEploid' (Zhu et.al. 2018 <doi:10.1093/bioinformatics/btx530>) is designed for deconvoluting mixed genomes with unknown proportions. Traditional phasing programs are limited to diploid organisms. Our method modifies Li and Stephen’s algorithm with Markov chain Monte Carlo (MCMC) approaches, and builds a generic framework that allows haloptype searches in a multiple infection setting. This package provides R functions to support data analysis and results interpretation.
Maintained by Joe Zhu. Last updated 4 months ago.
2.18 score 1 dependents