Showing 6 of total 6 results (show query)
bioc
OUTRIDER:OUTRIDER - OUTlier in RNA-Seq fInDER
Identification of aberrant gene expression in RNA-seq data. Read count expectations are modeled by an autoencoder to control for confounders in the data. Given these expectations, the RNA-seq read counts are assumed to follow a negative binomial distribution with a gene-specific dispersion. Outliers are then identified as read counts that significantly deviate from this distribution. Furthermore, OUTRIDER provides useful plotting functions to analyze and visualize the results.
Maintained by Christian Mertes. Last updated 5 months ago.
immunooncologyrnaseqtranscriptomicsalignmentsequencinggeneexpressiongeneticscount-datadiagnosticsexpression-analysismendelian-geneticsoutlier-detectionrna-seqopenblascpp
50 stars 9.07 score 110 scripts 1 dependents
drj001
ASMap:Linkage Map Construction using the MSTmap Algorithm
Functions for Accurate and Speedy linkage map construction, manipulation and diagnosis of Doubled Haploid, Backcross and Recombinant Inbred 'R/qtl' objects. This includes extremely fast linkage map clustering and optimal marker ordering using 'MSTmap' (see Wu et al.,2008).
Maintained by Julian Taylor. Last updated 5 months ago.
2 stars 6.73 score 79 scriptsbioc
iSEEde:iSEE extension for panels related to differential expression analysis
This package contains diverse functionality to extend the usage of the iSEE package, including additional classes for the panels or modes facilitating the analysis of differential expression results. This package does not perform differential expression. Instead, it provides methods to embed precomputed differential expression results in a SummarizedExperiment object, in a manner that is compatible with interactive visualisation in iSEE applications.
Maintained by Kevin Rue-Albrecht. Last updated 5 months ago.
softwareinfrastructuredifferentialexpressionbioconductorhacktoberfestiseeu
1 stars 5.38 score 15 scripts
devpsylab
petersenlab:A Collection of R Functions by the Petersen Lab
A collection of R functions that are widely used by the Petersen Lab. Included are functions for various purposes, including evaluating the accuracy of judgments and predictions, performing scoring of assessments, generating correlation matrices, conversion of data between various types, data management, psychometric evaluation, extensions related to latent variable modeling, various plotting capabilities, and other miscellaneous useful functions. By making the package available, we hope to make our methods reproducible and replicable by others and to help others perform their data processing and analysis methods more easily and efficiently. The codebase is provided in Petersen (2025) <doi:10.5281/zenodo.7602890> and on 'CRAN': <doi: 10.32614/CRAN.package.petersenlab>. The package is described in "Principles of Psychological Assessment: With Applied Examples in R" (Petersen, 2024, 2025) <doi:10.1201/9781003357421>, <doi:10.25820/work.007199>, <doi:10.5281/zenodo.6466589>.
Maintained by Isaac T. Petersen. Last updated 1 months ago.
data-analysisdata-analysis-in-rdata-managementpsychometrics
1 stars 4.10 score 1 scripts
tdjorgensen
simsem:SIMulated Structural Equation Modeling
Provides an easy framework for Monte Carlo simulation in structural equation modeling, which can be used for various purposes, such as such as model fit evaluation, power analysis, or missing data handling and planning.
Maintained by Terrence D. Jorgensen. Last updated 4 years ago.
3.40 score 276 scriptsbioc
cpvSNP:Gene set analysis methods for SNP association p-values that lie in genes in given gene sets
Gene set analysis methods exist to combine SNP-level association p-values into gene sets, calculating a single association p-value for each gene set. This package implements two such methods that require only the calculated SNP p-values, the gene set(s) of interest, and a correlation matrix (if desired). One method (GLOSSI) requires independent SNPs and the other (VEGAS) can take into account correlation (LD) among the SNPs. Built-in plotting functions are available to help users visualize results.
Maintained by Caitlin McHugh. Last updated 5 months ago.
geneticsstatisticalmethodpathwaysgenesetenrichmentgenomicvariation
3.30 score 3 scripts