Package: OutSeekR 1.0.0

OutSeekR: Statistical Approach to Outlier Detection in RNA-Seq and Related Data

An approach to outlier detection in RNA-seq and related data based on five statistics. 'OutSeekR' implements an outlier test by comparing the distributions of these statistics in observed data with those of simulated null data.

Authors:Jee Yun Han [aut], John Sahrmann [aut], Jaron Arbet [ctb], Paul Boutros [aut, cre, cph]

OutSeekR_1.0.0.tar.gz
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OutSeekR.pdf |OutSeekR.html✨
OutSeekR/json (API)
NEWS

# Install 'OutSeekR' in R:

install.packages('OutSeekR', repos = c('https://pboutros.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

example.data.for.calculate.p.values - Example.data.for.calculate.p.values
outliers - Example data set for outlier testing

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.00 score 2 scripts 519 downloads 11 exports 18 dependencies

Last updated 3 months agofrom:d264f12af4. Checks:8 OK. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Feb 18 2025
R-4.5-win	OK	Feb 18 2025
R-4.5-mac	OK	Feb 18 2025
R-4.5-linux	OK	Feb 18 2025
R-4.4-win	OK	Feb 18 2025
R-4.4-mac	OK	Feb 18 2025
R-4.3-win	OK	Feb 18 2025
R-4.3-mac	OK	Feb 18 2025

Exports:calculate.p.values calculate.residuals detect.outliers identify.bic.optimal.data.distribution identify.bic.optimal.residuals.distribution kmeans.fraction outlier.detection.cosine quantify.outliers simulate.null trim.sample zrange

Dependencies:codetools digest future future.apply gamlss gamlss.data gamlss.dist globals lattice listenv lsa MASS Matrix nlme parallelly SnowballC survival truncnorm

Introduction to OutSeekR

Rendered fromintroduction.Rmdusingknitr::rmarkdownon Feb 18 2025.

Last update: 2024-11-19
Started: 2024-11-19

Citation

Readme and manuals

Help Manual

Help page	Topics
Calculate p-values	calculate.p.values
Calculate residuals	calculate.residuals
Detect outliers	detect.outliers
example.data.for.calculate.p.values	example.data.for.calculate.p.values
Identify optimal distribution of data	identify.bic.optimal.data.distribution
Identify optimal distribution of residuals	identify.bic.optimal.residuals.distribution
k-means fraction	kmeans.fraction
Cosine similarity	outlier.detection.cosine
Example data set for outlier testing	outliers
Compute quantities for outlier detection	quantify.outliers
Simulate from a null distribution	simulate.null
Trim a vector of numbers	trim.sample
Range of z-scores	zrange