R Observatory: Metrics for ttScreening version 1.8

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

ttScreening

1.8Package record

Genome-Wide DNA Methylation Sites Screening by Use of Training and Testing Samples

0packages depend

2.8Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Meredith RayCRAN page ↗

A screening process utilizing training and testing samples to filter out uninformative DNA methylation sites. Surrogate variables (SVs) of DNA methylation are included in the filtering process to explain unknown factor effects. This package also provides two screening functions for screening high-dimensional predictors when the events are rare. The firth method is called 'Rare-Screening' which employs a repeated random sampling with replacement and using linear modeling with Bayes adjustment. The Second method is called 'Firth-ttScreening' which uses 'ttScreening' method with additional Firth correction term in the maximum likelihood for the logistic regression model. These methods handle the high-dimensionality and low event rates.

Install

R (CRAN)Ubuntu (r2u)

install.packages("ttScreening", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-ttscreening

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 4.6 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-27
ERROR12 OK, 1 ERROR2026-06-21
OK13 OK2026-06-09

Show 11 earlier changesHide 11 earlier changes

ERROR12 OK, 1 ERROR2026-06-08
WARNING12 OK, 1 WARNING2026-06-07
OK13 OK2026-05-11
WARNING12 OK, 1 WARNING2026-05-10
OK13 OK2026-05-06
ERROR12 OK, 1 ERROR2026-05-04
OK14 OK2026-04-16
ERROR13 OK, 1 ERROR2026-04-15
OK14 OK2026-04-09
ERROR13 OK, 1 ERROR2026-04-07
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.8

READMENoVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 7includes a package overview page
Examples that run: 0%3 never run
Exported functions with examples: 50%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 71%

How these are measured

Downloads

2.8K

CRAN downloads in the past year

Rank #15,258 · ~8/day · ~236/mo

Releases R versions

Daily download trend is not available in this view yet.

28230 days

80490 days

2.8K1 year

Compare downloads with other packages →

Also on80 r2u

How downloads are counted

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Installing ttScreening adds 11 packages (5 with compiled code, 5.3 MB of source tarballs). Heaviest: brglm2 2.3 MB, colorspace 2.0 MB, matrixStats 207 KB. 2 more not on CRAN are not measured.

Depends (3)

matrixStats sva limma

Imports (6)

graphicsstatscorpcor simsalaparMASSbrglm2

LinkingTo (0)

none

Suggests (1)

mvtnorm

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (5)

Meredith Ray

Author, Maintainer since 1.1 (2013)

Mohammad Nahian Ferdous Abrar

Author · added in 1.8

Yu Jiang

Author · added in 1.8

Xin Tong

Author

Hongmei Zhang

Author

Previously maintained by Xin Tong (1.0).

Releases (9)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.8Latest
record
2026-01-30 · current release · diff ↗ ·
added 2 exports
Rare_Screening, firth_screening
unarchivedReturned to CRAN
2025-07-04
1.7
record
2025-07-04 · diff ↗
archivedRemoved from CRAN
2025-06-13
issues were not corrected despite reminders
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
1.6
record
2018-10-12 · diff ↗
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03

Show 9 earlier eventsHide 9 earlier events

R
R 3.2.0 released · 2015-04-16
1.5
record
2014-11-14 · diff ↗
1.4
record
2014-08-29 · diff ↗ ·
added 1 export
num.sv2
R
R 3.1.0 released · 2014-04-10
1.3
record
2014-02-28 · diff ↗
1.2
record
2013-10-08 · diff ↗
1.1
record
2013-10-06 · diff ↗
1.0
record
2013-10-05
R
R 3.0.0 released · 2013-04-03

Package metadata

First published: 2013-10-05
Total releases: 9 / 13 yrs
License: Artistic-2.0 OSI
Download size: 14 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("ttScreening")

Format

Ray, M., Abrar, M. N. F., Jiang, Y., Tong, X., & Zhang, H. (2026). ttScreening: Genome-Wide DNA Methylation Sites Screening by Use of Training and Testing Samples (Version 1.8) [Computer software]. https://doi.org/10.32614/CRAN.package.ttScreening

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for ttScreening version 1.8 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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