R Observatory: Metrics for ttScreening version 1.8

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

ttScreening

1.8

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

0packages depend

2.6Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Meredith RayFirst published 2013-10-059 releasesCRAN 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.

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

Health

CRAN checks

13OK

Slowest check: 4.7 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

9

Dependencies · direct

Check history

OK2026-08-04
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-27
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-21
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 11 earlier snapshots

ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
WARNING2026-06-07
12 OK · 0 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE
OK2026-05-11
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
WARNING2026-05-10
12 OK · 0 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE
OK2026-05-06
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-05-04
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-16
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-15
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-09
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-07
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 0%
Documented parameters: 100%
Return-value docs: 100%
References docs: 71%

Downloads

2.6K

CRAN downloads in the past year

Rank #17,536 · ~7/day · ~219/mo

Releases R versions

Daily download trend is not available in this view yet.

16630 days

63190 days

2.6K1 year

Compare downloads with other packages →

Also on113 r2u

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

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.

Code & Tests

People & History

People (5)

Maintainer (1)

Meredith Ray

Author, Maintainer

Authors (5)

Meredith Ray

Author, Maintainer

Mohammad Nahian Ferdous Abrar

Author · added in 1.8

Yu Jiang

Author · added in 1.8

Xin Tong

Author

Hongmei Zhang

Author

Package Timeline

9 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.8Latest
2026-01-30 · current release · diff ↗
1.7
2025-07-04 · diff ↗
unarchivedReturned to CRAN
2025-07-04
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
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 events

R
R 3.2.0 released · 2015-04-16
1.5
2014-11-14 · diff ↗
1.4
2014-08-29 · diff ↗
R
R 3.1.0 released · 2014-04-10
1.3
2014-02-28 · diff ↗
1.2
2013-10-08 · diff ↗
1.1
2013-10-06 · diff ↗
1.0
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
Installed size: not tracked yet
With dependencies: not tracked yet

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 is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 v2026-08-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →