R Observatory: Metrics for ADAPTS version 1.0.22

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

ADAPTS

1.0.22Package record

Automated Deconvolution Augmentation of Profiles for Tissue Specific Cells

1packages depend

5.5Kdownloads / year

–test coverage

0/13flavors OK

Overview

About

Maintained by Samuel A DanzigerCRAN page ↗

Tools to construct (or add to) cell-type signature matrices using flow sorted or single cell samples and deconvolve bulk gene expression data. Useful for assessing the quality of single cell RNAseq experiments, estimating the accuracy of signature matrices, and determining cell-type spillover. Please cite: Danziger SA et al. (2019) ADAPTS: Automated Deconvolution Augmentation of Profiles for Tissue Specific cells doi:10.1371/journal.pone.0224693.

Install

R (CRAN)Ubuntu (r2u)

install.packages("ADAPTS", 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-adapts

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

13NOTE

Check messages

NOTERd filesr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64

checkRd: (-1) SVMDECON.Rd:23: Lost braces; missing escapes or markup?
    23 | and the best result from three values of v = {0.25, 0.5, 0.75}
       |                                              ^

NOTECRAN incoming feasibilityr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Maintainer: ‘Samuel A Danziger <sam.danziger@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = c("Samuel", "A"),
                    family = "Danziger",
                    role = c("aut", "cre"),
                    email = "sam.danziger@gmail.com")
as necessary.

CRAN check page ↗

Slowest check: 2.2 min · r-devel-windows-x86_64

Status changes

NOTE13 NOTENow
NOTE14 NOTE2026-03-13
ERROR13 NOTE, 1 ERROR2026-03-12
NOTE14 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.22

READMEYes · 111 wordsVignettesYes · 5 · staticNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 40
Examples that run: 94%33 run in a plain check · 2 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 94%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (5)

How these are measured

Downloads

5.5K

CRAN downloads in the past year

Rank #4,692 · ~15/day · ~454/mo

Releases R versions

Daily download trend is not available in this view yet.

64430 days

1.8K90 days

5.5K1 year

Compare downloads with other packages →

Also on280 r2u62 c2d4u

How downloads are counted

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Installing ADAPTS adds 38 packages (19 with compiled code, 19 MB of source tarballs). Heaviest: glmnet 2.7 MB, Rcpp 1.8 MB, RcppEigen 1.7 MB. 2 more not on CRAN are not measured.

Depends (1)

R >= 3.3.0

Imports (12)

missForest e1071 ComICS pheatmap doParallelutilsquantmod preprocessCore pcaMethods foreach nnls ranger

LinkingTo (0)

none

Suggests (3)

R.rsp DeconRNASeq WGCNA

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Imports 1

Depends, Imports or LinkingTo, most downloaded first

scMappR

How these are counted

Code & Tests

Datasets

People & History

People (from the free-text Author field) (1)

Samuel A Danziger

Maintainer since 0.9.14 (2019)

Releases (9)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
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
1.0.22Latest
record
2022-09-14 · current release · diff ↗
R
R 4.2.0 released · 2022-04-22
1.0.21
record
2021-10-05 · diff ↗ ·
added 1 export
matrixToGenelist
R
R 4.1.0 released · 2021-05-18
1.0.6
record
2020-10-17 · diff ↗ ·
added 1 export
meanResults
1.0.5
record
2020-08-31 · diff ↗ ·
added 2 exports
loopTillConvergence, testAllSigMatrices
1.0.3
record
2020-08-06 · diff ↗ ·
added 9 exports
buildSeed, calcAcc, gListFromRF, getF1mcc, plotKappas, scSample, shrinkByKappa, shrinkSigMatrix, splitSCdata
R
R 4.0.0 released · 2020-04-24
0.9.26
record
2019-10-29 · diff ↗ ·
added 1 export
estCellPercent
0.9.21
record
2019-08-07 · diff ↗
0.9.20
record
2019-06-18 · diff ↗ ·
removed 2 exports
heirarchicalClassify, heirarchicalSplit

added 3 exports
estCellPercent.nnls, hierarchicalClassify, hierarchicalSplit
0.9.14
record
2019-05-17

Show 1 earlier eventHide 1 earlier event

R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-05-17
Total releases: 9 / 7 yrs
License: MIT + file LICENSE OSI
Copyright: Bristol-Myers Squibb
Minimum R: ≥ 3.3.0
Bundled data: 188 KB / 3 files
Download size: 4.6 MB

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("ADAPTS")

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 ADAPTS version 1.0.22 [Data set]. HJJB, LLC. Data release v2026-10-20. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-20, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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