ADAPTS

1.0.22

Automated Deconvolution Augmentation of Profiles for Tissue Specific Cells

1packages depend

5.2Kdownloads / year

–test coverage

0/13checks pass

Overview

About

Maintained by Samuel A DanzigerFirst published 2019-05-179 releasesCRAN 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.

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

Health

CRAN checks

13NOTE

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc
NOTE r-devel-linux-x86_64-fedora-clang
NOTE r-devel-linux-x86_64-fedora-gcc
NOTE r-devel-windows-x86_64
NOTE r-oldrel-macos-arm64
NOTE r-oldrel-macos-x86_64
NOTE r-oldrel-windows-x86_64
NOTE r-patched-linux-x86_64
NOTE r-release-linux-x86_64
NOTE r-release-macos-arm64
NOTE r-release-macos-x86_64
NOTE r-release-windows-x86_64

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

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-03-13
0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-03-12
0 OK · 13 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 111 wordsVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 94%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

5.2K

CRAN downloads in the past year

Rank #7,713 · ~14/day · ~430/mo

Releases R versions

Daily download trend is not available in this view yet.

45730 days

1.4K90 days

5.2K1 year

Compare downloads with other packages →

Also on253 r2u26 c2d4u

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

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

scMappR

Code & Tests

Code Composition

R 2,774 (63%)Rd 1,613 (37%)Other 30 (1%)

Code characteristics

Cyclomatic complexity: 5.0 median / 36 max

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

38 34 exported

Complexity

6.3 avg / 36 max

Call network

38 nodes / 42 edges

Call graph

Open call graph →

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Lowest coverage

Per-function coverage is not measured for this package yet.

Datasets

Bundled datasets · 2

Name	Class	Rows × Cols	Also ships in
LM22	data.frame	547 × 22	–
MGSM27	data.frame	601 × 27	–

People & History

People (0)

Author records are not tracked yet for this package.

Listed in earlier versions (1)

Samuel A Danziger

no longer listed · 0.9.14 to 1.0.22

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
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
2022-09-14 · current release · diff ↗
R
R 4.2.0 released · 2022-04-22
1.0.21
2021-10-05 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.0.6
2020-10-17 · diff ↗
1.0.5
2020-08-31 · diff ↗
1.0.3
2020-08-06 · diff ↗
R
R 4.0.0 released · 2020-04-24
0.9.26
2019-10-29 · diff ↗
0.9.21
2019-08-07 · diff ↗
0.9.20
2019-06-18 · diff ↗
0.9.14
2019-05-17

Show 1 earlier events

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
Minimum R: ≥ 3.3.0
Bundled data: 188 KB / 3 files
Download size: 4.6 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

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