cellOrigins

0.1.3

Finds RNASeq Source Tissues Using In Situ Hybridisation Data

0packages depend

2.4Kdownloads / year

–test coverage

11/13checks pass

Overview

About

Maintained by David MolnarFirst published 2020-06-051 releasesCRAN page ↗

Finds the most likely originating tissue(s) and developmental stage(s) of tissue-specific RNA sequencing data. The package identifies both pure transcriptomes and mixtures of transcriptomes. The most likely identity is found through comparisons of the sequencing data with high-throughput in situ hybridisation patterns. Typical uses are the identification of cancer cell origins, validation of cell culture strain identities, validation of single-cell transcriptomes, and validation of identity and purity of flow-sorting and dissection sequencing products.

Install

R (CRAN)Ubuntu (r2u)openSUSE (OBS)

install.packages("cellOrigins", 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-cellorigins

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

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-cellOrigins

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

2NOTE11OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 54 s · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

None

Vignettes

README

Dependencies · direct

Check history

NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Downloads

2.4K

CRAN downloads in the past year

Rank #19,020 · ~7/day · ~199/mo

Releases R versions

Daily download trend is not available in this view yet.

27530 days

62190 days

2.4K1 year

Compare downloads with other packages →

Also on296 r2u24 autocran

Dependencies

Declared dependencies

1 external dependency (excludes base and recommended)

Depends (0)

none

Imports (1)

iterpc

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

Rd 554 (77%)R 167 (23%)

Code characteristics

Object systems

S32

Cyclomatic complexity: 1.0 median / 3 max

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

12 0 exported

Complexity

1.7 avg / 3 max

Call network

12 nodes / 3 edges

Test coverage has not been measured for this package yet; nodes fall back to a neutral fill.

Call graph

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Lowest coverage

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

People & History

People (0)

Author records are not tracked yet for this package.

Release timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.1.3Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2020-06-05
Total releases: 1 / 6 yrs
License: CC BY-NC-SA 4.0
Bundled data: 52 KB / 1 file
Download size: 323 KB
Installed size: not tracked yet
With dependencies: not tracked yet