smfishHmrf

0.1

Hidden Markov Random Field for Spatial Transcriptomic Data

0packages depend

3Kdownloads / year

–test coverage

11/13checks pass

Overview

About

Maintained by Qian ZhuFirst published 2020-11-031 releasesCRAN page ↗Bitbucket ↗

Discovery of spatial patterns with Hidden Markov Random Field. This package is designed for spatial transcriptomic data and single molecule fluorescent in situ hybridization (FISH) data such as sequential fluorescence in situ hybridization (seqFISH) and multiplexed error-robust fluorescence in situ hybridization (MERFISH). The methods implemented in this package are described in Zhu et al. (2018) doi:10.1038/nbt.4260.

Install

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

install.packages("smfishHmrf", 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-smfishhmrf

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

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-smfishHmrf

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# 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-smfishHmrf

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: 1.4 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-05-10
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
WARNING2026-05-09
11 OK · 1 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 323 wordsVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 97%
Return-value docs: 50%
References docs: 23%

Downloads

CRAN downloads in the past year

Rank #12,388 · ~8/day · ~248/mo

Releases R versions

Daily download trend is not available in this view yet.

24930 days

86290 days

3K1 year

Compare downloads with other packages →

Also on400 r2u28 autocran

Repository

Bitbucket ↗ qzhudfci/smfishhmrf-r

Repository practices

Upstream repositoryBeta

Repository bitbucket.org/qzhudfci/smfishhmrf-r is linked, but repository-practices checks have not run for it yet. Checks are GitHub-only for now.

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

3 external dependencies (excludes base and recommended)

Depends (3)

R >= 3.5.0pracma fs

Imports (1)

Rdpack

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

R 942 (52%)Rd 749 (41%)C 123 (7%)

Code characteristics

Cyclomatic complexity: 2.0 median / 9 max

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

31 10 exported

Complexity

2.9 avg / 9 max

Call network

31 nodes / 30 edges

Call graph

Open call graph →

Loading call graph…

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.

Listed in earlier versions (2)

Guo-Cheng Yuan

no longer listed · 0.1

Qian Zhu

no longer listed · 0.1

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.1Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2020-11-03
Total releases: 1 / 6 yrs
License: GPL
Minimum R: ≥ 3.5.0
Bundled data: 483 KB / 1 file
Download size: 636 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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