R Observatory: Metrics for SMDIC version 0.1.6

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

SMDIC

0.1.6Package record

Identification of Somatic Mutation-Driven Immune Cells

0packages depend

3.4Kdownloads / year

–test coverage

12/13flavors OK

Overview

About

Maintained by Junwei HanCRAN page ↗

A computing tool is developed to automated identify somatic mutation-driven immune cells. The operation modes including: i) inferring the relative abundance matrix of tumor-infiltrating immune cells and integrating it with a particular gene mutation status, ii) detecting differential immune cells with respect to the gene mutation status and converting the abundance matrix of significant differential immune cell into two binary matrices (one for up-regulated and one for down-regulated), iii) identifying somatic mutation-driven immune cells by comparing the gene mutation status with each immune cell in the binary matrices across all samples, and iv) visualization of immune cell abundance of samples in different mutation status..

Install

R (CRAN)Ubuntu (r2u)

install.packages("SMDIC", 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-smdic

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

1ERROR12OK

Check messages

ERRORpackage dependenciesr-patched-linux-x86_64

Package required but not available: ‘GSVA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

CRAN check page ↗

Slowest check: 10.5 min · r-oldrel-windows-x86_64

Status changes

ERROR12 OK, 1 ERROR2026-10-15
OK13 OK2026-09-24
ERROR12 OK, 1 ERROR2026-09-17
OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07

Show 15 earlier changesHide 15 earlier changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-07-26
ERROR12 OK, 1 ERROR2026-07-19
OK13 OK2026-06-27
ERROR12 OK, 1 ERROR2026-06-21
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-10
ERROR12 OK, 1 ERROR2026-05-03
OK13 OK2026-04-30
ERROR13 OK, 1 ERROR2026-04-09
OK14 OK2026-03-16
ERROR13 OK, 1 ERROR2026-03-13
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.6

READMEYes · 159 wordsVignettesYes · 1 · dynamicNEWSNoCitation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 16includes a package overview page
Examples that run: 100%9 run in a plain check
Exported functions with examples: 90%
Documented parameters: 97%
Return-value docs: 60%
Help pages citing references: 38%

Vignettes (1)

SMDIC HTML

How these are measured

Downloads

3.4K

CRAN downloads in the past year

Rank #10,135 · ~9/day · ~284/mo

Releases R versions

Daily download trend is not available in this view yet.

35430 days

1K90 days

3.4K1 year

Compare downloads with other packages →

Also on116 r2u

How downloads are counted

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Installing SMDIC adds 113 packages (62 with compiled code, 100 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, bslib 5.6 MB. 4 more not on CRAN are not measured.

Depends (2)

R >= 4.3.0GSVA

Imports (14)

samr e1071parallelpreprocessCore pheatmap maftoolsgrDevicessurvivalsurvminerMASSpracmastatsRColorBrewer backports

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown R.utils

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (2)

Junwei Han

Maintainer since 0.1.0 (2020)

Baotong Zheng

Author

Releases (7)

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
0.1.6Latest
record
2024-10-16 · current release · diff ↗
R
R 4.4.0 released · 2024-04-24
0.1.5
record
2024-01-12 · diff ↗
0.1.4
record
2023-08-29 · diff ↗
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
unarchivedReturned to CRAN
2020-11-13
0.1.3
record
2020-11-13 · diff ↗
archivedRemoved from CRAN
2020-10-02
check issues were not corrected in time
0.1.2
record
2020-07-05 · diff ↗
0.1.1
record
2020-06-21 · diff ↗
0.1.0
record
2020-06-16
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-06-16
Total releases: 7 / 6 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 4.3.0
Bundled data: 1.9 MB / 2 files
Download size: 3.3 MB

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' entry:

citation("SMDIC")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.3389/fcell.2021.715275.

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 SMDIC version 0.1.6 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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