This package was removed from CRAN on 2023-01-10. Its history is shown below.

Reason: issues were not corrected in time

Details below reflect version 1.1.3, its last release before removal.

scImmuneGraph

1.1.3

Visualize the Basic Characteristics of Single-Cell Immune Repertoire

0packages depend

–downloads / year

–test coverage

–checks pass

Overview

About

Maintained by Fenfei Zhao1 releasesCRAN page ↗GitHub ↗

Statistics and visualization of the distribution, diversity and composition of clonotypes, the abundance and length distribution of CDR3, the respective abundance distribution of V and J genes, and the abundance of V-J gene pairs are the basic requirements for single-cell immune group analysis. 'scImmuneGraph' is designed to process data from 10x Genomics Chromium Immune Profiling for T cell receptor (TCR) and immunoglobulin (Ig) enrichment workflows.

Install

R (source archive)pak (dev)Ubuntu (r2u)

url <- "https://cran.r-project.org/src/contrib/Archive/scImmuneGraph/scImmuneGraph_1.1.3.tar.gz"
pkgFile <- "scImmuneGraph_1.1.3.tar.gz"
download.file(url, pkgFile)
install.packages(pkgFile, type = "source", repos = NULL)

This package is no longer on CRAN, so install.packages() cannot fetch it by name. This downloads the last archived source (1.1.3) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("zff-excellent/scImmuneGraph")

Development version from zff-excellent/scImmuneGraph. Installs pak first if it is not already available.

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-scimmunegraph

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

CRAN check results are not tracked yet.

Code health

Yes

Tests · ratio 0.01

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

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

Downloads

scImmuneGraph Releases R versions

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Also on104 r2u

Dependencies

Declared dependencies

19 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.0

Imports (16)

RColorBrewer scales ggplot2 cowplot tibble stringr tidyverse readr tidyr dplyr purrr gtools plyr forcats easypackages BiocStyle

LinkingTo (0)

none

Suggests (3)

rmarkdown knitr testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

Code & Tests

People & History

People (1)

Other (1)

Fenfei Zhao

Contributor

Package Timeline

1 release. R releases are shown for context.

R
R 4.3.0 released · 2023-04-21
archivedRemoved from CRAN
2023-01-10
issues were not corrected in time
R
R 4.2.0 released · 2022-04-22
1.1.3
2021-12-10
R
R 4.1.0 released · 2021-05-18

Package metadata

Total releases: 1
License: GPL (>= 2) OSI
Minimum R: ≥ 4.0
Bundled data: 658 KB / 2 files
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

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