lfproQC

1.4.3

Quality Control for Label-Free Proteomics Expression Data

0packages depend

2.6Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Kabilan SFirst published 2024-05-238 releasesCRAN page ↗GitHub ↗

Label-free bottom-up proteomics expression data is often affected by data heterogeneity and missing values. Normalization and missing value imputation are commonly used techniques to address these issues and make the dataset suitable for further downstream analysis. This package provides an optimal combination of normalization and imputation methods for the dataset. The package utilizes three normalization methods and three imputation methods.The statistical evaluation measures named pooled co-efficient of variance, pooled estimate of variance and pooled median absolute deviation are used for selecting the best combination of normalization and imputation method for the given dataset. The user can also visualize the results by using various plots available in this package. The user can also perform the differential expression analysis between two sample groups with the function included in this package. The chosen three normalization methods, three imputation methods and three evaluation measures were chosen for this study based on the research papers published by Välikangas et al. (2016) doi:10.1093/bib/bbw095, Jin et al. (2021) doi:10.1038/s41598-021-81279-4 and Srivastava et al. (2023) doi:10.2174/1574893618666230223150253.This work has published by Sakthivel et al. (2025) doi:10.1021/acs.jproteome.4c00552.

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("lfproQC", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

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

Development version from kabilansbio/lfproQC. 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-lfproqc

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

13OK

Slowest check: 2.1 min · r-devel-linux-x86_64-fedora-clang

Code health

None

Tests · ratio 0.00

not tracked

Coverage

90%

Documentation · exports

Dependencies · direct

Check history

OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 88 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 0% structuredCode of conductNoContributing guideNo

Examples that run: 78%
Documented parameters: 100%
Return-value docs: 100%
References docs: 7%

Downloads

2.6K

CRAN downloads in the past year

Rank #12,095 · ~7/day · ~215/mo

Releases R versions

Daily download trend is not available in this view yet.

19130 days

88290 days

2.6K1 year

Compare downloads with other packages →

Also on118 r2u

Repository

GitHub ↗ kabilansbio/lfproqc

1Stars

0Forks

0Open issues

0Open PRs

0Releases

31Commits

1Contributors

31 commits · Last activity 2026-05-06

Stars over time

2025-05-07 · 12026-07-07 · 1

Repository practices

Upstream repositoryBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/kabilansbio/lfproqc on 2026-07-19.

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

20 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.2

Imports (17)

VIM dplyr limma matrixStats pcaMethods vsn reshape2 laeken ggplot2 Hmisc reshapestatstidyr magrittr plotlyMASStidyselect

LinkingTo (0)

none

Suggests (5)

knitr plyr rmarkdown testthat tibble

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (9)

Maintainer (1)

Kabilan S

Author, Maintainer

Authors (3)

Kabilan S

Author, Maintainer

Dr Shashi Bhushan Lal

Author, Thesis advisor

Dr Sudhir Srivastava

Author, Thesis advisor

Contributors (2)

Dr Girish Kumar Jha

Contributor

Dr Sharanbasappa

Contributor · added in 1.4.2

Other (4)

Dr Dwijesh Chandra Mishra

Thesis advisor · added in 1.4.3

Dr Krishna Kumar Chaturvedi

Thesis advisor

Dr Ramasubramanian V

Thesis advisor

Dr Yasin Jeshima K

Thesis advisor

Package Timeline

8 releases. Pick two to compare their code metrics. R releases are shown for context.

1.4.3Latest
2026-05-06 · current release · diff ↗
1.4.2
2026-05-01 · diff ↗
R
R 4.6.0 released · 2026-04-24
1.4.1
2025-07-03 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.4.0
2024-10-10 · diff ↗
1.3.0
2024-09-30 · diff ↗
0.3.0
2024-09-13 · diff ↗
0.2.0
2024-09-06 · diff ↗
0.1.0
2024-05-23
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2024-05-23
Total releases: 8 / 2 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.2
Bundled data: 104 KB / 4 files
Download size: 1.5 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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