Package: repli 0.99.0

Dick Zijlmans

repli: Replicate-based Imputation for Randomly Missing Data in Quantitative Proteomics

Implements replicate-based imputation for missing at random (MAR) values in proteomics data. The method leverages existing measurements from other replicates to determine imputation parameters (mean of observed values and global standard deviation).

Authors:Dick Zijlmans [aut, cre]

repli_0.99.0.tar.gz
repli_0.99.0.zip(r-4.7-any)repli_0.99.0.zip(r-4.6-any)repli_0.99.0.zip(r-4.5-any)
repli_0.99.0.tgz(r-4.6-any)repli_0.99.0.tgz(r-4.5-any)
repli_0.99.0.tar.gz(r-4.7-any)repli_0.99.0.tar.gz(r-4.6-any)
repli_0.99.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
repli/json (API)

# Install 'repli' in R:

install.packages('repli', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/biocstaging/repli/issues

Datasets:

example_dataset - Example Proteomics Dataset
example_se - Example Proteomics SummarizedExperiment

On CRAN:

proteomics massspectrometry software

3.18 score 7 exports 36 dependencies

Last updated from:65bb55f532. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	175
linux-devel	OK	219
source / vignettes	OK	277
linux-release	OK	174
macos-release	OK	134
macos-oldrel	OK	149
windows-devel	OK	2190
windows-release	OK	2080
windows-oldrel	OK	2098
wasm-release	OK	143

Exports:%>%impute_replicate impute_replicate_mixed_se impute_replicate_se prepare_imputation_data prepare_imputation_data_se reconstruct_se

Dependencies:abind Biobase BiocGenerics cli cpp11 DelayedArray dplyr generics GenomicRanges glue IRanges lattice lifecycle magrittr Matrix MatrixGenerics matrixStats pillar pkgconfig purrr R6 rlang S4Arrays S4Vectors Seqinfo SparseArray stringi stringr SummarizedExperiment tibble tidyr tidyselect utf8 vctrs withr XVector

Getting started with replicate-based imputation

Rendered fromrepli.Rmdusingknitr::rmarkdown

Last update: 2026-11-12
Started: 2026-08-26

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Example Proteomics Dataset	example_dataset
Example Proteomics SummarizedExperiment	example_se
Perform replicate-based imputation	impute_replicate
Perform mixed MAR/MNAR imputation on a SummarizedExperiment object	impute_replicate_mixed_se
Perform replicate-based imputation on a SummarizedExperiment object	impute_replicate_se
Prepare data for replicate-based imputation	prepare_imputation_data
Prepare a SummarizedExperiment for replicate-based imputation	prepare_imputation_data_se
Reconstruct a SummarizedExperiment after replicate-based imputation	reconstruct_se