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Package: FIRM 0.1.2

Jingsi Ming

FIRM: Flexible Integration of Single-Cell RNA-Seq Data

Provides functions for the flexible integration of heterogeneous scRNA-seq datasets across multiple tissue types, platforms, and experimental batches. Implements the method described in Ming (2022) <doi:10.1093/bib/bbac167>. The package incorporates modified 'C++' source code from the 'flashpca' library (Abraham, 2014-2016 <https://github.com/gabraham/flashpca>) for efficient principal component analysis, and the 'Spectra' library (Qiu, 2016-2025) for large-scale eigenvalue and singular value decomposition; see 'inst/COPYRIGHTS' for details on third-party code.

Authors:Jingsi Ming [aut, cre, cph], Shuzhen Ding [ctb], Gad Abraham [ctb, cph], Yixuan Qiu [ctb, cph], Anna Araslanova [ctb, cph], Felipe Zapata [ctb, cph], Nicolas Renaud [ctb, cph], Jens Wehner [ctb, cph], Gael Guennebaud [ctb, cph], Jitse Niesen [ctb, cph]

FIRM_0.1.2.tar.gz
FIRM_0.1.2.tar.gz(r-4.7-arm64)FIRM_0.1.2.tar.gz(r-4.7-x86_64)FIRM_0.1.2.tar.gz(r-4.6-arm64)FIRM_0.1.2.tar.gz(r-4.6-x86_64)
FIRM_0.1.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
FIRM/json (API)

# Install 'FIRM' in R:

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

Bug tracker:https://github.com/mingjingsi/firm/issues

Uses libs:

openblas– Optimized BLAS
c++– GNU Standard C++ Library v3

Datasets:

ExampleData - Example single-cell datasets

On CRAN:

openblas cpp

1.70 score 159 downloads 9 exports 142 dependencies

Last updated from:6e88aee1b0. Checks:6 OK. Indexed: no.

Target	Result	Time
linux-devel-arm64	OK	317
linux-devel-x86_64	OK	255
source / vignettes	OK	280
linux-release-arm64	OK	273
linux-release-x86_64	OK	292
wasm-release	OK	206

Exports:FIRM label_trans label_trans_prob Local_Struct match_score Mixing_Metric prep_data Select_hvg SelectGene

Dependencies:abind askpass base64enc BH bitops bslib cachem caTools cli cluster codetools commonmark cowplot cpp11 crosstalk curl data.table deldir digest dotCall64 dplyr dqrng evaluate farver fastDummies fastmap fitdistrplus FNN fontawesome fs future future.apply generics ggplot2 ggrepel ggridges globals glue goftest gplots gridExtra gtable gtools here highr htmltools htmlwidgets httpuv httr ica igraph irlba isoband jquerylib jsonlite KernSmooth knitr labeling later lattice lazyeval lifecycle listenv lmtest magrittr MASS Matrix matrixStats memoise mime miniUI nlme openssl otel parallelly patchwork pbapply pillar pkgconfig plotly plyr png polyclip progressr promises purrr R6 RANN rappdirs RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppHNSW RcppProgress RcppTOML reshape2 reticulate rlang rmarkdown ROCR rprojroot RSpectra Rtsne S7 sass scales scattermore sctransform Seurat SeuratObject shiny sitmo sourcetools sp spam spatstat.data spatstat.explore spatstat.geom spatstat.random spatstat.sparse spatstat.univar spatstat.utils stringi stringr survival sys tensor tibble tidyr tidyselect tinytex utf8 uwot vctrs viridisLite withr xfun xtable yaml zoo

Help page	Topics
Example single-cell datasets	ExampleData
Flexible Integration of Single-Cell RNA-Seq Data	FIRM
Label transfer via k-NN (hard assignment)	label_trans
Label transfer via k-NN (soft assignment / probabilities)	label_trans_prob
Local structure preservation metric	Local_Struct
Match score between query and reference neighbourhoods	match_score
k-NN Mixing Metric	Mixing_Metric
Data preprocessing for FIRM integration	prep_data
Combine or select top HVGs from saved prep_data outputs	Select_hvg
Select consensus genes across multiple HVG lists	SelectGene

Package: FIRM 0.1.2

FIRM: Flexible Integration of Single-Cell RNA-Seq Data

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)