Package: BatChef 1.1.0

Elena Zuin

BatChef: Single-cell RNA-seq batch effects correction methods interface

This package implements a variety of methods for batch correction in single-cell RNA sequencing (scRNA-seq) data. It incorporates quantitative metrics (e.g. Wasserstein distance, Adjusted Rand Index) to evaluate their performance. Furthermore, the package assists users in identifying and applying the optimal method for specific datasets.

Authors:Elena Zuin [aut, cre], Chiara Romualdi [ctb], Davide Risso [ctb], Gabriele Sales [ctb]

BatChef_1.1.0.tar.gz

BatChef_1.1.0.tgz(r-4.6-x86_64)BatChef_1.1.0.tgz(r-4.6-arm64)BatChef_1.1.0.tgz(r-4.5-x86_64)BatChef_1.1.0.tgz(r-4.5-arm64)
BatChef_1.1.0.tar.gz(r-4.6-arm64)BatChef_1.1.0.tar.gz(r-4.6-x86_64)
BatChef_1.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
BatChef/json (API)
NEWS

# Install 'BatChef' in R:

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

Bug tracker:https://github.com/zuinelena3/batchef/issues

Uses libs:

c++– GNU Standard C++ Library v3

On BioConductor:BatChef-1.1.0(bioc 3.24)BatChef-1.0.1(bioc 3.23)

batcheffect singlecell sequencing cpp

4.51 score 4 stars 2 scripts 157 downloads 27 exports 300 dependencies

Last updated from:b4ef68ead2. Checks:1 NOTE, 5 FAIL, 7 ERROR, 1 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	385
linux-devel-arm64	FAIL	246
linux-devel-x86_64	FAIL	278
source / vignettes	ERROR	524
linux-release-arm64	ERROR	641
linux-release-x86_64	ERROR	740
macos-release-arm64	ERROR	508
macos-release-x86_64	ERROR	1044
macos-oldrel-arm64	ERROR	505
macos-oldrel-x86_64	ERROR	891
windows-devel	FAIL	134
windows-release	FAIL	278
windows-oldrel	FAIL	162
wasm-release	OK	337

Exports:adjusted_rand_index average_silhouette_width batchCorrect CombatParams combatRun compute_lisi FastMNNParams fastMNNRun HarmonyParams harmonyRun leiden_clustering LigerParams ligerRun LimmaParams limmaRun local_inverse_simpson_index metrics normalized_mutual_info ScMerge2Params scMerge2Run SeuratV3Params seuratV3Run SeuratV5Params seuratV5Run simulate_data suggested_method wasserstein_distance

Dependencies:abind anndata annotate AnnotationDbi aricode askpass assertthat assorthead backports base64enc basilisk batchelor bbmle bdsmatrix beachmat beeswarm BH Biobase BiocGenerics biocmake BiocNeighbors BiocParallel BiocSingular Biostrings bit bit64 bitops blob bluster bslib cachem Cairo callr caTools checkmate circlize class classInt cli cluster codetools colorspace commonmark cowplot cpp11 crayon crosstalk curl cvTools data.table DBI DelayedArray DelayedMatrixStats deldir densEstBayes DEoptimR desc digest dir.expiry distr distributional dotCall64 dplyr dqrng e1071 easy.utils edgeR evaluate farver fastDummies fastmap fastmatch filelock fitdistrplus FNN fontawesome forcats foreign formatR Formula fs futile.logger futile.options future future.apply genefilter generics GenomicRanges ggbeeswarm ggplot2 ggprism ggrastr ggrepel ggridges GlobalOptions globals glue goftest gplots gridExtra gtable gtools h5mread harmony HDF5Array hdf5r hdf5r.Extra here HighFive highr Hmisc hms htmlTable htmltools htmlwidgets httpuv httr ica igraph inline IRanges irlba isoband janitor jquerylib jsonlite KEGGREST KernSmooth knitr labeling lambda.r later lattice lazyeval leidenAlg lifecycle limma listenv lmtest locfit loo lubridate M3Drop magrittr MASS Matrix MatrixGenerics matrixStats mclust mcprogress memoise metapod mgcv mime miniUI mvtnorm nlme nnet numDeriv openssl otel paletteer parallelly patchwork pbapply pbmcapply pheatmap pillar pkgbuild pkgconfig plotly plyr png polyclip posterior prismatic pROC processx progressr promises proxy proxyC ps purrr QuickJSR R6 ragg RANN rappdirs RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppHNSW RcppML RcppParallel RcppPlanc RcppProgress RcppTOML reldist rematch2 reshape2 ResidualMatrix reticulate rhdf5 rhdf5filters Rhdf5lib RhpcBLASctl Rigraphlib rlang rliger rmarkdown robustbase ROCR rpart rprojroot RSpectra RSQLite rstan rstantools rstudioapi rsvd Rtsne ruv s2 S4Arrays S4Vectors S7 sass ScaledMatrix scales scater scattermore sccore scCustomize scMerge scran scrapper sctransform scuttle Seqinfo Seurat SeuratObject sf sfsmisc shape shiny SingleCellExperiment sitmo snakecase snow sourcetools sp spam SparseArray sparseMatrixStats spatstat.data spatstat.explore spatstat.geom spatstat.random spatstat.sparse spatstat.univar spatstat.utils splatter StanHeaders startupmsg statmod stringi stringr SummarizedExperiment survival sva sys systemfonts tensor tensorA textshaping tibble tidyr tidyselect timechange tinytex transport units utf8 uwot vctrs vipor viridis viridisLite withr wk xfun XML xtable XVector yaml zellkonverter zoo

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Readme and manuals

Help Manual

Help page	Topics
Adjusted Rand Index (ARI)	adjusted_rand_index
Average Silhouette Width (ASW)	average_silhouette_width
Batch effects strength	batch_params
batchCorrect	batchCorrect batchCorrect,CombatParams-method batchCorrect,FastMNNParams-method batchCorrect,HarmonyParams-method batchCorrect,LigerParams-method batchCorrect,LimmaParams-method batchCorrect,ScMerge2Params-method batchCorrect,SeuratV3Params-method batchCorrect,SeuratV5Params-method
Capture parameters of the correction methods	capture_params
Convert into a SingleCellExperiment object for clustering	clustInput clustInput,AnnDataR6,AnnDataR6-method clustInput,AnnDataR6-method clustInput,Seurat,Seurat-method clustInput,Seurat-method clustInput,SingleCellExperiment,SingleCellExperiment-method clustInput,SingleCellExperiment-method
ComBat method	combatRun
Local Inverse Simpson Index (LISI)	compute_lisi
Compute the Local Inverse Simpson Index (LISI)	compute_simpson_index
Extract data characteristics	extract_features
Convert fastMNN output	fastMNNPost fastMNNPost,AnnDataR6,AnnDataR6-method fastMNNPost,AnnDataR6-method fastMNNPost,Seurat,Seurat-method fastMNNPost,Seurat-method fastMNNPost,SingleCellExperiment,SingleCellExperiment-method fastMNNPost,SingleCellExperiment-method
fastMNN method	fastMNNRun
Convert Harmony output	harmonyPost harmonyPost,AnnDataR6,AnnDataR6-method harmonyPost,AnnDataR6-method harmonyPost,Seurat,Seurat-method harmonyPost,Seurat-method harmonyPost,SingleCellExperiment,SingleCellExperiment-method harmonyPost,SingleCellExperiment-method
Harmony method	harmonyRun
Kullback-Leibler (KL) divergence) between two Gamma distributions	kl_gamma
Leiden clustering	leiden_clustering
Library size parameters	lib_size_params
Convert to a LIGER compatible object	ligerInput ligerInput,AnnDataR6,AnnDataR6-method ligerInput,AnnDataR6-method ligerInput,Seurat,Seurat-method ligerInput,Seurat-method ligerInput,SingleCellExperiment,SingleCellExperiment-method ligerInput,SingleCellExperiment-method
Convert the LIGER output	ligerPost ligerPost,AnnDataR6,AnnDataR6-method ligerPost,AnnDataR6-method ligerPost,Seurat,Seurat-method ligerPost,Seurat-method ligerPost,SingleCellExperiment,SingleCellExperiment-method ligerPost,SingleCellExperiment-method
LIGER method	ligerRun
BatChefParams methods	BatChefParams-class BBKNNParams-class CombatParams CombatParams-class FastMNNParams FastMNNParams-class HarmonyParams HarmonyParams-class LigerParams LigerParams-class LimmaParams LimmaParams-class ScanoramaParams-class ScMerge2Params ScMerge2Params-class SCVIParams-class SeuratV3Params SeuratV3Params-class SeuratV5Params SeuratV5Params-class
limma method	limmaRun
Convert into a SingleCellExperiment object for linear model based methods	linearInput linearInput,AnnDataR6,AnnDataR6-method linearInput,AnnDataR6-method linearInput,Seurat,Seurat-method linearInput,Seurat-method linearInput,SingleCellExperiment,SingleCellExperiment-method linearInput,SingleCellExperiment-method
Convert the output of linear models	linearPost linearPost,AnnDataR6,AnnDataR6-method linearPost,AnnDataR6-method linearPost,Seurat,Seurat-method linearPost,Seurat-method linearPost,SingleCellExperiment,SingleCellExperiment-method linearPost,SingleCellExperiment-method
Median of Local Inverse Simposon Index (LISI)	local_inverse_simpson_index
A shifted log transformation	log_transf
Parameters merging	merge_params
Performance evaluation metrics.	metrics
Normalization	normalized
Normalized Mutual Information (NMI)	normalized_mutual_info
Highly expressed genes probability	outlier_params
Gamma parameters estimation of batch factors	params_btc_factors
Prediction plot	prediction_plot
Convert into a SingleCellExperiment object	sceInput sceInput,AnnDataR6,AnnDataR6-method sceInput,AnnDataR6-method sceInput,Seurat,Seurat-method sceInput,Seurat-method sceInput,SingleCellExperiment,SingleCellExperiment-method sceInput,SingleCellExperiment-method
Convert the scMerge2 output	scMerge2Post scMerge2Post,AnnDataR6,AnnDataR6-method scMerge2Post,AnnDataR6-method scMerge2Post,Seurat,Seurat-method scMerge2Post,Seurat-method scMerge2Post,SingleCellExperiment,SingleCellExperiment-method scMerge2Post,SingleCellExperiment-method
scMerge2 method	scMerge2Run
Convert to a SeuratV3 compatible object	seuratv3Input seuratv3Input,AnnDataR6,AnnDataR6-method seuratv3Input,AnnDataR6-method seuratv3Input,Seurat,Seurat-method seuratv3Input,Seurat-method seuratv3Input,SingleCellExperiment,SingleCellExperiment-method seuratv3Input,SingleCellExperiment-method
Convert the SeuratV3 output	seuratv3Post seuratv3Post,AnnDataR6,AnnDataR6-method seuratv3Post,AnnDataR6-method seuratv3Post,Seurat,Seurat-method seuratv3Post,Seurat-method seuratv3Post,SingleCellExperiment,SingleCellExperiment-method seuratv3Post,SingleCellExperiment-method
Seurat V3 method	seuratV3Run
Convert to a SeuratV5 compatible object	seuratv5Input seuratv5Input,AnnDataR6,AnnDataR6-method seuratv5Input,AnnDataR6-method seuratv5Input,Seurat,Seurat-method seuratv5Input,Seurat-method seuratv5Input,SingleCellExperiment,SingleCellExperiment-method seuratv5Input,SingleCellExperiment-method
Convert the SeuratV5 output	seuratv5Post seuratv5Post,AnnDataR6,AnnDataR6-method seuratv5Post,AnnDataR6-method seuratv5Post,Seurat,Seurat-method seuratv5Post,Seurat-method seuratv5Post,SingleCellExperiment,SingleCellExperiment-method seuratv5Post,SingleCellExperiment-method
Seurat V5 method	seuratV5Run
Function to simulate data	simulate_data
Suggested method prediction	suggested_method
Wasserstein distance	wasserstein_distance
Winsorization	winsorization