Introduction | Installation | Basic workflow | Retrieve data and signatures | Preprocessing and imputation | Score and plot data
Package: Seqtometry 1.1.1
Robert Kousnetsov
Seqtometry: Signature scoring for single cell analysis
This package provides functions used in Seqtometry (Kousnetsov et al. 2024), a method for analyzing single cell (scRNA-seq or scATAC-seq) data via signature (gene set) enrichment scores. The Seqtometry scores may be useful for annotating or characterizing cells, either in a flow cytometry like workflow (where scores are standalone features used for progressive partitoning as described in the Seqtometry publication) or in a cluster-based workflow (as features of clusters). The exported impute function (a port of Python's MAGIC-impute, van Dijk et al. 2018), may also be useful for single cell analysis on its own.
Authors:
Seqtometry_1.1.1.tar.gz
Seqtometry_1.1.1.zip(r-4.7-x86_64)Seqtometry_1.1.1.zip(r-4.7-arm64)Seqtometry_1.1.1.zip(r-4.6-x86_64)Seqtometry_1.1.1.zip(r-4.6-arm64)Seqtometry_1.1.1.zip(r-4.5-x86_64)
Seqtometry_1.1.1.tgz(r-4.6-x86_64)Seqtometry_1.1.1.tgz(r-4.6-arm64)Seqtometry_1.1.1.tgz(r-4.5-x86_64)Seqtometry_1.1.1.tgz(r-4.5-arm64)
Seqtometry_1.1.1.tar.gz(r-4.7-arm64)Seqtometry_1.1.1.tar.gz(r-4.7-x86_64)Seqtometry_1.1.1.tar.gz(r-4.6-arm64)Seqtometry_1.1.1.tar.gz(r-4.6-x86_64)
Seqtometry_1.1.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Seqtometry/json (API)
| # Install 'Seqtometry' in R: |
| install.packages('Seqtometry', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/hawigerlab/seqtometry/issues
On BioConductor:Seqtometry-1.1.1(bioc 3.24)Seqtometry-1.0.1(bioc 3.23)
singlecellgenesetenrichmentgeneexpressioncpp
Last updated from:9432878f7e. Checks:1 NOTE, 13 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 348 | ||
| linux-devel-arm64 | WARNING | 339 | ||
| linux-devel-x86_64 | WARNING | 473 | ||
| source / vignettes | OK | 505 | ||
| linux-release-arm64 | WARNING | 458 | ||
| linux-release-x86_64 | WARNING | 610 | ||
| macos-release-arm64 | WARNING | 379 | ||
| macos-release-x86_64 | WARNING | 732 | ||
| macos-oldrel-arm64 | WARNING | 396 | ||
| macos-oldrel-x86_64 | WARNING | 622 | ||
| windows-devel-arm64 | WARNING | 437 | ||
| windows-devel-x86_64 | WARNING | 2362 | ||
| windows-release-arm64 | WARNING | 443 | ||
| windows-release-x86_64 | WARNING | 1698 | ||
| windows-oldrel-x86_64 | WARNING | 1390 | ||
| wasm-release | OK | 326 |
Dependencies:abindassortheadbackportsbeachmatBHBiocGenericsBiocParallelBiocSingularcheckmateclicodetoolscpp11data.tableDelayedArrayDelayedMatrixStatsdigestformatRfutile.loggerfutile.optionsfuturefuture.applygenericsglobalsglueIRangesirlbalambda.rlatticelifecyclelistenvmagrittrMatrixMatrixGenericsmatrixStatsparallellypurrrRcppRcppArmadilloRcppEigenRcppHNSWrlangRSpectrarsvdS4ArraysS4VectorsScaledMatrixsnowSparseArraysparseMatrixStatsvctrsXVectorzeallot
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Signature scoring for single cell analysis | Seqtometry-package Seqtometry |
| Perform data diffusion | .apply_diff_op |
| Compute diffusion operator | .calc_diff_op |
| PCA wrapper | .calc_pca |
| Parameter validation | .check_params |
| Finds row indices of signature genes | .gene_indices |
| PCA inversion | .invert_pca |
| Minmax transform | .minmax_scale |
| LogCP10K transform | .normalize |
| Procrustes disparity | .procrustes |
| MAGIC imputation (van Dijk et al. 2018) | impute |
| Seqtometry scoring (Kousnetsov et al. 2024) | score |
| Helper function for performing a weighted Kolmogorov-Smirnov-like procedure. | wks |