diffcyt - Differential discovery in high-dimensional cytometry via high-resolution clustering

Statistical methods for differential discovery analyses in high-dimensional cytometry data (including flow cytometry, mass cytometry or CyTOF, and oligonucleotide-tagged cytometry), based on a combination of high-resolution clustering and empirical Bayes moderated tests adapted from transcriptomics.

Last updated 24 days ago

immunooncologyflowcytometryproteomicssinglecellcellbasedassayscellbiologyclusteringfeatureextractionsoftware

8.71 score 19 stars 5 packages 200 scripts 889 downloads

nnSVG - Scalable identification of spatially variable genes in spatially-resolved transcriptomics data

Method for scalable identification of spatially variable genes (SVGs) in spatially-resolved transcriptomics data. The method is based on nearest-neighbor Gaussian processes and uses the BRISC algorithm for model fitting and parameter estimation. Allows identification and ranking of SVGs with flexible length scales across a tissue slide or within spatial domains defined by covariates. Scales linearly with the number of spatial locations and can be applied to datasets containing thousands or more spatial locations.

Last updated 24 days ago

spatialsinglecelltranscriptomicsgeneexpressionpreprocessing

7.52 score 11 stars 1 packages 249 scripts 266 downloads

ggspavis - Visualization functions for spatial transcriptomics data

Visualization functions for spatial transcriptomics data. Includes functions to generate several types of plots, including spot plots, feature (molecule) plots, reduced dimension plots, spot-level quality control (QC) plots, and feature-level QC plots, for datasets from the 10x Genomics Visium and other technological platforms. Datasets are assumed to be in either SpatialExperiment or SingleCellExperiment format.

Last updated 24 days ago

spatialsinglecelltranscriptomicsgeneexpressionqualitycontroldimensionreduction

6.45 score 2 stars 142 scripts 338 downloads

regsplice - L1-regularization based methods for detection of differential splicing

Statistical methods for detection of differential splicing (differential exon usage) in RNA-seq and exon microarray data, using L1-regularization (lasso) to improve power.

Last updated 24 days ago

immunooncologyalternativesplicingdifferentialexpressiondifferentialsplicingsequencingrnaseqmicroarrayexonarrayexperimentaldesignsoftware

5.86 score 3 stars 27 scripts 171 downloads

smoothclust - smoothclust

Method for segmentation of spatial domains and spatially-aware clustering in spatial transcriptomics data. The method generates spatial domains with smooth boundaries by smoothing gene expression profiles across neighboring spatial locations, followed by unsupervised clustering. Spatial domains consisting of consistent mixtures of cell types may then be further investigated by applying cell type compositional analyses or differential analyses.

Last updated 24 days ago

spatialsinglecelltranscriptomicsgeneexpressionclustering

3.74 score 1 stars 7 scripts 184 downloads