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.
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immunooncologyflowcytometryproteomicssinglecellcellbasedassayscellbiologyclusteringfeatureextractionsoftware
10.29 score 25 stars 6 dependents 402 scripts 1.0k downloadsnnSVG - 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.
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spatialsinglecelltranscriptomicsgeneexpressionpreprocessing
8.20 score 24 stars 2 dependents 367 scripts 664 downloadsHDCytoData - Collection of high-dimensional cytometry benchmark datasets in Bioconductor object formats
Data package containing a set of publicly available high-dimensional cytometry benchmark datasets, formatted into SummarizedExperiment and flowSet Bioconductor object formats, including all required metadata. Row metadata includes sample IDs, group IDs, patient IDs, reference cell population or cluster labels (where available), and labels identifying 'spiked in' cells (where available). Column metadata includes channel names, protein marker names, and protein marker classes (cell type or cell state).
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experimenthubexperimentdataexpressiondataflowcytometrydatasinglecelldatahomo_sapiens_dataimmunooncologydatadatapkg
7.73 score 12 stars 1 dependents 83 scriptsggspavis - 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.
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spatialsinglecelltranscriptomicsgeneexpressionqualitycontroldimensionreduction
7.44 score 5 stars 694 scripts 854 downloadsOSTA - Orchestrating Spatial Transcriptomics Analysis with Bioconductor
This package contains source files for the "Orchestrating Spatial Transcriptomics Analysis with Bioconductor" online book. This book provides interactive examples and discussion on key principles of computational analysis workflows for spatial transcriptomics data using Bioconductor in R. The book contains chapters describing individual analysis steps as well as extended workflows, each with examples including R code and datasets.
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spatialsinglecellgeneexpressiontranscriptomicsanalysis-workflowsbioconductorspatial-transcriptomicsspatially-resolved-transcriptomicsdatapkgopenjdk
7.19 score 116 starsSTexampleData - Collection of spatial transcriptomics datasets in SpatialExperiment Bioconductor format
Collection of spatial transcriptomics datasets stored in SpatialExperiment Bioconductor format, for use in examples, demonstrations, and tutorials. The datasets are from several different platforms and have been sourced from various publicly available sources. Several datasets include images and/or reference annotation labels.
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experimentdataexperimenthubreproducibleresearchexpressiondatasinglecelldataspatialdatahomo_sapiens_datamus_musculus_datadatapkg
7.07 score 2 stars 1 dependents 246 scriptsregsplice - 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.
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immunooncologyalternativesplicingdifferentialexpressiondifferentialsplicingsequencingrnaseqmicroarrayexonarrayexperimentaldesignsoftware
5.76 score 4 stars 16 scripts 508 downloadsWeberDivechaLCdata - Spatially-resolved transcriptomics and single-nucleus RNA-sequencing data from the locus coeruleus (LC) in postmortem human brain samples
Spatially-resolved transcriptomics (SRT) and single-nucleus RNA-sequencing (snRNA-seq) data from the locus coeruleus (LC) in postmortem human brain samples. Data were generated with the 10x Genomics Visium SRT and 10x Genomics Chromium snRNA-seq platforms. Datasets are stored in SpatialExperiment and SingleCellExperiment formats.
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experimentdataexperimenthubreproducibleresearchexpressiondatasequencingdatarnaseqdatasinglecelldataspatialdatahomo_sapiens_datadatapkg
4.94 score 1 stars 29 scriptssmoothclust - smoothclust
Tools for spatial domain analysis in spatial transcriptomics data. Includes spatial smoothing of gene expression profiles for downstream clustering and a boundary density (BD) metric for summarizing spatial domain organization. The smoothing function returns processed expression values for subsequent clustering. BD requires only spatial coordinates and categorical labels, and provides local and sample-level summaries of label transitions.
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spatialsinglecelltranscriptomicsgeneexpressionclustering
4.60 score 1 stars 10 scripts 334 downloads