zellkonverter - Conversion Between scRNA-seq Objects
Provides methods to convert between Python AnnData objects and SingleCellExperiment objects. These are primarily intended for use by downstream Bioconductor packages that wrap Python methods for single-cell data analysis. It also includes functions to read and write H5AD files used for saving AnnData objects to disk.
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singlecelldataimportdatarepresentationbioconductorconversionscrna-seq
12.02 score 210 stars 6 dependents 1.4k scripts 4.0k downloads
clustree - Visualise Clusterings at Different Resolutions
Deciding what resolution to use can be a difficult question when approaching a clustering analysis. One way to approach this problem is to look at how samples move as the number of clusters increases. This package allows you to produce clustering trees, a visualisation for interrogating clusterings as resolution increases.
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clusteringclustering-treesvisualisationvisualization
11.85 score 258 stars 5 dependents 3.2k scripts 4.7k downloadssplatter - Simple Simulation of Single-cell RNA Sequencing Data
Splatter is a package for the simulation of single-cell RNA sequencing count data. It provides a simple interface for creating complex simulations that are reproducible and well-documented. Parameters can be estimated from real data and functions are provided for comparing real and simulated datasets.
Last updated
singlecellrnaseqtranscriptomicsgeneexpressionsequencingsoftwareimmunooncologybioconductorbioinformaticsscrna-seqsimulation
11.63 score 235 stars 1 dependents 532 scripts 848 downloads
anndataR - AnnData interoperability in R
Bring the power and flexibility of AnnData to the R ecosystem, allowing you to effortlessly manipulate and analyse your single-cell data. This package lets you work with backed h5ad and zarr files, directly access various slots (e.g. X, obs, var), or convert the data into SingleCellExperiment and Seurat objects.
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singlecelldataimportdatarepresentationanndatah5adinteroperability
11.58 score 188 stars 3 dependents 302 scriptszellkonverter - Conversion Between scRNA-seq Objects
Provides methods to convert between Python AnnData objects and SingleCellExperiment objects. These are primarily intended for use by downstream Bioconductor packages that wrap Python methods for single-cell data analysis. It also includes functions to read and write H5AD files used for saving AnnData objects to disk.
Last updated
singlecelldataimportdatarepresentationbioconductorconversionscrna-seq
11.39 score 210 stars 6 dependents 1.3k scriptssplatter - Simple Simulation of Single-cell RNA Sequencing Data
Splatter is a package for the simulation of single-cell RNA sequencing count data. It provides a simple interface for creating complex simulations that are reproducible and well-documented. Parameters can be estimated from real data and functions are provided for comparing real and simulated datasets.
Last updated
singlecellrnaseqtranscriptomicsgeneexpressionsequencingsoftwareimmunooncologybioconductorbioinformaticsscrna-seqsimulation
10.97 score 235 stars 1 dependents 700 scriptsdoilinker - Link Preprints And Publications By DOI
Links preprints to publications using the method described in Cabanac G, Oikonomidi T, Boutron I. "Day-to-day discovery of preprint-publication links". Scientometrics. 2021;1–20. DOI: 10.1007/s11192-021-03900-7.
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doipreprintpublication
3.40 score 5 stars 3 scripts