SingleR - Reference-Based Single-Cell RNA-Seq Annotation
Performs unbiased cell type recognition from single-cell RNA sequencing data, by leveraging reference transcriptomic datasets of pure cell types to infer the cell of origin of each single cell independently.
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softwaresinglecellgeneexpressiontranscriptomicsclassificationclusteringannotationbioconductorsinglercpp
13.89 score 205 stars 7 dependents 4.0k scripts 9.1k downloadsBiocSingular - Singular Value Decomposition for Bioconductor Packages
Implements exact and approximate methods for singular value decomposition and principal components analysis, in a framework that allows them to be easily switched within Bioconductor packages or workflows. Where possible, parallelization is achieved using the BiocParallel framework.
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softwaredimensionreductionprincipalcomponentbioconductor-packagehuman-cell-atlassingular-value-decompositioncpp
12.64 score 8 stars 121 dependents 1.2k scripts 35k downloadsscuttle - Legacy Utilities for Single-Cell RNA-Seq Analysis
Provides some legacy utility functions for performing single-cell analyses. Most of these functions are deprecated in favor of newer, more performant alternatives. We just keep this package around for back-compatibility and to point to the replacement functions.
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immunooncologysinglecellrnaseqqualitycontrolpreprocessingnormalizationtranscriptomicsgeneexpressionsequencingsoftwaredataimportopenblascpp
12.48 score 10 stars 97 dependents 3.6k scripts 26k downloadsBiocNeighbors - Nearest Neighbor Detection for Bioconductor Packages
Implements exact and approximate methods for nearest neighbor detection, in a framework that allows them to be easily switched within Bioconductor packages or workflows. Exact searches can be performed using the k-means for k-nearest neighbors algorithm, vantage point trees, or an exhaustive search. Approximate searches can be performed using the Annoy or HNSW libraries. Each search can be performed with a variety of different distance metrics, parallelization, and variable numbers of neighbors. Range-based searches (to find all neighbors within a certain distance) are also supported.
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clusteringclassificationbioconductor-packagehuman-cell-atlasnearest-neighbor-searchcpp
12.08 score 6 stars 115 dependents 814 scripts 30k downloadsscran - Methods for Single-Cell RNA-Seq Data Analysis
Implements miscellaneous functions for interpretation of single-cell RNA-seq data. Methods are provided for assignment of cell cycle phase, detection of highly variable and significantly correlated genes, identification of marker genes, and other common tasks in routine single-cell analysis workflows.
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immunooncologynormalizationsequencingrnaseqsoftwaregeneexpressiontranscriptomicssinglecellclusteringbioconductor-packagehuman-cell-atlassingle-cell-rna-seqopenblascpp
11.52 score 48 stars 39 dependents 72 scripts 16k downloadsbeachmat - Compiling Bioconductor to Handle Each Matrix Type
Provides a consistent C++ class interface for reading from a variety of commonly used matrix types. Ordinary matrices and several sparse/dense Matrix classes are directly supported, along with a subset of the delayed operations implemented in the DelayedArray package. All other matrix-like objects are supported by calling back into R.
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datarepresentationdataimportinfrastructurebioconductor-packagehuman-cell-atlasmatrix-librarycpp
11.51 score 6 stars 201 dependents 34 scripts 39k downloadsbasilisk - Freezing Python Dependencies Inside Bioconductor Packages
Installs a self-contained conda instance that is managed by the R/Bioconductor installation machinery. This aims to provide a consistent Python environment that can be used reliably by Bioconductor packages. Functions are also provided to enable smooth interoperability of multiple Python environments in a single R session.
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infrastructurebioconductor-package
10.64 score 29 stars 44 dependents 158 scripts 9.1k downloadsbluster - Clustering Algorithms for Bioconductor
Wraps common clustering algorithms in an easily extended S4 framework. Backends are implemented for hierarchical, k-means and graph-based clustering. Several utilities are also provided to compare and evaluate clustering results.
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immunooncologysoftwaregeneexpressiontranscriptomicssinglecellclusteringcpp
10.24 score 63 dependents 1.1k scripts 17k downloadscelldex - Index of Reference Cell Type Datasets
Provides a collection of reference expression datasets with curated cell type labels, for use in procedures like automated annotation of single-cell data or deconvolution of bulk RNA-seq.
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experimenthubexperimentdataexpressiondatasequencingdatarnaseqdatadatapkg
9.70 score 68 stars 4 dependents 2.1k scriptsassorthead - Assorted Header-Only C++ Libraries
Vendors an assortment of useful header-only C++ libraries. Bioconductor packages can use these libraries in their own C++ code by LinkingTo this package without introducing any additional dependencies. The use of a central repository avoids duplicate vendoring of libraries across multiple R packages, and enables better coordination of version updates across cohorts of interdependent C++ libraries.
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singlecellqualitycontrolnormalizationdatarepresentationdataimportdifferentialexpressionalignment
9.34 score 1 stars 224 dependents 27k downloadsalabaster.base - Save Bioconductor Objects to File
Save Bioconductor data structures into file artifacts, and load them back into memory. This is a more robust and portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.
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datarepresentationdataimportcurlopensslzlibcpp
8.79 score 4 stars 23 dependents 63 scripts 8.0k downloadsScaledMatrix - Creating a DelayedMatrix of Scaled and Centered Values
Provides delayed computation of a matrix of scaled and centered values. The result is equivalent to using the scale() function but avoids explicit realization of a dense matrix during block processing. This permits greater efficiency in common operations, most notably matrix multiplication.
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softwaredatarepresentation
8.60 score 128 dependents 12 scripts 29k downloadscsaw - ChIP-Seq Analysis with Windows
Detection of differentially bound regions in ChIP-seq data with sliding windows, with methods for normalization and proper FDR control.
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multiplecomparisonchipseqnormalizationsequencingcoveragegeneticsannotationdifferentialpeakcallingcurlbzip2xz-utilszlibcpp
8.52 score 9 dependents 635 scripts 1.3k downloadsdir.expiry - Managing Expiration for Cache Directories
Implements an expiration system for access to versioned directories. Directories that have not been accessed by a registered function within a certain time frame are deleted. This aims to reduce disk usage by eliminating obsolete caches generated by old versions of packages.
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softwareinfrastructure
8.37 score 500 dependents 8 scripts 15k downloadsscrapper - Bindings to C++ Libraries for Single-Cell Analysis
Implements R bindings to C++ code for analyzing single-cell (expression) data, mostly from various libscran libraries. Each function performs an individual step in the single-cell analysis workflow, ranging from quality control to clustering and marker detection. Additional wrappers are provided for easy construction of end-to-end workflows involving Bioconductor objects like SingleCellExperiments.
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normalizationrnaseqsoftwaregeneexpressiontranscriptomicssinglecellbatcheffectqualitycontroldifferentialexpressionfeatureextractionprincipalcomponentclusteringopenblascpp
8.24 score 10 stars 15 dependents 5 scripts 2.7k downloadsmetapod - Meta-Analyses on P-Values of Differential Analyses
Implements a variety of methods for combining p-values in differential analyses of genome-scale datasets. Functions can combine p-values across different tests in the same analysis (e.g., genomic windows in ChIP-seq, exons in RNA-seq) or for corresponding tests across separate analyses (e.g., replicated comparisons, effect of different treatment conditions). Support is provided for handling log-transformed input p-values, missing values and weighting where appropriate.
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multiplecomparisondifferentialpeakcallingcpp
8.24 score 2 stars 55 dependents 13k downloadsbiocmake - CMake for Bioconductor
Manages the installation of CMake for building Bioconductor packages. This avoids the need for end-users to manually install CMake on their system. No action is performed if a suitable version of CMake is already available.
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infrastructure
7.93 score 1 stars 378 dependents 5 scripts 3.7k downloadsscRNAseq - Collection of Public Single-Cell RNA-Seq Datasets
Gene-level counts for a collection of public scRNA-seq datasets, provided as SingleCellExperiment objects with cell- and gene-level metadata.
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experimenthubexperimentdataexpressiondatasequencingdatarnaseqdatasinglecelldatadatapkg
7.76 score 8 dependents 1.6k scriptsInteractionSet - Base Classes for Storing Genomic Interaction Data
Provides the GInteractions, InteractionSet and ContactMatrix objects and associated methods for storing and manipulating genomic interaction data from Hi-C and ChIA-PET experiments.
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infrastructuredatarepresentationsoftwarehiccpp
7.36 score 44 dependents 2.9k downloadsbatchelor - Single-Cell Batch Correction Methods
Implements a variety of methods for batch correction of single-cell (RNA sequencing) data. This includes methods based on detecting mutually nearest neighbors, as well as several efficient variants of linear regression of the log-expression values. Functions are also provided to perform global rescaling to remove differences in depth between batches, and to perform a principal components analysis that is robust to differences in the numbers of cells across batches.
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sequencingrnaseqsoftwaregeneexpressiontranscriptomicssinglecellbatcheffectnormalizationcpp
7.14 score 9 dependents 6 scripts 9.4k downloadsTileDBArray - Using TileDB as a DelayedArray Backend
Implements a DelayedArray backend for reading and writing dense or sparse arrays in the TileDB format. The resulting TileDBArrays are compatible with all Bioconductor pipelines that can accept DelayedArray instances.
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datarepresentationinfrastructuresoftware
6.88 score 11 stars 1 dependents 29 scripts 433 downloadsalabaster.se - Load and Save SummarizedExperiments from File
Save SummarizedExperiments into file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.
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dataimportdatarepresentation
6.87 score 12 dependents 19 scripts 7.2k downloadsalabaster.matrix - Load and Save Artifacts from File
Save matrices, arrays and similar objects into file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.
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dataimportdatarepresentationcpp
6.85 score 11 dependents 12 scripts 7.2k downloadsBumpyMatrix - Bumpy Matrix of Non-Scalar Objects
Implements the BumpyMatrix class and several subclasses for holding non-scalar objects in each entry of the matrix. This is akin to a ragged array but the raggedness is in the third dimension, much like a bumpy surface - hence the name. Of particular interest is the BumpyDataFrameMatrix, where each entry is a Bioconductor data frame. This allows us to naturally represent multivariate data in a format that is compatible with two-dimensional containers like the SummarizedExperiment and MultiAssayExperiment objects.
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softwareinfrastructuredatarepresentation
6.85 score 1 stars 19 dependents 52 scripts 1.2k downloadsResidualMatrix - Creating a DelayedMatrix of Regression Residuals
Provides delayed computation of a matrix of residuals after fitting a linear model to each column of an input matrix. Also supports partial computation of residuals where selected factors are to be preserved in the output matrix. Implements a number of efficient methods for operating on the delayed matrix of residuals, most notably matrix multiplication and calculation of row/column sums or means.
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softwaredatarepresentationregressionbatcheffectexperimentaldesign
6.74 score 1 stars 10 dependents 10 scripts 9.2k downloadsalabaster.schemas - Schemas for the Alabaster Framework
Stores all schemas required by various alabaster.* packages. No computation should be performed by this package, as that is handled by alabaster.base. We use a separate package instead of storing the schemas in alabaster.base itself, to avoid conflating management of the schemas with code maintenence.
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datarepresentationdataimport
6.67 score 24 dependents 2 scripts 6.4k downloadsalabaster.ranges - Load and Save Ranges-related Artifacts from File
Save GenomicRanges, IRanges and related data structures into file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.
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dataimportdatarepresentation
6.62 score 13 dependents 9 scripts 7.1k downloadsgypsum - Interface to the gypsum REST API
Client for the gypsum REST API (https://gypsum.artifactdb.com), a cloud-based file store in the ArtifactDB ecosystem. This package provides functions for uploads, downloads, and various adminstrative and management tasks. Check out the documentation at https://github.com/ArtifactDB/gypsum-worker for more details.
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dataimport
6.61 score 1 stars 10 dependents 21 scripts 6.4k downloadsRigraphlib - igraph library as an R package
Vendors the igraph C source code and builds it into a static library. Other Bioconductor packages can link to libigraph.a in their own C/C++ code. This is intended for packages wrapping C/C++ libraries that depend on the igraph C library and cannot be easily adapted to use the igraph R package.
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clusteringgraphandnetwork
6.35 score 1 stars 15 dependents 2.5k downloadsTrajectoryUtils - Single-Cell Trajectory Analysis Utilities
Implements low-level utilities for single-cell trajectory analysis, primarily intended for re-use inside higher-level packages. Include a function to create a cluster-level minimum spanning tree and data structures to hold pseudotime inference results.
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geneexpressionsinglecell
6.22 score 1 stars 8 dependents 21 scripts 5.4k downloadsbasilisk.utils - Centralized Conda Installation for Bioconductor Packages
Provides a centralized conda installation for use by other Bioconductor packages. If conda is not already available on the system, it is downloaded and installed from the Miniforge project; otherwise, no action is performed. Historically, this package was used to provide a Python installation for basilisk, hence the name.
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infrastructure
5.89 score 2 dependents 18 scripts 4.8k downloadsaugere.core - Core Utilities for Automatically Generated Reports
Provides utility functions for automatic generation of reports in the augere framework. This mostly involves parsing and dynamically editing Rmarkdown files, controlling inputs into the augere pipelines. Each pipeline generates and executes a self-contained Rmarkdown file for a common bioinformatics analysis; see downstream packages like augere.de and augere.screen for examples of some analysis pipelines.
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workflowmanagementreportwriting
5.78 score 4 dependents 116 downloadsalabaster.sce - Load and Save SingleCellExperiment from File
Save SingleCellExperiment into file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.
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dataimportdatarepresentation
5.73 score 5 dependents 12 scripts 2.0k downloadsscrapbook - Single-cell RNA-seq analyses with scrapper
Demonstrates some basic analysis of single-cell RNA-seq data with scrapper. This includes quality control, normalization, feature selection, various forms of dimensionality reduction, clustering into subpopulations, and detection of marker genes. It is intended for users who already have some familiarity with R and want to get hands-on with some basic single-cell analyses.
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workflowsinglecellworkflowdatapkg
5.52 score 1 stars 2 dependentsbeachmat.hdf5 - beachmat bindings for HDF5-backed matrices
Extends beachmat to support initialization of tatami matrices from HDF5-backed arrays. This allows C++ code in downstream packages to directly call the HDF5 C/C++ library to access array data, without the need for block processing via DelayedArray. Some utilities are also provided for direct creation of an in-memory tatami matrix from a HDF5 file.
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datarepresentationdataimportinfrastructurecurlopensslcpp
5.43 score 1 dependents 12 scripts 404 downloadsDropletTestFiles - Test Files for Single-Cell Droplet Utilities
Assorted files generated from droplet-based single-cell protocols, to be used for testing functions in DropletUtils. Primarily intended for storing files that directly come out of processing pipelines like 10X Genomics' CellRanger software, prior to the formation of a SingleCellExperiment object. Unlike other packages, this is not designed to provide objects that are immediately ready for analysis.
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experimenthubexperimentdataexpressiondatasequencingdatarnaseqdatasinglecelldatadatapkg
5.36 score 5 dependents 76 scriptsaugere.de - Automatic Generation of Differential Expression Analyses
Implements pipelines for generating differential expression analysis reports in the augere framework. This includes analyses with edgeR or voom-limma, with a variety of options for contrasts, blocking and covariates. Each pipeline function generates a self-contained Rmarkdown report with all of the steps required to reproduce the DE analysis.
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workflowmanagementreportwritingdifferentialexpressiontranscription
5.30 score 2 dependents 11 scripts 139 downloadsSingleRBook - The Book of SingleR
Comprehensive guide to using the SingleR Bioconductor package (https://bioconductor.org/packages/SingleR) for automated cell annotation in single-cell RNA-seq datasets. Includes theoretical explanations, worked examples with code, and demonstrations of advanced functionality.
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immunooncologyworkflowworkflowsinglecellworkflowbioconductorsinglerdatapkg
5.26 score 6 starsalabaster.spatial - Save and Load Spatial 'Omics Data to/from File
Save SpatialExperiment objects and their images into file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.
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dataimportdatarepresentation
5.08 score 2 dependents 8 scripts 393 downloadsalabaster.string - Save and Load Biostrings to/from File
Save Biostrings objects to file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.
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dataimportdatarepresentation
4.95 score 2 dependents 6 scripts 343 downloadsDelayedRandomArray - Delayed Arrays of Random Values
Implements a DelayedArray of random values where the realization of the sampled values is delayed until they are needed. Reproducible sampling within any subarray is achieved by chunking where each chunk is initialized with a different random seed and stream. The usual distributions in the stats package are supported, along with scalar, vector and arrays for the parameters.
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datarepresentationcpp
4.95 score 1 dependents 397 downloadsmumosa - Multi-Modal Single-Cell Analysis Methods
Assorted utilities for multi-modal analyses of single-cell datasets. Includes functions to combine multiple modalities for downstream analysis, perform MNN-based batch correction across multiple modalities, and to compute correlations between assay values for different modalities.
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immunooncologysinglecellrnaseq
4.86 score 1 dependents 16 scripts 455 downloadsalabaster.mae - Load and Save MultiAssayExperiments
Save MultiAssayExperiments into file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.
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dataimportdatarepresentation
4.78 score 1 dependents 4 scripts 373 downloadsbeachmat.tiledb - beachmat bindings for TileDB-backed matrices
Extends beachmat to initialize tatami matrices from TileDB-backed arrays. This allows C++ code in downstream packages to directly call the TileDB C/C++ library to access array data, without the need for block processing via DelayedArray. Developers only need to import this package to automatically extend the capabilities of beachmat::initializeCpp to TileDBArray instances.
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datarepresentationdataimportinfrastructurecpp
4.78 score 4 scripts 215 downloadsscreenCounter - Counting Reads in High-Throughput Sequencing Screens
Provides functions for counting reads from high-throughput sequencing screen data (e.g., CRISPR, shRNA) to quantify barcode abundance. Currently supports single barcodes in single- or paired-end data, and combinatorial barcodes in paired-end data.
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crispralignmentfunctionalgenomicsfunctionalpredictionzlibcpp
4.78 score 4 stars 15 scripts 339 downloadscydar - Using Mass Cytometry for Differential Abundance Analyses
Identifies differentially abundant populations between samples and groups in mass cytometry data. Provides methods for counting cells into hyperspheres, controlling the spatial false discovery rate, and visualizing changes in abundance in the high-dimensional marker space.
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immunooncologyflowcytometrymultiplecomparisonproteomicssinglecellcpp
4.78 score 566 downloadsgesel - Search for Interesting Gene Sets
Query the gesel indices to identify interesting gene sets. Users can test for enrichment in their own list of genes and/or search by text in the set names or descriptions. The indices can be hosted remotely or on a local filesystem.
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genesetenrichmentdataimportpathwayszlibcpp
4.70 score 1 stars 350 downloadsalabaster.bumpy - Save and Load BumpyMatrices to/from file
Save BumpyMatrix objects into file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.
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dataimportdatarepresentation
4.69 score 1 dependents 11 scripts 358 downloadsalabaster.vcf - Save and Load Variant Data to/from File
Save variant calling SummarizedExperiment to file and load them back as VCF objects. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.
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dataimportdatarepresentation
4.65 score 1 dependents 9 scripts 318 downloadsaugere.gsea - Automatic Generation of Gene Set Enrichment Analyses
Implements pipelines for generating gene set enrichment analysis reports in the augere framework. This includes various competitive and self-contained gene sets from a variety of Bioconductor packages. Each pipeline function generates a self-contained Rmarkdown report with all of the steps required to reproduce the gene set enrichment analysis.
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workflowmanagementreportwritinggenesetenrichment
4.48 score 129 downloadsaugere.screen - Automatic Generation of Functional Screen Analyses
Implements pipelines for generating functional screen analysis reports in the augere framework. This uses voom to test for differential abundance of barcodes with consolidation into gene-level statistics. Each pipeline function generates a self-contained Rmarkdown report with all of the steps required to reproduce the analysis.
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workflowmanagementreportwritinggenetargetfunctionalgenomics
4.40 score 121 downloadsalabaster.files - Wrappers to Save Common File Formats
Save common bioinformatics file formats within the alabaster framework. This includes BAM, BED, VCF, bigWig, bigBed, FASTQ, FASTA and so on. We save and load additional metadata for each file, and we support linkage between each file and its corresponding index.
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datarepresentationdataimport
4.34 score 11 scripts 330 downloadsaugere.solo - Automatic Generation of Single-Cell Analyses
Implements pipelines for generating single-cell analysis reports in the augere framework. This uses scrapper to execute routine steps such as quality control, normalization, feature selection, clustering and marker detection. We also implement a pipeline for automatic cell type annotation against a labelled reference with SingleR. Each pipeline function generates a self-contained Rmarkdown report with all of the steps required to reproduce its analysis.
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workflowmanagementreportwritingsinglecell
4.30 score 123 downloadsalabaster - Umbrella for the Alabaster Framework
Umbrella for the alabaster suite, providing a single-line import for all alabaster.* packages. Installing this package ensures that all known alabaster.* packages are also installed, avoiding problems with missing packages when a staging method or loading function is dynamically requested. Obviously, this comes at the cost of needing to install more packages, so advanced users and application developers may prefer to install the required alabaster.* packages individually.
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datarepresentationdataimport
4.00 score 3 scripts 348 downloadschihaya - Save Delayed Operations to a HDF5 File
Saves the delayed operations of a DelayedArray to a HDF5 file. This enables efficient recovery of the DelayedArray's contents in other languages and analysis frameworks.
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dataimportdatarepresentationcurlopensslcpp
4.00 score 428 downloadscsawBook - The Book of csaw
Describes how to use the csaw package to detect differentially bound regions in ChIP-seq data. This provides instructions on how to read in BAM files to obtain a per-window count matrix, filtering to obtain high-abundance windows of interest, normalization of sample-specific biases, testing for differential binding, consolidation of per-window results to obtain per-region statistics, and annotation and visualization of the DB results.
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workflowepigeneticsworkflowdatapkg
4.00 scorerebook - Re-using Content in Bioconductor Books
Provides utilities to re-use content across chapters of a Bioconductor book. This is mostly based on functionality developed while writing the OSCA book, but generalized for potential use in other large books with heavy compute. Also contains some functions to assist book deployment.
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softwareinfrastructurereportwriting
3.90 score 398 scripts 472 downloadschipseqDBData - Data for the chipseqDB Workflow
Sorted and indexed BAM files for ChIP-seq libraries, for use in the chipseqDB workflow. BAM indices are also included.
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sequencingdatachipseqdataexperimenthubdatapkg
3.60 score 20 scriptssimpleSingleCell - A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor
Once a proud workflow package, this is now a shell of its former self. Almost all of its content has been cannibalized for use in the "Orchestrating Single-Cell Analyses with Bioconductor" book at https://osca.bioconductor.org. Most vignettes here are retained as reminders of the glory that once was, also providing redirection for existing external links to the relevant OSCA book chapters.
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immunooncologyworkflowworkflowsinglecellworkflow
1.30 score