scran - 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.
Last updated 23 days ago
immunooncologynormalizationsequencingrnaseqsoftwaregeneexpressiontranscriptomicssinglecellclusteringbioconductor-packagehuman-cell-atlassingle-cell-rna-seq
13.21 score 40 stars 36 packages 7.6k scripts 8.2k downloadsSingleR - 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.
Last updated 4 days ago
softwaresinglecellgeneexpressiontranscriptomicsclassificationclusteringannotationbioconductorsingler
12.45 score 177 stars 1 packages 2.0k scripts 6.2k 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.
Last updated 23 days ago
softwaredimensionreductionprincipalcomponentbioconductor-packagehuman-cell-atlassingular-value-decomposition
12.03 score 7 stars 98 packages 1.0k scripts 21k 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.
Last updated 10 days ago
datarepresentationdataimportinfrastructurebioconductor-packagehuman-cell-atlasmatrix-library
10.94 score 4 stars 136 packages 21 scripts 28k 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.
Last updated 23 days ago
infrastructurebioconductor-package
10.72 score 27 stars 37 packages 70 scripts 5.5k downloadsscuttle - Single-Cell RNA-Seq Analysis Utilities
Provides basic utility functions for performing single-cell analyses, focusing on simple normalization, quality control and data transformations. Also provides some helper functions to assist development of other packages.
Last updated 23 days ago
immunooncologysinglecellrnaseqqualitycontrolpreprocessingnormalizationtranscriptomicsgeneexpressionsequencingsoftwaredataimport
10.14 score 76 packages 1.6k scripts 16k 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 or with vantage point trees. Approximate searches can be performed using the Annoy or HNSW libraries. Searching on either Euclidean or Manhattan distances is supported. Parallelization is achieved for all methods by using BiocParallel. Functions are also provided to search for all neighbors within a given distance.
Last updated 23 days ago
clusteringclassification
9.97 score 85 packages 582 scripts 18k 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.
Last updated 23 days ago
immunooncologysoftwaregeneexpressiontranscriptomicssinglecellclustering
9.37 score 48 packages 592 scripts 9.1k 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.
Last updated 10 days ago
datarepresentationdataimport
8.44 score 3 stars 14 packages 55 scripts 3.1k downloadsassorthead - 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.
Last updated 3 days ago
singlecellqualitycontrolnormalizationdatarepresentationdataimportdifferentialexpressionalignment
8.23 score 150 packages 5.1k 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.
Last updated 23 days ago
sequencingrnaseqsoftwaregeneexpressiontranscriptomicssinglecellbatcheffectnormalization
7.99 score 7 packages 1.2k scripts 6.4k downloadsInteractionSet - 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.
Last updated 23 days ago
infrastructuredatarepresentationsoftwarehic
7.92 score 36 packages 233 scripts 2.8k downloadsbasilisk.utils - Basilisk Installation Utilities
Implements utilities for installation of the basilisk package, primarily for creation of the underlying Conda instance. This allows us to avoid re-writing the same R code in both the configure script (for centrally administered R installations) and in the lazy installation mechanism (for distributed package binaries). It is highly unlikely that developers - or, heaven forbid, end-users! - will need to interact with this package directly; they should be using the basilisk package instead.
Last updated 23 days ago
infrastructure
7.22 score 38 packages 7 scripts 4.9k 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.
Last updated 1 days ago
dataimportdatarepresentation
7.05 score 8 packages 13 scripts 3.6k 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.
Last updated 23 days ago
softwareinfrastructure
6.97 score 40 packages 6 scripts 5.2k 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.
Last updated 23 days ago
softwaredatarepresentation
6.75 score 102 packages 8 scripts 20k 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.
Last updated 23 days ago
multiplecomparisondifferentialpeakcalling
6.68 score 46 packages 15 scripts 7.8k 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.
Last updated 23 days ago
multiplecomparisonchipseqnormalizationsequencingcoveragegeneticsannotationdifferentialpeakcalling
6.48 score 7 packages 474 scripts 893 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.
Last updated 23 days ago
dataimportdatarepresentation
6.47 score 6 packages 8 scripts 3.3k 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.
Last updated 23 days ago
datarepresentationinfrastructuresoftware
6.41 score 10 stars 26 scripts 146 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.
Last updated 23 days ago
dataimportdatarepresentation
6.41 score 7 packages 8 scripts 2.7k 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.
Last updated 23 days ago
dataimport
6.32 score 1 packages 20 scripts 3.5k 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.
Last updated 23 days ago
datarepresentationdataimport
6.21 score 15 packages 2.4k 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.
Last updated 23 days ago
geneexpressionsinglecell
6.04 score 9 packages 15 scripts 3.0k 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.
Last updated 23 days ago
softwaredatarepresentationregressionbatcheffectexperimentaldesign
5.91 score 1 stars 8 packages 6 scripts 5.6k 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.
Last updated 23 days ago
dataimportdatarepresentation
5.61 score 3 packages 4 scripts 1.0k 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. It is mostly intended for other Bioconductor package developers to build more user-friendly end-to-end workflows.
Last updated 3 days ago
normalizationrnaseqsoftwaregeneexpressiontranscriptomicssinglecellbatcheffectqualitycontroldifferentialexpressionfeatureextractionprincipalcomponentclustering
5.37 score 29 scriptsBumpyMatrix - 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.
Last updated 23 days ago
softwareinfrastructuredatarepresentation
5.32 score 1 stars 11 packages 32 scripts 805 downloadsalabaster.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.
Last updated 13 days ago
dataimportdatarepresentation
5.08 score 1 packages 5 scripts 151 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.
Last updated 23 days ago
dataimportdatarepresentation
5.08 score 2 packages 5 scripts 200 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.
Last updated 23 days ago
dataimportdatarepresentation
4.95 score 1 packages 5 scripts 166 downloadsdiffHic - Differential Analysis of Hi-C Data
Detects differential interactions across biological conditions in a Hi-C experiment. Methods are provided for read alignment and data pre-processing into interaction counts. Statistical analysis is based on edgeR and supports normalization and filtering. Several visualization options are also available.
Last updated 23 days ago
multiplecomparisonpreprocessingsequencingcoveragealignmentnormalizationclusteringhic
4.88 score 38 scripts 273 downloadsbeachmat.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.
Last updated 13 days ago
datarepresentationdataimportinfrastructure
4.88 score 6 scripts 209 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.
Last updated 23 days ago
immunooncologyflowcytometrymultiplecomparisonproteomicssinglecell
4.86 score 48 scripts 217 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.
Last updated 23 days ago
dataimportdatarepresentation
4.78 score 1 packages 5 scripts 156 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.
Last updated 23 days ago
crispralignmentfunctionalgenomicsfunctionalprediction
4.65 score 3 stars 10 scripts 138 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.
Last updated 23 days ago
datarepresentationdataimport
4.62 score 21 scripts 104 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.
Last updated 23 days ago
immunooncologysinglecellrnaseq
4.51 score 13 scripts 154 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.
Last updated 23 days ago
datarepresentation
4.43 score 1 packages 6 scripts 133 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.
Last updated 23 days ago
dataimportdatarepresentation
4.38 score 16 scripts 198 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.
Last updated 23 days ago
datarepresentationdataimport
4.18 score 3 scripts 144 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.
Last updated 23 days ago
dataimportdatarepresentation
3.78 score 1 packages 6 scripts 188 downloadsrebook - 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.
Last updated 23 days ago
softwareinfrastructurereportwriting
3.63 score 211 scripts 220 downloads