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.

Last updated 4 months ago

softwaresinglecellgeneexpressiontranscriptomicsclassificationclusteringannotation

170 stars 7.18 score 47 dependencies 1 dependents

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 2 days ago

immunooncologynormalizationsequencingrnaseqsoftwaregeneexpressiontranscriptomicssinglecellclusteringbioconductor-packagehuman-cell-atlassingle-cell-rna-seq

40 stars 7.09 score 64 dependencies 34 dependents

beachmat - 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 3 days ago

datarepresentationdataimportinfrastructurebioconductor-packagehuman-cell-atlasmatrix-library

4 stars 6.92 score 16 dependencies 133 dependents

BiocSingular - 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 2 months ago

softwaredimensionreductionprincipalcomponent

7 stars 6.23 score 28 dependencies 98 dependents

ScaledMatrix - 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 4 months ago

softwaredatarepresentation

6.19 score 14 dependencies 100 dependents

scuttle - 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 25 days ago

immunooncologysinglecellrnaseqqualitycontrolpreprocessingnormalizationtranscriptomicsgeneexpressionsequencingsoftwaredataimport

5.80 score 40 dependencies 77 dependents

BiocNeighbors - 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 3 days ago

clusteringclassification

5.77 score 2 dependencies 83 dependents

basilisk - 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 1 months ago

infrastructure

27 stars 4.77 score 15 dependencies 35 dependents

bluster - 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 2 days ago

immunooncologysoftwaregeneexpressiontranscriptomicssinglecellclustering

4.70 score 25 dependencies 48 dependents

metapod - 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 4 months ago

multiplecomparisondifferentialpeakcalling

4.54 score 1 dependencies 44 dependents

InteractionSet - 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 4 months ago

infrastructuredatarepresentationsoftwarehic

4.35 score 29 dependencies 34 dependents

dir.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 4 months ago

softwareinfrastructure

4.26 score 1 dependencies 38 dependents

basilisk.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 1 months ago

infrastructure

4.23 score 2 dependencies 36 dependents

csaw - 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 4 months ago

multiplecomparisonchipseqnormalizationsequencingcoveragegeneticsannotationdifferentialpeakcalling

4.18 score 47 dependencies 7 dependents

alabaster.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 11 days ago

datarepresentationdataimport

2 stars 3.43 score 11 dependencies 14 dependents

batchelor - 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 2 months ago

sequencingrnaseqsoftwaregeneexpressiontranscriptomicssinglecellbatcheffectnormalization

3.03 score 58 dependencies 7 dependents

alabaster.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 4 months ago

datarepresentationdataimport

2.89 score 0 dependencies 15 dependents

alabaster.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 4 days ago

dataimportdatarepresentation

2.60 score 25 dependencies 8 dependents

diffHic - 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 4 months ago

multiplecomparisonpreprocessingsequencingcoveragealignmentnormalizationclusteringhic

2.50 score 61 dependencies

BumpyMatrix - 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 4 months ago

softwareinfrastructuredatarepresentation

2.50 score 5 dependencies 11 dependents

TrajectoryUtils - 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 4 months ago

geneexpressionsinglecell

2.35 score 38 dependencies 9 dependents

assorthead - 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 2 days ago

singlecellqualitycontrolnormalizationdatarepresentationdataimportdifferentialexpressionalignment

2.27 score 0 dependencies 7 dependents

ResidualMatrix - 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 3 months ago

softwaredatarepresentationregressionbatcheffectexperimentaldesign

1 stars 2.22 score 14 dependencies 8 dependents

alabaster.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 2 months ago

dataimportdatarepresentation

2.18 score 39 dependencies 6 dependents

alabaster.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 3 months ago

dataimportdatarepresentation

2.14 score 25 dependencies 7 dependents

gypsum - 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 3 months ago

dataimport

1.90 score 16 dependencies 1 dependents

cydar - 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 2 days ago

immunooncologyflowcytometrymultiplecomparisonproteomicssinglecell

1.75 score 91 dependencies

alabaster.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 4 months ago

dataimportdatarepresentation

1.51 score 41 dependencies 3 dependents

beachmat.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 3 days ago

datarepresentationdataimportinfrastructure

1.08 score 21 dependencies

DelayedRandomArray - 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 2 months ago

datarepresentation

1.00 score 18 dependencies 1 dependents

alabaster.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 4 months ago

dataimportdatarepresentation

1.00 score 26 dependencies 2 dependents

alabaster.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 4 months ago

dataimportdatarepresentation

0.91 score 77 dependencies 1 dependents

screenCounter - 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 28 days ago

crispralignmentfunctionalgenomicsfunctionalprediction

0.82 score 38 dependencies

TileDBArray - 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 2 months ago

datarepresentationinfrastructuresoftware

0.82 score 26 dependencies

alabaster.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 4 months ago

dataimportdatarepresentation

0.82 score 62 dependencies 1 dependents

alabaster.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 4 months ago

dataimportdatarepresentation

0.71 score 83 dependencies 1 dependents

alabaster.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 4 months ago

dataimportdatarepresentation

0.71 score 16 dependencies 1 dependents

chihaya - 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 4 months ago

dataimportdatarepresentation

0.49 score 19 dependencies

mumosa - 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 2 days ago

immunooncologysinglecellrnaseq

0.36 score 75 dependencies

alabaster.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 4 months ago

datarepresentationdataimport

0.23 score 39 dependencies

alabaster - 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 4 months ago

datarepresentationdataimport

0.23 score 110 dependencies

rebook - 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 4 months ago

softwareinfrastructurereportwriting

0.09 score 36 dependencies