Seurat - Tools for Single Cell Genomics
A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.
Last updated 27 days ago
human-cell-atlassingle-cell-genomicssingle-cell-rna-seqcpp
17.39 score 2.3k stars 70 dependents 49k scripts 45k downloadsS4Vectors - Foundation of vector-like and list-like containers in Bioconductor
The S4Vectors package defines the Vector and List virtual classes and a set of generic functions that extend the semantic of ordinary vectors and lists in R. Package developers can easily implement vector-like or list-like objects as concrete subclasses of Vector or List. In addition, a few low-level concrete subclasses of general interest (e.g. DataFrame, Rle, Factor, and Hits) are implemented in the S4Vectors package itself (many more are implemented in the IRanges package and in other Bioconductor infrastructure packages).
Last updated 10 days ago
infrastructuredatarepresentationbioconductor-packagecore-package
13.21 score 18 stars 1.8k dependents 1.0k scriptsIRanges - Foundation of integer range manipulation in Bioconductor
Provides efficient low-level and highly reusable S4 classes for storing, manipulating and aggregating over annotated ranges of integers. Implements an algebra of range operations, including efficient algorithms for finding overlaps and nearest neighbors. Defines efficient list-like classes for storing, transforming and aggregating large grouped data, i.e., collections of atomic vectors and DataFrames.
Last updated 9 days ago
infrastructuredatarepresentationbioconductor-packagecore-package
13.07 score 22 stars 1.8k dependents 2.1k scriptsDelayedArray - A unified framework for working transparently with on-disk and in-memory array-like datasets
Wrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, ordinary arrays and, data frames.
Last updated 7 days ago
infrastructuredatarepresentationannotationgenomeannotationbioconductor-packagecore-packageu24ca289073
12.94 score 26 stars 1.2k dependents 538 scriptsremotes - R Package Installation from Remote Repositories, Including 'GitHub'
Download and install R packages stored in 'GitHub', 'GitLab', 'Bitbucket', 'Bioconductor', or plain 'subversion' or 'git' repositories. This package provides the 'install_*' functions in 'devtools'. Indeed most of the code was copied over from 'devtools'.
Last updated 1 years ago
12.86 score 248 dependents 5.7k scripts 480k downloadsSeuratObject - Data Structures for Single Cell Data
Defines S4 classes for single-cell genomic data and associated information, such as dimensionality reduction embeddings, nearest-neighbor graphs, and spatially-resolved coordinates. Provides data access methods and R-native hooks to ensure the Seurat object is familiar to other R users. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, and Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, Hao Y, Hao S, et al (2021) <doi:10.1016/j.cell.2021.04.048> and Hao Y, et al (2023) <doi:10.1101/2022.02.24.481684> for more details.
Last updated 2 months ago
cpp
12.32 score 25 stars 87 dependents 1.2k scripts 35k downloadstiledb - Modern Database Engine for Complex Data Based on Multi-Dimensional Arrays
The modern database 'TileDB' introduces a powerful on-disk format for storing and accessing any complex data based on multi-dimensional arrays. It supports dense and sparse arrays, dataframes and key-values stores, cloud storage ('S3', 'GCS', 'Azure'), chunked arrays, multiple compression, encryption and checksum filters, uses a fully multi-threaded implementation, supports parallel I/O, data versioning ('time travel'), metadata and groups. It is implemented as an embeddable cross-platform C++ library with APIs from several languages, and integrations. This package provides the R support.
Last updated 2 days ago
arrayhdfss3storage-managertiledbcpp
11.85 score 107 stars 4 dependents 306 scripts 1.2k downloadsSeuratObject - Data Structures for Single Cell Data
Defines S4 classes for single-cell genomic data and associated information, such as dimensionality reduction embeddings, nearest-neighbor graphs, and spatially-resolved coordinates. Provides data access methods and R-native hooks to ensure the Seurat object is familiar to other R users. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, and Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031> for more details.
Last updated 1 years ago
cpp
11.62 score 25 stars 86 dependents 1.2k scripts 35k downloadsBiocGenerics - S4 generic functions used in Bioconductor
The package defines many S4 generic functions used in Bioconductor.
Last updated 14 days ago
infrastructurebioconductor-packagecore-package
11.20 score 12 stars 2.2k dependents 612 scriptsSparseArray - High-performance sparse data representation and manipulation in R
The SparseArray package provides array-like containers for efficient in-memory representation of multidimensional sparse data in R (arrays and matrices). The package defines the SparseArray virtual class and two concrete subclasses: COO_SparseArray and SVT_SparseArray. Each subclass uses its own internal representation of the nonzero multidimensional data: the "COO layout" and the "SVT layout", respectively. SVT_SparseArray objects mimic as much as possible the behavior of ordinary matrix and array objects in base R. In particular, they suppport most of the "standard matrix and array API" defined in base R and in the matrixStats package from CRAN.
Last updated 1 days ago
infrastructuredatarepresentationbioconductor-packagecore-packageopenmp
10.81 score 8 stars 1.2k dependents 79 scriptsMatrixGenerics - S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects
S4 generic functions modeled after the 'matrixStats' API for alternative matrix implementations. Packages with alternative matrix implementation can depend on this package and implement the generic functions that are defined here for a useful set of row and column summary statistics. Other package developers can import this package and handle a different matrix implementations without worrying about incompatibilities.
Last updated 1 months ago
infrastructuresoftwarebioconductor-packagecore-package
9.77 score 12 stars 1.3k dependents 129 scriptstiledbsoma - 'TileDB' Stack of Matrices, Annotated ('SOMA')
Interface for working with 'TileDB'-based Stack of Matrices, Annotated ('SOMA'): an open data model for representing annotated matrices, like those commonly used for single cell data analysis. It is documented at <https://github.com/single-cell-data>; a formal specification available is at <https://github.com/single-cell-data/SOMA/blob/main/abstract_specification.md>.
Last updated 17 hours ago
cpp
9.56 score 97 stars 1 dependents 34 scriptsS4Arrays - Foundation of array-like containers in Bioconductor
The S4Arrays package defines the Array virtual class to be extended by other S4 classes that wish to implement a container with an array-like semantic. It also provides: (1) low-level functionality meant to help the developer of such container to implement basic operations like display, subsetting, or coercion of their array-like objects to an ordinary matrix or array, and (2) a framework that facilitates block processing of array-like objects (typically on-disk objects).
Last updated 13 days ago
infrastructuredatarepresentationbioconductor-packagecore-package
9.47 score 5 stars 1.2k dependents 8 scriptsggseurat - ggplot2 Bindings for Seurat Objects
Provides methods to allow Seurat objects to be utilized directly in the ggplot2 ecosystem.
Last updated 3 months ago
3.30 score 4 stars 2 scriptstinyexpect - What the Package Does (One Line, Title Case)
What the package does (one paragraph).
Last updated 7 months ago
2.00 scorepbmc3k - Raw and Processed Matrices of the PBMC 3k Dataset
What the package does (one paragraph).
Last updated 8 months ago
1.00 score