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 2 months ago

human-cell-atlassingle-cell-genomicssingle-cell-rna-seq

16.67 score 2.3k stars 69 packages 46k scripts 45k downloads

S4Vectors - 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 6 days ago

infrastructuredatarepresentationbioconductor-packagecore-package

13.22 score 18 stars 1.8k packages 1.0k scripts

remotes - 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 11 months ago

13.13 score 241 packages 5.7k scripts 467k downloads

IRanges - 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 6 days ago

infrastructuredatarepresentationbioconductor-packagecore-package

13.07 score 22 stars 1.8k packages 2.1k scripts

DelayedArray - 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-package

12.86 score 25 stars 1.2k packages 554 scripts

SeuratObject - 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 7 months ago

11.86 score 24 stars 83 packages 1.0k scripts 43k downloads

tiledb - 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 3 days ago

arrayhdfss3storage-managertiledb

11.59 score 103 stars 3 packages 324 scripts 967 downloads

SeuratObject - 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

11.58 score 24 stars 83 packages 1.0k scripts 44k downloads

BiocGenerics - S4 generic functions used in Bioconductor

The package defines many S4 generic functions used in Bioconductor.

Last updated 7 days ago

infrastructurebioconductor-packagecore-package

11.01 score 12 stars 2.2k packages 606 scripts

MatrixGenerics - 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 23 days ago

infrastructuresoftwarebioconductor-packagecore-package

9.63 score 12 stars 1.3k packages 117 scripts

SparseArray - 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 8 days ago

infrastructuredatarepresentationbioconductor-packagecore-package

9.56 score 8 stars 1.2k packages 45 scripts

S4Arrays - 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 23 days ago

infrastructuredatarepresentationbioconductor-packagecore-package

9.49 score 5 stars 1.2k packages 7 scripts

tiledbsoma - '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 5 hours ago

9.35 score 92 stars 1 packages 30 scripts

ggseurat - ggplot2 Bindings for Seurat Objects

Provides methods to allow Seurat objects to be utilized directly in the ggplot2 ecosystem.

Last updated 2 years ago

2.30 score 4 stars 2 scripts

tinyexpect - What the Package Does (One Line, Title Case)

What the package does (one paragraph).

Last updated 4 months ago

2.00 score

mamisc - Miscellaneous Functions by Paul Hoffman

More about what it does (maybe more than one line) Use four spaces when indenting paragraphs within the Description.

Last updated 2 years ago

1.70 score

pbmc3k.sce - PBMC 3k Dataset as a SingleCellExperiment

The PBMC 3k dataset provided as a SingleCellExperiment object. Also includes a processed version, pbmc3k.sce.final, using Bioc-equivalents of the Seurat standard workflow

Last updated 6 months ago

1.30 score

pbmc3k - Raw and Processed Matrices of the PBMC 3k Dataset

What the package does (one paragraph).

Last updated 5 months ago

1.00 score