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 6 days ago
human-cell-atlassingle-cell-genomicssingle-cell-rna-seq
2.2k stars 11.97 score 145 dependencies 66 dependentsremotes - 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 9 months ago
8.40 score 0 dependencies 238 dependentsSeuratObject - 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 12 months ago
22 stars 6.29 score 14 dependencies 78 dependentstiledb - Modern Database Engine for Multi-Modal Data via Sparse and Dense Multidimensional Arrays
The modern database 'TileDB' introduces a powerful on-disk format for multi-modal data based on 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.
Last updated 7 months ago
arrayhdfss3storage-managertiledb
102 stars 4.76 score 11 dependencies 3 dependentstiledbsoma - '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 months ago
83 stars 4.65 score 36 dependencies 1 dependentsggseurat - ggplot2 Bindings for Seurat Objects
Provides methods to allow Seurat objects to be utilized directly in the ggplot2 ecosystem.
Last updated 2 years ago
4 stars 0.49 score 43 dependenciestinyexpect - What the Package Does (One Line, Title Case)
What the package does (one paragraph).
Last updated 2 months ago
0.23 score 2 dependenciespbmc3k - Raw and Processed Matrices of the PBMC 3k Dataset
What the package does (one paragraph).
Last updated 3 months ago
0.09 score 2 dependenciesmamisc - 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
0.00 score 1 dependencies