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 1 years ago

human-cell-atlassingle-cell-genomicssingle-cell-rna-seqcpp

16.56 score 2.3k stars 68 dependents 49k scripts 36k 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

cpp

11.52 score 24 stars 83 dependents 1.2k scripts 30k downloads

enrichR - Provides an R Interface to 'Enrichr'

Provides an R interface to all 'Enrichr' databases. 'Enrichr' is a web-based tool for analysing gene sets and returns any enrichment of common annotated biological features. Quoting from their website 'Enrichment analysis is a computational method for inferring knowledge about an input gene set by comparing it to annotated gene sets representing prior biological knowledge.' See <https://maayanlab.cloud/Enrichr/> for further details.

Last updated 2 days ago

9.99 score 85 stars 6 dependents 920 scripts 167 downloads

presto - Fast Functions for Differential Expression using Wilcox and AUC

Scalable implementation of the Wilcoxon rank sum test and auROC statistic. Interfaces to dense and sparse matrices, as well as genomics analysis frameworks Seurat and SingleCellExperiment.

Last updated 11 months ago

cpp

7.61 score 173 stars 592 scripts