slingshot - Tools for ordering single-cell sequencing

Provides functions for inferring continuous, branching lineage structures in low-dimensional data. Slingshot was designed to model developmental trajectories in single-cell RNA sequencing data and serve as a component in an analysis pipeline after dimensionality reduction and clustering. It is flexible enough to handle arbitrarily many branching events and allows for the incorporation of prior knowledge through supervised graph construction.

Last updated 25 days ago

clusteringdifferentialexpressiongeneexpressionrnaseqsequencingsoftwaresinglecelltranscriptomicsvisualization

11.98 score 268 stars 4 packages 1.1k scripts 2.4k downloads

scry - Small-Count Analysis Methods for High-Dimensional Data

Many modern biological datasets consist of small counts that are not well fit by standard linear-Gaussian methods such as principal component analysis. This package provides implementations of count-based feature selection and dimension reduction algorithms. These methods can be used to facilitate unsupervised analysis of any high-dimensional data such as single-cell RNA-seq.

Last updated 25 days ago

dimensionreductiongeneexpressionnormalizationprincipalcomponentrnaseqsoftwaresequencingsinglecelltranscriptomics

7.34 score 19 stars 115 scripts 560 downloads

VDJdive - Analysis Tools for 10X V(D)J Data

This package provides functions for handling and analyzing immune receptor repertoire data, such as produced by the CellRanger V(D)J pipeline. This includes reading the data into R, merging it with paired single-cell data, quantifying clonotype abundances, calculating diversity metrics, and producing common plots. It implements the E-M Algorithm for clonotype assignment, along with other methods, which makes use of ambiguous cells for improved quantification.

Last updated 25 days ago

softwareimmunooncologysinglecellannotationrnaseqtargetedresequencing

5.32 score 7 stars 1 scripts 136 downloads

mazing - Utilities for Making and Plotting Mazes

Functionality for generating and plotting random mazes. The mazes are based on matrices, so can only consist of vertical and horizontal lines along a regular grid. But there is no need to use every possible space, so they can take on many different shapes.

Last updated 7 months ago

4.30 score 4 stars 4 scripts 157 downloads