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.
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clusteringdifferentialexpressiongeneexpressionrnaseqsequencingsoftwaresinglecelltranscriptomicsvisualization
12.34 score 337 stars 3 dependents 1.7k scripts 3.9k downloadsscry - 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.
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dimensionreductiongeneexpressionnormalizationprincipalcomponentrnaseqsoftwaresequencingsinglecelltranscriptomics
8.07 score 23 stars 1 dependents 171 scripts 742 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.
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softwareimmunooncologysinglecellannotationrnaseqtargetedresequencingcpp
5.77 score 13 stars 5 scripts 288 downloadsfourinarow - Play "Four in a Row"
Play or simulate games of "Four in a Row" in the R console. This package is designed for educational purposes, encouraging users to write their own functions to play the game automatically. It contains a collection of built-in functions that play the game at various skill levels, for users to test their own functions against.
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quarto
4.40 score 1 scripts 155 downloadsmazing - 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.
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4.30 score 4 stars 4 scripts 223 downloads