Starred repositories
A collection of Rfast functions for data analysis. Note 1: The vast majority of the functions accept matrices only, not data.frames. Note 2: Do not have matrices or vectors with have missing data (…
Highly specific clustering of T cell receptor CDR3s
Ultrafast TCR clustering algorithm based on geometric isometry
CUT&RUN and CUT&Tag data processing and analysis
SCAVENGE is a method to optimize the inference of functional and genetic associations to specific cells at single-cell resolution.
EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.
R package containing useful functions for mutational signature analysis
R package for extracting and visualizing mutational patterns in base substitution catalogues
ggplot extension: options for tailored facets, multiple colourscales and miscellaneous
Tools for copy number signature analysis of allele-specific copy number profiles. Includes: matrix generation, simulation of CN profiles, plotting of CN profiles, artificial genome doubling of sign…
Assignment of known mutational signatures to individual samples and individual somatic mutations
SigProfilerSingleSample allows attributing a known set of mutational signatures to an individual sample. The tool identifies the activity of each signature in the sample and assigns the probability…
📦 Automate Absolute Copy Number Calling using 'ABSOLUTE' package
Quantifying copy number signatures from absolute copy number profiles
Discovering copy number signatures from TCGA and new cohorts.
Main repository for Drews et al. (Nature, 2022)
Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.
🌲 An easy-to-use and scalable toolkit for genomic alteration signature (a.k.a. mutational signature) analysis and visualization in R https://shixiangwang.github.io/sigminer/reference/index.html
https://hub.docker.com/r/pp535/metamutationalsigs
Package to wrangle and visualize genomic data in R
Comprehensive list of color palettes available in R ❤️🧡💛💚💙💜
An R package to create forestplots of measures of effects with their confidence intervals.
Venn Diagram by ggplot2, with really easy-to-use API.
Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.