R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data
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Updated
Jan 6, 2024 - R
R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data
An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
🧬 Immunarch: an R Package for Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires
Analysis Pipeline for Single Cell ATAC-seq
Community-provided extensions to Seurat
R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
Haplotype-aware CNV analysis from single-cell RNA-seq
A collection of 50+ trajectory inference methods within a common interface 📥📤
Similarity Weighted Nonnegative Embedding (SWNE), a method for visualizing high dimensional datasets
HMM-integrated Bayesian approach for detecting CNV and LOH events from single-cell RNA-seq data
R package to visualize gene expression data based on weighted kernel density estimation
SCAVENGE is a method to optimize the inference of functional and genetic associations to specific cells at single-cell resolution.
Bi-order integration (in silico multi-omics data) of single cell RNA sequencing, single cell ATAC sequencing, spacial transcriptomics and CyTOF data
SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.
A web-based interactive (wizard style) application to perform a guided single-cell RNA-seq data analysis and clustering based on Seurat v3
Code repository for single cell RNA-seq
Comparison of dimensionality reduction methods
Calculation of Reference/Cluster Similarity Spectrum (RSS/CSS)
BEER: Batch EffEct Remover for single-cell data
SCASA: Single cell transcript quantification tool
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