Analysing RE-RRSeq with GTDB taxonomic framework

UniverSC: a flexible cross-platform single-cell data processing pipeline

Single Cell Analysis of Five'Ends

This library provides implementations of many algorithms and data structures that are useful for bioinformatics. All provided implementations are rigorously tested via continuous integration.

Treefit: R implementaion

Implementation of the Leiden algorithm for various quality functions to be used with igraph in Python.

A Julia implementation of the Leiden algorithm for community detection.

Annotated data.

R toolkit for single cell genomics

A fast and sensitive gapped read aligner

A SingleCell RNASeq pre-processing snakemake workflow

Rphenograph: R implementation of the PhenoGraph algorithm

Table of software for the analysis of single-cell RNA-seq data.

Simple simulation of single-cell RNA sequencing data

R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets

Accurate and robust imputation of scRNA-seq data

Differential Correlation across Ranked Samples

Visualise Clusterings at Different Resolutions

A curated list of awesome Machine Learning frameworks, libraries and software.

⛔ ARCHIVED ⛔ Wraps UMAP Algorithm for Dimension Reduction

Subpopulation detection in high-dimensional single-cell data

Code for the MNN manuscript figures

Deep count autoencoder for denoising scRNA-seq data

RNA velocity estimation in R

Reproducible machine learning analysis of gene expression and alternative splicing data

Course material in notebook format for learning about single cell bioinformatics methods

Mapping out the coarse-grained connectivity structures of complex manifolds.

Software for processing and analyzing STARmap experiments.