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awesome-single-cell

List of software packages for single-cell data analysis, including RNA-seq, ATAC-seq, etc.

basilisk

Clone of the Bioconductor repository for the basilisk package.

biscuit_singlecell_imm_icml_2016

R Codebase for BISCUIT: Infinite Mixture Model to cluster and impute single cells.

bookdown

Authoring Books and Technical Documents with R Markdown

cnmf

Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data

colorramppalettealpha

Helper functions for adding transparency to colors in R and preserving the alpha channel when using colorRampPalette

deconv_benchmark

latex-proposal

The Proposal package for LaTeX

monocle-release

powsim

This package underwent major revisions and is now available as powsimR!

powsimr

Power analysis is essential to optimize the design of RNA-seq experiments and to assess and compare the power to detect differentially expressed genes. PowsimR is a flexible tool to simulate and evaluate differential expression from bulk and especially single-cell RNA-seq data making it suitable for a priori and posterior power analyses.

powsimrdata

pyeng

Python for engineers

rgcop

Regularized Copula based Feature Selection

scrna-seq-pipelines

Compendium to "A Systematic Evaluation of Single Cell RNA-Seq Analysis Pipelines"

scrna-tools

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

simulation-comparison

Snakemake workflow to benchmark scRNA-seq data simulators

zinbwavezinger

Integrating zingeR with ZINB-WaVE weights

zumis

zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs