229 Open source projects that are alternatives of or similar to single-cell-papers-with-code

An unofficial demultiplexing strategy for SPLiT-seq RNA-Seq data

A deep learning-based tool for alignment and integration of single cell genomic data across multiple datasets, species, conditions, batches

ReproZip is a tool that simplifies the process of creating reproducible experiments from command-line executions, a frequently-used common denominator in computational science.

🔬 Empirical CLI

Examples and demos for ReproZip

Deep learning model for single-cell inference of multi-omic profiles from a single input modality.

Everware is about re-useable science, it allows people to jump right in to your research code.

Clustering scRNAseq by genotypes

Reference mapping for single-cell genomics

Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing

No description or website provided.

Harmony framework for connecting scRNA-seq data from discrete time points

Short course on reproducible science: what, why, how

Reproducible research and reusable acyclic workflows in Python. Execute code on HPC systems as if you executed them on your personal computer!

rrtools: Tools for Writing Reproducible Research in R

Sacred is a tool to help you configure, organize, log and reproduce experiments developed at IDSIA.

Simulating single-cell data using gene regulatory networks 📠

Empirical Software Engineering journal (EMSE) open science and reproducible research initiative

Validation and manipulation of FASTQ files, scRNA-seq barcode pre-processing and UMI quantification.

Reproducible Data Science in Python (SciPy 2019 Tutorial)

A DSL for data-driven computational pipelines

A curated list of reproducible research case studies, projects, tutorials, and media

A tool for semi-automatic cell type annotation

🐳 Containerize R Markdown documents for continuous reproducibility

Fully reproducible, open source scientific articles in LaTeX.

Single cell type annotation guided by cell atlases, with freedom to be queer

NOTE: This repo is archived. Please see https://github.com/benmarwick/rrtools for my current approach

Clone identification from single-cell data

Future Gadget Machine

A pipeline for preprocessing NGS data from Illumina, Nanopore and PacBio technologies

Source code for the CERN Analysis Preservation portal

Future Gadget Laboratory

Software Papers as Software Modules: Towards a Culture of Reusable Results

Package an R workspace and all dependencies as a Docker container

ukbREST: efficient and streamlined data access for reproducible research of large biobanks

Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.

Data-driven Network-based Bayesian Inference of Drivers

Data analysis scripts for Datlinger et. al, 2017 (doi:10.1038/nmeth.4177)

R API and htmlwidget for Vitessce

Quantifying experimental perturbations at single cell resolution

IMS Machine Learning Lab publications.

pytask is a workflow management system which facilitates reproducible data analyses.

Cell type specific enrichments using finemapped variants and quantitative epigenetic data

Reproducible reanalysis of a combined ChIP-Seq & RNA-Seq data set

#nowplaying-RS: Music Recommendation using Factorization Machines

Open solution to the Google AI Object Detection Challenge 🍁

Collective Knowledge extension with unified and customizable benchmarks (with extensible JSON meta information) to be easily integrated with customizable and portable Collective Knowledge workflows. You can easily compile and run these benchmarks using different compilers, environments, hardware and OS (Linux, MacOS, Windows, Android). More info:

💡 💾 💽 A simple, intuitive and Efficient single cell binary Data Storage format

Rmarkdown templates for reproducible science

Enjoy your transcriptomic data and analysis responsibly - like sipping a cocktail

cTPnet Package

Differential expression (DE); gene set Enrichment Analysis (GSEA); single cell RNAseq studies (scRNAseq)

A minimal example data analysis project with the targets R package

spatial transcriptome, single cell

Cookbook examples for the Insight Toolkit documented with Sphinx

A robust, extensible metagenomics pipeline

Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data

Conversion between scRNA-seq objects

A comprehensive dimensional reduction framework to recover the latent topology from high-dimensional data.

Non-official Git repository for R package cellrangerRkit (currently not available elsewhere; I'm not affiliated with 10x)