91 Open source projects that are alternatives of or similar to Nebulosa

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

An online companion to the OSCA manuscript demonstrating Bioconductor resources and workflows for single-cell RNA-seq analysis.

Graph-linked unified embedding for single-cell multi-omics data integration

🧬 Immunarch by ImmunoMind: R Package for Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires

🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.

A collection of 50+ trajectory inference methods within a common interface 📥📤

Simulating single-cell data using gene regulatory networks 📠

Manuscript for functional prediction of transcriptomic “dark matter” across species

Expression Weighted Celltype Enrichment. See the package website for up-to-date instructions on usage.

spatial transcriptome, single cell

Experimental design framework for scRNAseq population studies (eQTL and DE)

mgatk: mitochondrial genome analysis toolkit

No description or website provided.

Clone identification from single-cell data

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

Methods for detecting doublets in single-cell sequencing data

Multiome GRN inference.

Dynamical systems methods for RNA velocity analysis

R API and htmlwidget for Vitessce

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

All-in-one analysis pipeline

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

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

Covarying neighborhood analysis (CNA) is a method for finding structure in- and conducting association analysis with multi-sample single-cell datasets.

GCModeller: genomics CAD(Computer Assistant Design) Modeller system in .NET language

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

kallisto | bustools workflow for pre-processing single-cell RNA-seq data

R package to do the Ligand Receptor Analysis Visualization

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

Wasserstein Generative Adversarial Network for analysing scRNAseq data

characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular densities

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

Single-cell copy number calling and event history reconstruction.

VoxHunt: Resolving human brain organoid heterogeneity through single-cell genomic comparison to spatial brain maps

A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data

Pileup biallelic SNPs from single-cell and bulk RNA-seq data

Bead-based single-cell atac processing

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

CellRank for directed single-cell fate mapping

Cell type specific enrichments using finemapped variants and quantitative epigenetic data

Inference of switch-like differential expression along single-cell trajectories

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

Deep Learning based cell composition analysis with Scaden.

netSmooth: A Network smoothing based method for Single Cell RNA-seq imputation

A tool for semi-automatic cell type annotation

Fast visualization tool for large-scale and high dimensional single-cell data

R package (compatible with SCope) to create generic .loom files and extend them with other data e.g.: SCENIC regulons, Seurat clusters and markers, ...

Reference mapping for single-cell genomics

CUT&RUN and CUT&Tag data processing and analysis

<<------ Use SnapATAC!!

Single-Cell Omics Preparation Entity Tools

A fast, accurate, and modularized dimensionality reduction approach based on diffusion harmonics and graph layouts. Escalates to millions of samples on a personal laptop. Adds high-dimensional big data intrinsic structure to your clustering and data visualization workflow.

Software for exploration of gene expression data from single-cell RNA sequencing.

Efficient genotyping bi-allelic SNPs on single cells

Tools for single-cell data processing

Conditional out-of-distribution prediction

A tool that allows to get UMI counts from a single cell protein assay

Next-Gen Sequencing tools from the Horvath Lab

A Bayesian model for compositional single-cell data analysis

Papers with code for single cell related papers