88 Open source projects that are alternatives of or similar to scAlign

Reference mapping for single-cell genomics

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

Papers with code for single cell related papers

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

A tool for semi-automatic cell type annotation

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

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.

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

Clustering scRNAseq by genotypes

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

Tutorials, workflows, and convenience scripts for Single Cell Portal

Clone identification from single-cell data

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

Dynamical systems methods for RNA velocity analysis

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

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

Examples using Clustergrammer2 to explore high-dimensional datasets.

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.

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

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

cTPnet Package

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

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

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

Spatial Transcriptomics Dashboard

BEER: Batch EffEct Remover for single-cell data

Methods for detecting doublets in single-cell sequencing data

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

Reconstruction of complex single-cell trajectories using CellRouter

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

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

Conversion between scRNA-seq objects

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

SHARP: Single-cell RNA-seq Hyper-fast and Accurate processing via ensemble Random Projection

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

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

Single-cell Hierarchical Poisson Factorization

No description or website provided.

Pipeline for initial analysis of droplet-based single-cell RNA-seq data

spatial transcriptome, single cell

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

Imputation method for scRNA-seq based on low-rank approximation

mgatk: mitochondrial genome analysis toolkit

Cell type specific enrichments using finemapped variants and quantitative epigenetic data

Multiome GRN inference.

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

Demultiplexing pooled scRNA-seq data with or without genotype reference

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

R API and htmlwidget for Vitessce

Efficient and precise single-cell reference atlas mapping with Symphony

R package to do the Ligand Receptor Analysis Visualization

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

Spatial alignment of single cell transcriptomic data.

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

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

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

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

Discover differential transcript usage from polyA-captured single cell RNA-seq data

scGEAToolbox: Matlab toolbox for single-cell gene expression analyses

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