78 Open source projects that are alternatives of or similar to celltypist

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

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

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

Papers with code for single cell related papers

Clone identification from single-cell data

Reference mapping for single-cell genomics

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

R package to do the Ligand Receptor Analysis Visualization

R package to visualize gene expression data based on weighted kernel density estimation

Spatial Transcriptomics Dashboard

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

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

Mouse cell atlas

Examples using Clustergrammer2 to explore high-dimensional datasets.

Single-Cell Omics Preparation Entity Tools

Conditional out-of-distribution prediction

CUT&RUN and CUT&Tag data processing and analysis

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

Clustering scRNAseq by genotypes

Efficient genotyping bi-allelic SNPs on single cells

scGEAToolbox: Matlab toolbox for single-cell gene expression analyses

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

cTPnet Package

Next-Gen Sequencing tools from the Horvath Lab

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

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

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

Convert between AnnData and SingleCellExperiment

Bead-based single-cell atac processing

Efficient and precise single-cell reference atlas mapping with Symphony

Simulating single-cell data using gene regulatory networks 📠

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

Single cell analysis in the browser

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

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

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

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

Reconstruction of complex single-cell trajectories using CellRouter

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

Conversion between scRNA-seq objects

BEER: Batch EffEct Remover for single-cell data

Single-cell Hierarchical Poisson Factorization

Single-cell copy number calling and event history reconstruction.

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

Tools for single-cell data processing

Dynamical systems methods for RNA velocity analysis

A tool for fast and accurate summarizing of variant calling format (VCF) files

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

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

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.

No description or website provided.

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

Demultiplexing pooled scRNA-seq data with or without genotype reference

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

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

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.

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

Spatial alignment of single cell transcriptomic data.

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