81 Open source projects that are alternatives of or similar to babel

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

Papers with code for single cell related papers

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

A tool for semi-automatic cell type annotation

BEER: Batch EffEct Remover for single-cell data

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

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.

Clone identification from single-cell data

Reference mapping for single-cell genomics

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

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

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

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

Methods for detecting doublets in single-cell sequencing 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, ...

No description or website provided.

Bead-based single-cell atac processing

Single-cell Hierarchical Poisson Factorization

CUT&RUN and CUT&Tag data processing and analysis

Tools for single-cell data processing

Efficient and precise single-cell reference atlas mapping with Symphony

spatial transcriptome, single cell

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

A bioinformatics API and web-app to integrate multi-omics datasets & interface with public databases.

Spatial alignment of single cell transcriptomic data.

Cell type specific enrichments using finemapped variants and quantitative epigenetic data

Mouse cell atlas

Conversion between scRNA-seq objects

Reconstruction of complex single-cell trajectories using CellRouter

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

Model-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles

Multi-omics Autoencoder Integration: Deep learning-based heterogenous data analysis toolkit

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

mgatk: mitochondrial genome analysis toolkit

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

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

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

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

Single-Cell Omics Preparation Entity Tools

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

Efficient genotyping bi-allelic SNPs on single cells

Multiome GRN inference.

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

Demultiplexing pooled scRNA-seq data with or without genotype reference

R API and htmlwidget for Vitessce

Convert between AnnData and SingleCellExperiment

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

Single cell analysis in the browser

cTPnet Package

Conditional out-of-distribution prediction

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

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

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

scGEAToolbox: Matlab toolbox for single-cell gene expression analyses

Single-cell copy number calling and event history reconstruction.

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

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

Next-Gen Sequencing tools from the Horvath Lab

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

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