56 Open source projects that are alternatives of or similar to SCOPE-tools

CUT&RUN and CUT&Tag data processing and analysis

Efficient genotyping bi-allelic SNPs on single cells

Tools for single-cell data processing

Convert between AnnData and SingleCellExperiment

Mouse cell atlas

Single cell analysis in the browser

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

Conditional out-of-distribution prediction

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

Single-cell copy number calling and event history reconstruction.

Next-Gen Sequencing tools from the Horvath Lab

Simulating single-cell data using gene regulatory networks 📠

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

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

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

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

R package to do the Ligand Receptor Analysis Visualization

Clone identification from single-cell data

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

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

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

Dynamical systems methods for RNA velocity analysis

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

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

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

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

Reference mapping for single-cell genomics

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

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

Papers with code for single cell related papers

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

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

No description or website provided.

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

spatial transcriptome, single cell

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

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

Methods for detecting doublets in single-cell sequencing data

mgatk: mitochondrial genome analysis toolkit

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

Multiome GRN inference.

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

R API and htmlwidget for Vitessce

Cell type specific enrichments using finemapped variants and quantitative epigenetic data

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

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

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

🧬 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

A tool for semi-automatic cell type annotation

kallisto | bustools workflow for pre-processing 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, ...

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

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

Bead-based single-cell atac processing