140 Open source projects that are alternatives of or similar to scarches

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

Tutorials, workflows, and convenience scripts for Single Cell Portal

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

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

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

scGEAToolbox: Matlab toolbox for single-cell gene expression analyses

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

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

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

A tool for semi-automatic cell type annotation

Papers with code for single cell related papers

Detecting Hate Speech in Memes Using Multimodal Deep Learning Approaches: Prize-winning solution to Hateful Memes Challenge. https://arxiv.org/abs/2012.12975

spatial transcriptome, single cell

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

interactive Multi Objective K-mer Analysis

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

The official repository for the CVPR 2019 paper "Overcoming Limitations of Mixture Density Networks: A Sampling and Fitting Framework for Multimodal Future Prediction"

Multiome GRN inference.

Community-provided extensions to Seurat

Data-driven Network-based Bayesian Inference of Drivers

Cell type specific enrichments using finemapped variants and quantitative epigenetic data

Population Assignment using Genetic, Non-genetic or Integrated Data in a Machine-learning Framework. Methods in Ecology and Evolution. 2018;9:439–446.

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.

Reconstruction of complex single-cell trajectories using CellRouter

Discrete Distributional Differential Expression

cTPnet Package

mgatk: mitochondrial genome analysis toolkit

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

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

Configurable data bridge for permanent ETL jobs

Interactive Differential Expression AnaLysis - DE made accessible and reproducible

Single-cell Hierarchical Poisson Factorization

Template to deploy a Data Product for Batch data processing into a Data Landing Zone of the Data Management & Analytics Scenario (former Enterprise-Scale Analytics). The Data Product template can be used by cross-functional teams to ingest, provide and create new data assets within the platform.

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

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

R API and htmlwidget for Vitessce

Installer for Thymeflow, a personal knowledge management system.

Code accompanying our ECCV-2020 paper on 3D Neural Listeners.

The Read Origin Protocol (ROP) is a computational protocol that aims to discover the source of all reads, including those originating from repeat sequences, recombinant B and T cell receptors, and microbial communities.

Enjoy your transcriptomic data and analysis responsibly - like sipping a cocktail

Make rapid visualizations of RNA-seq data in R

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

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

No description or website provided.

A comprehensive dimensional reduction framework to recover the latent topology from high-dimensional data.

Multimodal Image Synthesis and Editing: A Survey

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.

Clustering scRNAseq by genotypes

A .NET class library that allows you to import data from different sources into a unified destination

This repository contains R code, with which you can create 3D UMAP and tSNE plots of Seurat analyzed scRNAseq data

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

Kuwala is the no-code data platform for BI analysts and engineers enabling you to build powerful analytics workflows. We are set out to bring state-of-the-art data engineering tools you love, such as Airbyte, dbt, or Great Expectations together in one intuitive interface built with React Flow. In addition we provide third-party data into data sc…

The code for our IEEE ACCESS (2020) paper Multimodal Emotion Recognition with Transformer-Based Self Supervised Feature Fusion.

A framework for Multimodal Intelligence research from Inspur HSSLAB.

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

Conversion between scRNA-seq objects

GREIN : GEO RNA-seq Experiments Interactive Navigator

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