108 Open source projects that are alternatives of or similar to EWCE

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

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

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

Multiome GRN inference.

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

Differential expression analysis for single-cell RNA-seq data.

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

Deep Learning based cell composition analysis with Scaden.

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

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

Single-cell Orientation Tracing

Example of Deconvnet in PyTorch for VGG16

A tool to identify, orient, trim and rescue full length cDNA reads

A prediction model for differential gene expression (DE) based on genome-wide regulatory interactions

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

spatial transcriptome, single cell

MERlin is an extensible analysis pipeline applied to decoding MERFISH data

A tool for semi-automatic cell type annotation

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

Pipeline for annotating genomes using long read transcriptomics data with pinfish

A general framework for optimizing DNN dataflow on systolic array

Discrete Distributional Differential Expression

scLearn：Learning for single cell assignment

Spatial Single Cell Analysis in Python

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

TransPi – a comprehensive TRanscriptome ANalysiS PIpeline for de novo transcriptome assembly

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

mgatk: mitochondrial genome analysis toolkit

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

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

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

just annotate it, dammit!

An R implementation of the SINCERA pipeline for single cell RNA-seq profiling analysis

Bead-based single-cell atac processing

Code pipeline for the PaccMann^RL in iScience: https://www.cell.com/iscience/fulltext/S2589-0042(21)00237-6

Reference-based transcript discovery from long RNA read

Single-cell exploratory data analysis for RNA-Seq

CUT&RUN and CUT&Tag data processing and analysis

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

Code for the empty droplet and cell detection project from the HCA Hackathon.

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

Processing of single cell RNAseq data for the recovery of TCRs in python

Causal Deconvolution of Networks by Algorithmic Generative Models

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.

R API and htmlwidget for Vitessce

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

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

A collection of 50+ trajectory inference methods within a common interface 📥📤

Cell type specific enrichments using finemapped variants and quantitative epigenetic data

Single-Cell Omics Preparation Entity Tools

No description or website provided.

scRNA-seq data visualization from scrattch

Digital Expression Explorer 2 (DEE2): a repository of uniformly processed RNA-seq data

Efficient genotyping bi-allelic SNPs on single cells

Tools for single-cell data processing

Metacell - Single-cell mRNA Analysis

PISCES is a pipeline for rapid transcript quantitation, genetic fingerprinting, and quality control assessment of RNAseq libraries using Salmon.

Scripts to run and benchmark scRNA-seq cell cluster labeling methods

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

Convert between AnnData and SingleCellExperiment