130 Open source projects that are alternatives of or similar to OrchestratingSingleCellAnalysis-release

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

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

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

CellO: Gene expression-based hierarchical cell type classification using the Cell Ontology

Deep Learning based cell composition analysis with Scaden.

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

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

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

Single cell analysis in the browser

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

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

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

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

Dynamical systems methods for RNA velocity analysis

Next-Gen Sequencing tools from the Horvath Lab

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

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

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

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

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

GREIN : GEO RNA-seq Experiments Interactive Navigator

Single-Cell Omics Preparation Entity Tools

Efficient genotyping bi-allelic SNPs on single cells

Single-cell Orientation Tracing

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

Create a cromphensive report of DEG list coming from any analysis of RNAseq data

Differential Gene Correlation Analysis

Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders

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

Single-cell exploratory data analysis for RNA-Seq

A proof of concept RNA-Seq pipeline with Nextflow

Lightweight and Fast; RNA-seq quantification at the event-level

Bead-based single-cell atac processing

scLearn：Learning for single cell assignment

CUT&RUN and CUT&Tag data processing and analysis

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

Tools for single-cell data processing

CWL tools and workflows for GGR

A graphical user interface for distributed data processing of high throughput genomics

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

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

Fast and accurate gene fusion detection from RNA-Seq data

R API and htmlwidget for Vitessce

scisorseqr is an R-package for processing of single-cell long read data and analyzing differential isoform expression across any two conditions

A tool for semi-automatic cell type annotation

Scripts to import your FeatureCounts output into DEXSeq

A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.

Convert between AnnData and SingleCellExperiment

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

PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data

Mouse cell atlas

A R framework for pipeline benchmarking, with application to single-cell RNAseq

Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

An automated RNA-seq pipeline using Nextflow

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

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

📊 Graphical User Interface for TCC package

Multi-omics analysis protocols by Lyu.

Pipeline for annotating genomes using long read transcriptomics data with pinfish

Conditional out-of-distribution prediction