109 Open source projects that are alternatives of or similar to iDEA

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

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

Dynamical systems methods for RNA velocity analysis

Single cell analysis in the browser

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

🐟 🔬🦀 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

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, ...

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

Bead-based single-cell atac processing

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

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

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

Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)

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

CUT&RUN and CUT&Tag data processing and analysis

Tools for single-cell data processing

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

Reference-free reconstruction and error correction of transcriptomes from Nanopore long-read sequencing

Multiome GRN inference.

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

Scripts to import your FeatureCounts output into DEXSeq

Convert between AnnData and SingleCellExperiment

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

Mouse cell atlas

Pipeline for annotating genomes using long read transcriptomics data with pinfish

Cell type specific enrichments using finemapped variants and quantitative epigenetic data

Differential Gene Correlation Analysis

Automated generation of tailored bioinformatics Jupyter Notebooks via a user interface.

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

CWL tools and workflows for GGR

A proof of concept RNA-Seq pipeline with Nextflow

A pipeline for the computational evaluation of RNA-Seq data

Single-Cell Omics Preparation Entity Tools

📊 Graphical User Interface for TCC package

Efficient genotyping bi-allelic SNPs on single cells

🐍 Snakefiles for common RNA-seq data analysis workflows.

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

Multi-omics analysis protocols by Lyu.

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

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

Fast and accurate gene fusion detection from RNA-Seq data

Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.

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

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

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

An automated RNA-seq pipeline using Nextflow

GREIN : GEO RNA-seq Experiments Interactive Navigator

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

Methods for detecting doublets in single-cell sequencing data

Conditional out-of-distribution prediction

A tool for semi-automatic cell type annotation

Deep Learning based cell composition analysis with Scaden.

R API and htmlwidget for Vitessce

A course on Analysing Next Generation (/High Throughput etc..) Sequencing data using Bioconductor

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

Single-cell copy number calling and event history reconstruction.

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

Summer school course materials collection