Stars
A modular graph-based Retrieval-Augmented Generation (RAG) system
Comprehensive pipeline for donor demultiplexing in single cell
Port of symphony algorithm of single-cell reference atlas mapping to Python
DrEval is a toolkit that ensures drug response prediction evaluations are statistically sound, biologically meaningful, and reproducible.
Pipeline for testing drug response prediction models in a statistically and biologically sound way.
rapids-singlecell: GPU-accelerated framework for scRNA analysis
Declarative creation of composable visualization for Python (Complex heatmap, Upset plot, Oncoprint and more~)
ATAC-seq peak-calling and QC analysis pipeline
ChIP-seq peak-calling, QC and differential analysis pipeline.
Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection
CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.
A single cell transcriptomics pipeline for QC, integration and making the data presentable
Bioinformatics pipeline that makes use of expression and open chromatin data to identify differentially active transcription factors across conditions.
circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data
Nextflow runs monitoring and organisation UI
A nextflow pipeline for processing sc-RNASeq data, performing QC and integration and preparing the results for further investigation using cellxgene.
Bioinformatics pipeline to identify differentially active transcription factors between conditions using expression and epigenetic data
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.