{"repo":"nf-core/hadge","free":true,"listed":false,"github":"https://github.com/nf-core/hadge","clone":"git clone https://github.com/nf-core/hadge.git","description":"Comprehensive pipeline for donor demultiplexing in single cell","language":"Nextflow","stars":26,"topics":["deconvolution","demultiplexing","single-cell","nextflow","nf-core","pipeline","workflow","cell-hashing","donor-assignment","genetic-demultiplexing"],"license":"MIT","category":"workflow-automation","readme_excerpt":"Introduction nf-core/hadge ( ha shing d econvolution combined with ge notype information) is a bioinformatics pipeline that combines 11 methods to perform both hashing- and genotype-based deconvolution on single cell multiplexing data. It takes a samplesheet with count matrices, BAM and VCF files as input, performs deconvolution with every method, joins all results and finally recovers previously discarded cells by combining the best performing methods (donor matching). 1. Untar matrices 2. Extract hto names from matrix 3. Perform genetic-based deconvolution 1. Get single cell genotype cellSNP 2. vireo 3. demuxlet 4. freemuxlet 5. souporcell 4. summarize assignments and classifications 5. Perform hashing-based deconvolution 1. htodemux 2. multiseq 3. bff 4. demuxem 5. gmm-demux 6. hasheddrops 7. hashsolo 6. summarize assignments and classifications 7. Join all results 8. Donor match 9. Find informative variants 10. Create AnnData and Mudata objects 11. MultiQC Usage [!NOTE] If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data. The profile test is used to test hadge's rescue mode, but you can also test the other modes with the profiles test genetic , test hashing and test donor match . First, prepare a samplesheet with your input data that looks as follows: samplesheet.csv : Each row contains data from a single-cell multiplexing experiment. The RNA","default_branch":null,"files":null,"tree":[],"storefront":"/r/nf-core","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/nf-core/hadge/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}