Nextflow Modules
Showing module(s) with keyword "single-cell"
| Module | Keywords | Description |
|---|---|---|
| cellgeni/anndata/concat | concatenation single-cell anndata | In-memory concatenation of AnnData objects using anndata.concat. |
| cellgeni/anndata/concatondisk | concatenation single-cell anndata | Memory-efficient on-disk concatenation of AnnData objects using anndata.experimental.concat_on_disk. |
| cellgeni/fetch10xmeta | metadata GEO SRA ENA ArrayExpress BioProject 10x single-cell public data | Fetches and parses metadata for public 10x datasets from GEO (GSE*), ArrayExpress (E-MTAB*), or BioProject (PRJ*). Downloads raw metadata from SRA/ENA/BioStudies, resolves sample-to-run mappings, classifies each run by download type, and produces a merged links file. |
| cellgeni/hmetacells | metacells hierarchical-clustering single-cell scRNA-seq scATAC-seq | Hierarchical metacell aggregation for single-cell genomics data. |
| cellgeni/scanpy/aggregate | pseudobulk aggregation single-cell scRNA-seq scanpy | Pseudobulk aggregation of an AnnData object using scanpy.get.aggregate. |
| cellgeni/seacells | metacells single-cell scRNA-seq scATAC-seq aggregation | SEACells aggregates single-cell profiles into metacells from scRNA-seq or scATAC-seq data. |
| nf-core/anndata/barcodes | single-cell barcodes anndata subsetting transcriptomics | Module to subset AnnData object to cells with matching barcodes from the csv file |
| nf-core/anndata/getsize | anndata single-cell scanpy | Get the size (n_cells or n_genes) of an anndata object stored as a h5ad file |
| nf-core/bff | demultiplexing hashing-based deconvolution single-cell | Generating cell hashing calls from a matrix of count data. |
| nf-core/cellbender/merge | single-cell scRNA-seq ambient RNA removal | Module to use CellBender to remove ambient RNA from single-cell RNA-seq data |
| nf-core/cellbender/removebackground | single-cell scRNA-seq ambient RNA removal | Module to use CellBender to estimate ambient RNA from single-cell RNA-seq data |
| nf-core/cellranger/mkvdjref | reference mkvdjref index immunoprofiling single-cell cellranger | Module to build the VDJ reference needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkvdjref command. |
| nf-core/cellranger/vdj | align vdj reference immunoprofiling single-cell cellranger | Module to use Cell Ranger's pipelines analyze sequencing data produced from Chromium Single Cell Immune Profiling. |
| nf-core/demuxem | demultiplexing hashing-based deconvoltion single-cell | Demultiplexing cell nucleus hashing data, using the estimated antibody background probability. |
| nf-core/doubletdetection | single-cell doublets doublet_detection | Doublet detection in single-cell RNA-seq data |
| nf-core/gmmdemux | demultiplexing hashing-based deconvolution single-cell | GMM-Demux is a Gaussian-Mixture-Model-based software for processing sample barcoding data (cell hashing and MULTI-seq). |
| nf-core/hasheddrops | demultiplexing hashing-based deconvolution single-cell | Generating cell hashing calls from a matrix of count data. |
| nf-core/htodemux | demultiplexing hashing-based deconvolution single-cell | Demultiplex samples based on data from cell hashing. |
| nf-core/kallistobustools/count | scRNA-seq count single-cell kallisto bustools | quantifies scRNA-seq data from fastq files using kb-python. |
| nf-core/kallistobustools/ref | scRNA-seq count single-cell kallisto |