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/cellbender/removebackground | cellbender single-cell RNA-seq ambient RNA empty droplets artifact removal | Removes ambient RNA and empty droplet artifacts from single-cell RNA-seq data using CellBender, producing a per-sample output directory with filtered count matrices. |
| cellgeni/cellranger/count | cellranger 10x single-cell RNA-seq count matrix | Runs Cell Ranger count on 10x single-cell RNA-seq FASTQs to align reads, generate feature-barcode matrices, and produce per-sample output directories. |
| 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. |
| cellgeni/starsolo10x | STARsolo STAR alignment single-cell 10x RNA-seq count matrix | Aligns 10x single-cell RNA-seq FASTQs to a reference genome using STARsolo, producing per-sample output directories with count matrices and summary statistics. |
| cellgeni/starsoloqc | STARsolo STAR QC quality control single-cell 10x RNA-seq | Collects QC statistics from STARsolo output directories, producing a merged TSV summary of alignment and cell-calling metrics across all samples in a dataset. |
| 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 |