Nextflow Modules
Showing module(s) with keyword "single-cell"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| cellgeni/anndata/concat | Process | concatenation single-cell anndata | In-memory concatenation of AnnData objects using anndata.concat. |
| cellgeni/anndata/concatondisk | Process | concatenation single-cell anndata | Memory-efficient on-disk concatenation of AnnData objects using anndata.experimental.concat_on_disk. |
| cellgeni/cellbender/qc | Process | cellbender single-cell RNA-seq quality control ambient RNA | Collects summary statistics from CellBender outputs and produces a QC report directory with PDF plots and per-sample RDS summaries. |
| cellgeni/cellbender/removebackground | Process | 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 | Process | 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 | Process | 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 | Process | metacells hierarchical-clustering single-cell scRNA-seq scATAC-seq | Hierarchical metacell aggregation for single-cell genomics data. |
| cellgeni/rename10xsample | Process | 10x single-cell FASTQ rename Cell Ranger sample | Collects per-run Cell Ranger-style FASTQs for a sample and renames them to a consistent sample-level naming scheme, ready for downstream alignment. |
| cellgeni/scanpy/aggregate | Process | pseudobulk aggregation single-cell scRNA-seq scanpy | Pseudobulk aggregation of an AnnData object using scanpy.get.aggregate. |
| cellgeni/seacells | Process | metacells single-cell scRNA-seq scATAC-seq aggregation | SEACells aggregates single-cell profiles into metacells from scRNA-seq or scATAC-seq data. |
| cellgeni/sra2fastq | Process | SRA FASTQ conversion single-cell 10x public data | Converts a local SRA file to split gzipped FASTQ files using parallel-fastq-dump, producing one FASTQ per read slot ready for downstream processing. |
| cellgeni/starsolo10x | Process | 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 | Process | 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 | Process | single-cell barcodes anndata subsetting transcriptomics | Module to subset AnnData object to cells with matching barcodes from the csv file |
| nf-core/anndata/convert | Process | single-cell anndata conversion | Convert an AnnData H5AD file to Seurat and SingleCellExperiment RDS objects |
| nf-core/anndata/getsize | Process | anndata single-cell scanpy |