Nextflow Modules
Showing module(s) with keyword "single-cell"
| Module | Keywords | Description |
|---|---|---|
| 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 bustools index | index creation for kb count quantification of single-cell data. |
| nf-core/multiseqdemux | demultiplexing hashing-based deconvolution single-cell | Identify singlets, doublets and negative cells from multiplexing experiments. Annotate singlets by tags. |
| nf-core/qcatch | single-cell quality control alevin-fry cell filtering QC report | Cell-filtering and QC reporting tool for alevin-fry quantification results |
| nf-core/scanpy/filter | filter quality-control scanpy single-cell preprocessing | Filter cells and genes in single-cell RNA-seq data using Scanpy |
| nf-core/scanpy/hashsolo | anndata single-cell hashing demultiplexing scanpy | Probabilistic demultiplexing of cell hashing data |
| nf-core/scanpy/pca | pca principal-component-analysis scanpy single-cell dimensionality-reduction | Perform principal component analysis (PCA) on single-cell RNA-seq data using Scanpy |
| nf-core/scanpy/scrublet | scrublet doublet-detection scanpy single-cell | Detect doublets in single-cell RNA-seq data using Scrublet via Scanpy |