Nextflow Modules
Showing module(s) with keyword "transcriptomics"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| 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/arcane/filter | Process | single-cell rnaseq filter gtf fasta transcriptomics | Filter GTF annotations and genome sequence for alignment-free single-cell RNA-seq quantification with Arcane |
| nf-core/arcane/index | Process | single-cell rnaseq index kmer hash transcriptomics | Build a k-mer hash index from a filtered reference for alignment-free single-cell RNA-seq quantification with Arcane |
| nf-core/ciri2 | Process | circRNA detection genomics transcriptomics | Circular RNA identification based on multiple seed matching |
| nf-core/cpc2 | Process | coding potential genomics transcriptomics | Coding Potential Calculator 2 |
| nf-core/proseg/proseg | Process | segmentation spatial transcriptomics | Proseg (probabilistic segmentation) is a cell segmentation method for in situ spatial transcriptomics. |
| nf-core/proseg/proseg2baysor | Process | segmentation spatial transcriptomics | Convert proseg outputs to baysor format for import to Xenium explorer |
| nf-core/rtn/tni | Process | regulatory network transcriptomics transcription factors | Uses the RTN R package for transcriptional regulatory network inference (TNI). |
| nf-core/scds | Process | doublet single-cell transcriptomics | Module to use scds for doublet scoring |
| nf-core/soupx | Process | single-cell transcriptomics ambient | Estimation and removal of cell free mRNA contamination in droplet based single cell RNA-seq data. The filtered counts are preprocessed with Seurat (LogNormalize, PCA, kNN graph, clustering) to provide cluster assignments to SoupX, which then estimates per-cluster contamination and adjusts counts. The adjusted counts are written to the output H5AD as an `ambient` layer. |
| nf-core/spotiflow | Process | imaging image microscopy transcriptomics spatial spot detection | Spotiflow, accurate and efficient spot detection with stereographic flow. |
| nf-core/telescope/assign | Process | EM single-locus transcriptomics | The telescope assign program finds overlapping reads between an alignment (SAM/BAM) and an annotation (GTF) then reassigns reads using a statistical model. |
| nf-core/tetranscripts | Process | transposable TE transcriptomics | Runs TEtranscripts which summarises transposable element content of a bam file. |