Nextflow Modules
Showing module(s) with keyword "quantification"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/arcane/express | Process | single-cell rnaseq quantification mapping counts transcriptomics | Runs barcode correction, mapping, and UMI resolution in one go for single-cell RNA-seq quantification with Arcane |
| nf-core/centrifuger/quantification | Process | metagenomics quantification Centrifuger | Quantification (taxonomic profiling) of Centrifuger model |
| nf-core/diann | Process | proteomics mass spectrometry DIA spectral library quantification | Generic DIA-NN module for running any DIA-NN operation including in-silico library generation, preliminary analysis, empirical library assembly, individual analysis, and final quantification |
| nf-core/dia_proteomics_analysis | Workflow | diann proteomics dia quantification spectral library quantms-utils | Complete DIA-NN proteomics analysis pipeline including in-silico library generation, preliminary analysis, empirical library assembly, individual analysis, and final quantification. This subworkflow combines DIA-NN modules with quantms-utils for comprehensive data-independent acquisition (DIA) proteomics data processing. |
| nf-core/mcquant | Process | quantification image_analysis mcmicro highly_multiplexed_imaging | Mcquant extracts single-cell data given a multi-channel image and a segmentation mask. |
| nf-core/oarfish/alignmentmode | Process | bam transcript quantification alignment-mode | oarfish is a program for quantifying transcript-level expression from long-read sequencing technologies. Quantify pre-computed alignments of reads to the transcriptome (a name-sorted BAM, e.g. from minimap2/pbmm2). |
| nf-core/oarfish/alignmentprojectionmode | Process | fastq transcript quantification read-mode | oarfish is a program for quantifying transcript-level expression from long-read sequencing technologies. Project an existing spliced genome BAM (e.g. from minimap2 -ax splice) onto the annotated transcripts, then quantify. |
| nf-core/oarfish/readmode | Process | fastq transcript quantification read-mode | oarfish is a program for quantifying transcript-level expression from long-read sequencing technologies. Map raw reads to the transcriptome internally with the built-in rammap mapper, then quantify. |
| nf-core/oarfish/readprojectionmode | Process | fastq transcript quantification read-mode | oarfish is a program for quantifying transcript-level expression from long-read sequencing technologies. Spliced-align raw reads to the genome, project each read's genomic alignments onto the annotated transcripts via bramble, then quantify. |
| nf-core/openms/featurefinderidentification | Process | quantification feature detection featureXML openms proteomics | Detects and quantifies features in MS1 data based on peptide identifications (targeted feature extraction). |
| nf-core/openms/idconflictresolver | Process | quantification consensusXML openms proteomics | Resolves ambiguous annotations of features with peptide identifications, keeping the best-scoring hit per feature. |
| nf-core/quantify_pseudo_alignment | Workflow | rnaseq quantification kallisto salmon | Perform quantification with Salmon or Kallisto to produce count tables and SummarizedExperiment objects |
| nf-core/quantify_rsem | Workflow | rnaseq quantification rsem tximport | Perform quantification with RSEM to produce count tables, legacy merge matrices, and SummarizedExperiment objects |
| nf-core/quant_tximport_summarizedexperiment | Workflow | rnaseq quantification tximport summarizedexperiment salmon kallisto rsem | Post-process transcript-level quantification results using tximport to produce count matrices and SummarizedExperiment objects |
| nf-core/rsem/calculateexpression | Process | rsem expression quantification | Calculate expression with RSEM |
| nf-core/sentieon/rsemcalculateexpression | Process | rsem expression quantification sentieon | Calculate expression with RSEM |
| nf-core/simpleaf/quant | Process | quantification gene expression SimpleAF |