Nextflow Modules
Showing module(s) with keyword "quantification"
| Module | Keywords | Description |
|---|---|---|
| nf-core/centrifuger/quantification | metagenomics quantification Centrifuger | Quantification (taxonomic profiling) of Centrifuger model |
| nf-core/diann | 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/mcquant | 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 | 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 | 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 | 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 | 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/rsem/calculateexpression | rsem expression quantification | Calculate expression with RSEM |
| nf-core/sentieon/rsemcalculateexpression | rsem expression quantification sentieon | Calculate expression with RSEM |
| nf-core/simpleaf/quant | quantification gene expression SimpleAF | simpleaf is a program to simplify and customize the running and configuration of single-cell processing with alevin-fry. |
| nf-core/slamdunk/all | slamseq rna-seq mapping snp quantification | Complete SLAMseq analysis pipeline including read mapping, filtering, SNP calling, and quantification |
| nf-core/stringtie/stringtie | transcript assembly quantification gtf | Transcript assembly and quantification for RNA-Se |