Nextflow Modules
Showing module(s) with keyword "counts"
| 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/bam_qc_picard | Workflow | statistics counts hs_metrics wgs_metrics bam sam cram | Produces comprehensive statistics from BAM file |
| nf-core/bam_stats_samtools | Workflow | statistics counts bam sam cram | Produces comprehensive statistics from SAM/BAM/CRAM file |
| nf-core/cobiontid/kmercounter | Process | cobiontid kmer counts npy fasta | A rust based tool based on Needletail's FASTA parser tallies k-mer counts for large sequencing rounds. Written with downstream processing with Tensorflow or numpy in mind. |
| nf-core/custom/collectfeaturecounts | Process | featurecounts collect counts tpm | Collects one or more subread/featureCounts raw output files (typically one per sample, for the same feature type/ORF caller) into a single long-format table with per-sample TPM (Transcripts Per Million) computed. |
| nf-core/custom/rsemmergecounts | Process | rsem merge counts gene expression | Merge per-sample RSEM results into wide and long format TSV matrices |
| nf-core/edger/differential | Process | differential expression rna-seq counts edger | Runs a differential expression analysis on count data with edgeR. Options are passed via `ext.args` as `--option value` pairs: `gene_id_col` (default `gene_id`), `sample_id_col` (`experiment_accession`), `blocking_variables` (`;`-separated sample sheet columns, not combinable with a formula), `subset_to_contrast_samples` (`FALSE`, needs a contrast variable), `exclude_samples_col` and `exclude_samples_values` (`;`-separated), `filter_by_expr` (`FALSE`), `min_count` (`10`), `norm_method` (`TMM`), `test_method` (`qlf` for glmQLFit/glmQLFTest or `lrt` for glmFit/glmLRT), `robust` (`TRUE`), `prior_count` (`2`), `adjust_method` (`BH`) and `round_digits` (no rounding). Defaults that differ from edgeR's own: `robust` is `TRUE` for both `estimateDisp` and `glmQLFit` (edgeR default `FALSE`), and `filterByExpr` is off by default because pipelines usually filter upstream; when enabled, `min_count` is passed as `min.count`. Sample sheet column names, including those used in a formula, are converted with `make.names()`. |
| nf-core/gatk4/determinegermlinecontigploidy | Process | copy number counts determinegermlinecontigploidy gatk4 | Determines the baseline contig ploidy for germline samples given counts data |
| nf-core/samtools/flagstat | Process | stats mapping counts bam sam cram | Counts the number of alignments in a BAM/CRAM/SAM file for each FLAG type |
| nf-core/samtools/idxstats | Process | stats mapping counts chromosome bam sam cram | Reports alignment summary statistics for a BAM/CRAM/SAM file |
| nf-core/samtools/stats | Process | statistics counts bam sam cram | Produces comprehensive statistics from SAM/BAM/CRAM file |
| nf-core/subread/featurecounts | Process | counts fasta genome reference | Count reads that map to genomic features |