Nextflow Modules
Showing module(s) with keyword "transcript"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/custom/tx2gene | Process | gene gtf pseudoalignment rsem transcript | Make a transcript/gene mapping from a GTF and cross-reference with transcript quantifications. |
| nf-core/evigene/tr2aacds | Process | genomics transcript assembly clean polish filter redundant duplicate | Uses evigene/scripts/prot/tr2aacds.pl to filter a transcript assembly |
| 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/rseqc/tin | Process | rnaseq transcript integrity | Calculate TIN (transcript integrity number) from RNA-seq reads |
| nf-core/stringtie/stringtie | Process | transcript assembly quantification gtf | Transcript assembly and quantification for RNA-Se |
| nf-core/summarizedexperiment/summarizedexperiment | Process | gene transcript sample matrix assay | SummarizedExperiment container |
| nf-core/transdecoder/longorf | Process | eucaryotes gff transcript coding | TransDecoder identifies candidate coding regions within transcript sequences. it is used to build gff file. |
| nf-core/tsebra | Process | genomics transcript selector gene prediction evidence | Transcript Selector for BRAKER TSEBRA combines gene predictions by selecting transcripts based on their extrisic evidence support |
| nf-core/tximeta/tximport | Process | gene kallisto pseudoalignment rsem salmon transcript | Import transcript-level abundances and estimated counts for gene-level analysis packages |