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nf-core/abotyper
0.0.0-4e7592c
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n/a
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A pipeline for characterising the Human Blood Group and Red Cell Antigens using Oxford Nanopore third-generation sequencing data.
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nf-core/airrflow
5.1.2
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airr b-cell immcantation immunorepertoire
+1
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B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework
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nf-core/alleleexpression
0.0.0-985ad30
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n/a
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Alleleexpression is a nf-core pipeline for allele-specific expression (ASE) analysis using STAR-WASP for alignment, UMI-tools for deduplication, and phaser for haplotype phasing and ASE detection.
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nf-core/ampliseq
3.0.0
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16s 18s amplicon-sequencing edna
+12
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Amplicon sequencing analysis workflow using DADA2 and QIIME2
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nf-core/atacseq
2.1.2
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atac-seq chromatin-accessibiity
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ATAC-seq peak-calling and QC analysis pipeline
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nf-core/bacass
2.6.1
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assembly bacterial-genomes denovo denovo-assembly
+4
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Simple bacterial assembly and annotation pipeline
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nf-core/bacmodel
0.0.0-c6948d4
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bacteria genome-scale-models metabolic-models metaomics
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Systems-based bacterial functional modeling pipeline
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nf-core/bactmap
1.0.0
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bacteria bacterial bacterial-genome-analysis genomics
+3
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A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences
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nf-core/bamtofastq
2.2.1
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bamtofastq conversion cramtofastq
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Converts bam or cram files to fastq format and does quality control.
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nf-core/cageseq
1.0.2
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cage cage-seq cageseq-data gene-expression
+1
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CAGE-sequencing analysis pipeline with trimming, alignment and counting of CAGE tags.
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nf-core/callingcards
1.0.0
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n/a
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A pipeline for processing calling cards data
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nf-core/cellpainting
0.0.0-ce04836
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n/a
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n/a
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nf-core/chipseq
2.1.0
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chip chip-seq chromatin-immunoprecipitation macs2
+1
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ChIP-seq peak-calling, QC and differential analysis pipeline.
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nf-core/circdna
1.1.0
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ampliconarchitect ampliconsuite circle-seq circular
+5
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Pipeline for the identification of extrachromosomal circular DNA (ecDNA) from Circle-seq, WGS, and ATAC-seq data that were generated from cancer and other eukaryotic cells.
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nf-core/circrna
0.0.0-23fdf1d
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circrna circrna-pipeline circrna-prediction circular-rna
+5
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circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data
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nf-core/clipseq
1.0.0
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clip clip-seq peak-calling rna-rbp-interactions
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CLIP sequencing analysis pipeline for QC, pre-mapping, genome mapping, UMI deduplication, and multiple peak-calling options.
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nf-core/coproid
2.0.1
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adna ancient-dna coprolite microbiome
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Coprolite host Identification pipeline
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nf-core/createpanelrefs
1.0.0
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n/a
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Generate Panel of Normals, models or other similar references from lots of samples
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nf-core/createtaxdb
3.1.0
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database database-builder metagenomic-profiling metagenomics
+2
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Parallelised and automated construction of metagenomic classifier databases of different tools
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nf-core/crisprseq
2.3.0
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crispr crispr-analysis crispr-cas ngs
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A pipeline for the analysis of CRISPR edited data. It allows the evaluation of the quality of gene editing experiments using targeted next generation sequencing (NGS) data (`targeted`) as well as the discovery of important genes from knock-out or activation CRISPR-Cas9 screens using CRISPR pooled DNA (`screening`).
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