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nf-core/hicar
1.0.0
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atac atac-seq hic hicar
+2
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Pipeline for HiCAR data, a robust and sensitive multi-omic co-assay for simultaneous measurement of transcriptome, chromatin accessibility and cis-regulatory chromatin contacts.
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nf-core/hlatyping
2.2.0
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dna hla hla-typing immunology
+3
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Precision HLA typing from next-generation sequencing data
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nf-core/imcyto
1.0.0
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cytometry image-analysis image-processing image-segmentation
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Image Mass Cytometry analysis pipeline
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nf-core/isoseq
3.0.1
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isoseq isoseq-3 rna tama
+1
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Genome annotation with PacBio Iso-Seq. Takes raw subreads as input, generate Full Length Non Chemiric (FLNC) sequences and produce a bed annotation.
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nf-core/kmermaid
0.1.0-alpha
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k-mer kmer kmer-counting kmer-frequency-count
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k-mer similarity analysis pipeline
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nf-core/liverctanalysis
0.0.0-800d619
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n/a
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UNDER CONSTRUCTION: pipeline for liver CT analysis
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nf-core/lncpipe
0.0.0-ac1ab61
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differential-expression lncrna long-non-coding non-coding
+3
|
UNDER DEVELOPMENT--- Analysis of long non-coding RNAs from RNA-seq datasets
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nf-core/longraredisease
1.0.0
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nanopore pacbio
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Long read sequencing pipeline to identify variants in patients with neurodevelopmental disorders
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nf-core/lsmquant
1.0.3
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3dunet image-analysis image-processing light-sheet-microcopy
+2
|
A pipeline for processing and analysis of light-sheet microscopy images.
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nf-core/mag
5.5.0
|
annotation assembly binning long-read-sequencing
+4
|
Assembly and binning of metagenomes
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nf-core/magmap
1.3.0
|
n/a
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Best-practice analysis pipeline for mapping reads to a (large) collections of genomes
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nf-core/marsseq
1.0.3
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facs-sorting mars-seq single-cell single-cell-rna-seq
+2
|
MARS-seq v2 pre-processing pipeline with velocity
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nf-core/mcmicro
2.0.0
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bioformats image-analysis image-processing microscopy
+8
|
An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.
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nf-core/meerpipe
0.0.0-2cf519f
|
n/a
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nf-core/meerpipe is a astronomy pipeline that processes MeerKAT pulsar data to produce images and data products for pulsar timing analysis
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nf-core/metaboigniter
2.0.1
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identification mass-spectrometry metabolomics ms1
+2
|
Pre-processing of mass spectrometry-based metabolomics data with quantification and identification based on MS1 and MS2 data.
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nf-core/metapep
1.0.0
|
n/a
|
From metagenomes to epitopes and beyond
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nf-core/metatdenovo
2.0.0
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eukaryotes metagenomics metatranscriptomics prokaryotes
+1
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Assembly and annotation of metatranscriptomic or metagenomic data for prokaryotic, eukaryotic and viruses.
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nf-core/methylarray
0.0.0-278890f
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n/a
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Process methylation data from Illumina arrays. Pre-processing, quality checks, confounder check and DMPs (differentially methylated positions) and DMRs (differentially methylated regions). Optionally estimates cell type composition and adjusts data for it.
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nf-core/methylong
2.0.0
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dna-methylation fiber-seq long-read ont
+1
|
Extract methylation calls from long reads (ONT/ PacBio)
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nf-core/methylseq
4.2.0
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bisulfite-sequencing dna-methylation em-seq epigenome
+6
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Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark/bwa-meth + MethylDackel or bwa-mem + rastair
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