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nf-core/spatialaxe
1.0.1
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10x-genomics atera image-processing spatial
+4
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A bioinformatics best-practice processing and quality control pipeline for Xenium and Artera data
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nf-core/spatialvi
0.0.0-17d6cb0
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10x-genomics 10xgenomics image-processing microscopy
+7
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Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.
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nf-core/spinningjenny
0.0.0-d41309a
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n/a
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Pipeline for simulating the first industrial revolution using Agent Based Models.
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nf-core/ssds
0.0.0-0cc3ee6
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chip-ssds dmc1-ssds dsbs ori-ssds
+4
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Single-stranded DNA Sequencing (SSDS) nf-core pipeline
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nf-core/stableexpression
1.1.0
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expression housekeeping-genes qpcr-analysis
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This pipeline is designed to identify the most stable genes in one or more expression datasets (RNA-seq / Microarray). The ideal use case is for determining the most suitable RT-qPCR reference genes for a given species.
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nf-core/taxmarker
0.0.0-acbf705
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mislabel-identification mislabeling sativa taxmarker
+2
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Identify taxonomically mislabelled sequences
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nf-core/taxprofiler
2.0.1
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classification illumina long-reads metagenomics
+7
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Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
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nf-core/tbanalyzer
0.0.0-7e2936d
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mycobacterium-tuberculosis mycobacterium-tuberculosis-complex
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An nf-core (meta) pipeline for analysis of different members of Mycobacterium tuberculosis complex.
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nf-core/tfactivity
0.0.0-5ed1431
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open-chromatin-regions transcription-factors transcriptomics
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Bioinformatics pipeline that makes use of expression and open chromatin data to identify differentially active transcription factors across conditions.
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nf-core/troughgraph
0.0.0-c3e250e
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permafrost
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A quantitative assessment of the underlying permafrost landscapes and, per extension, of the level of permafrost thaw in the region
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nf-core/tumourevo
1.0.0
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cancer-evolution cancer-genomics copy-number-variation mutational-signatures
+4
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Analysis pipeline to model tumour clonal evolution from WGS data (driver annotation, quality control of copy number calls, subclonal and mutational signature deconvolution)
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nf-core/variantbenchmarking
1.5.0
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benchmark small-variants structural-variants variant-calling
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Pipeline to evaluate and validate the accuracy of variant calling methods in genomic research
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nf-core/variantcatalogue
0.0.0-64de12d
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n/a
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Pipeline to generate variant catalogues, a list of variants and their frequencies in a population, from whole genome sequences.
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nf-core/variantprioritization
1.0.0
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n/a
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Bioinformatics analysis pipeline for the functional annotation and translation of somatic SNVs/InDels and copy number abberations for precision cancer medicine using Personal Cancer Genome Reporter (PCGR). The pipeline offers germline SNVs/INDELS intepretation and annotation using Cancer Predisposition Sequencing Reporter (CPSR).
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nf-core/vipr
0.0.0-6eef3b3
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genome-assembly metagenomics variant-calling viral
+5
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Assembly and intrahost / low-frequency variant calling for viral samples
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nf-core/viralintegration
0.1.1
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chimeric-alignment ctat viral-integration virus
+1
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Analysis pipeline for the identification of viral integration events in genomes using a chimeric read approach.
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nf-core/viralmetagenome
1.2.0
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epidemiology fastq ngs viral-metagenomics
+2
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A nf-core pipeline for untargeted whole genome reconstruction with iSNV detection from metagenomic samples.
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nf-core/viralrecon
3.0.0
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amplicon artic assembly covid-19
+11
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Assembly and intrahost/low-frequency variant calling for viral samples
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