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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/denovotranscript
1.2.1
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denovo-assembly rna-seq transcriptome
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A pipeline for de novo transcriptome assembly of paired-end short reads from bulk RNA-seq
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nf-core/differentialabundance
2.0.0
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atac-seq chip-seq deseq2 differential-abundance
+6
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Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
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nf-core/dualrnaseq
1.0.0
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dualrna-seq host-pathogen quantification readmapping
+1
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Analysis of Dual RNA-seq data - an experimental method for interrogating host-pathogen interactions through simultaneous RNA-seq.
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nf-core/lncpipe
0.0.0-ac1ab61
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differential-expression lncrna long-non-coding non-coding
+3
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UNDER DEVELOPMENT--- Analysis of long non-coding RNAs from RNA-seq datasets
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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
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MARS-seq v2 pre-processing pipeline with velocity
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nf-core/rnafusion
4.1.3
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fusion fusion-genes gene-fusion rna
+1
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RNA-seq analysis pipeline for detection of gene-fusions
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nf-core/rnaseq
3.27.0
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rna rna-seq
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RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
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nf-core/rnasplice
1.0.4
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alternative-splicing rna rna-seq splicing
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rnasplice is a bioinformatics pipeline for RNA-seq alternative splicing analysis
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nf-core/scflow
0.0.0-c2c9728
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rnaseq single-cell single-nuclei single-nuclei-rna-sequencing
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Please consider using/contributing to https://github.com/nf-core/scdownstream
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nf-core/scnanoseq
1.3.0
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10xgenomics long-read-sequencing nanopore rna-seq
+3
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Single-cell/nuclei pipeline for data derived from Oxford Nanopore and 10X Genomics
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nf-core/scrnaseq
4.2.0
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10x-genomics 10xgenomics alevin bustools
+5
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Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection
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nf-core/smrnaseq
2.4.1
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small-rna smrna-seq
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A small-RNA sequencing analysis pipeline
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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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