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nf-core/ampliseq
3.0.0
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16s 18s amplicon-sequencing edna
+12
|
Amplicon sequencing analysis workflow using DADA2 and QIIME2
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nf-core/cageseq
1.0.2
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cage cage-seq cageseq-data gene-expression
+1
|
CAGE-sequencing analysis pipeline with trimming, alignment and counting of CAGE tags.
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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
|
CLIP sequencing analysis pipeline for QC, pre-mapping, genome mapping, UMI deduplication, and multiple peak-calling options.
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nf-core/dartseq
0.0.0-da3db96
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dartseq rna-editing rnaseq
|
Pipeline for m6A detection in RNAseq data
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nf-core/denovotranscript
1.2.1
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denovo-assembly rna-seq transcriptome
|
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
|
atac-seq chip-seq deseq2 differential-abundance
+6
|
Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
|
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nf-core/dualrnaseq
1.0.0
|
dualrna-seq host-pathogen quantification readmapping
+1
|
Analysis of Dual RNA-seq data - an experimental method for interrogating host-pathogen interactions through simultaneous RNA-seq.
|
|
nf-core/hlatyping
2.2.0
|
dna hla hla-typing immunology
+3
|
Precision HLA typing from next-generation sequencing data
|
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nf-core/isoseq
3.0.1
|
isoseq isoseq-3 rna tama
+1
|
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/lncpipe
0.0.0-ac1ab61
|
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/marsseq
1.0.3
|
facs-sorting mars-seq single-cell single-cell-rna-seq
+2
|
MARS-seq v2 pre-processing pipeline with velocity
|
|
nf-core/nascent
2.3.0
|
gro-seq nascent pro-seq rna
+2
|
Nascent Transcription Processing Pipeline
|
|
nf-core/ncrnannotator
0.0.0-b3e953b
|
infernal ncrna rfam
|
nf-core pipeline for genome-level ncRNA annotation using Infernal
|
|
nf-core/oncoanalyser
3.0.0
|
cancer clinical ctdna dna
+9
|
A comprehensive cancer DNA/RNA analysis and reporting pipeline
|
|
nf-core/rnadnavar
1.0.0
|
n/a
|
Pipeline for RNA and DNA integrated analysis for somatic mutation detection
|
|
nf-core/rnafusion
4.1.3
|
fusion fusion-genes gene-fusion rna
+1
|
RNA-seq analysis pipeline for detection of gene-fusions
|
|
nf-core/rnaseq
3.27.0
|
rna rna-seq
|
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
|
alternative-splicing rna rna-seq splicing
|
rnasplice is a bioinformatics pipeline for RNA-seq alternative splicing analysis
|
|
nf-core/rnastructurome
1.0.0
|
dms map rna-structure rnacentral
+3
|
a bioinformatics pipeline for analysing chemical high-throughput RNA structure-probing data
|