nf-core / rnaseq
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
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RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
Repository to host tool-specific module files for the Nextflow DSL2 community!
Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.
Call and score variants from WGS/WES of rare disease patients.
Assembly and intrahost/low-frequency variant calling for viral samples
Analysis of Dual RNA-seq data - an experimental method for interrogating host-pathogen interactions through simultaneous RNA-seq.
Config files used to define parameters specific to compute environments at different Institutions
A pipeline to investigate horizontal gene transfer from NGS data
Pipeline for HiCAR data, a robust and sensitive multi-omic co-assay for simultaneous measurement of transcriptome, chromatin accessibility and cis-regulatory chromatin contacts.
gatk4 RNA variant calling pipeline
DEPRECIATED! Please use nf-core/tools instead
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Coprolite host Identification pipeline
Assembly and binning of metagenomes
A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences
ATAC-seq peak-calling and QC analysis pipeline
A fully reproducible and state-of-the-art ancient DNA analysis pipeline
Nanopore demultiplexing, QC and alignment pipeline
Identify and quantify MHC eluted peptides from mass spectrometry raw data
MNase-seq analysis pipeline using BWA and DANPOS2.
A single-cell RNAseq pipeline for 10X genomics data
Genome annotation with PacBio Iso-Seq. Takes raw subreads as input, generate Full Length Non Chemiric (FLNC) sequences and produce a bed annotation.
ChIP-seq peak-calling, QC and differential analysis pipeline.
Automated quantitative analysis of DIA proteomics mass spectrometry measurements.