43 results found Sort:

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984
mit
159
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
Created 2018-03-29
5,806 commits to master branch, last one 2 months ago
428
422
mit
134
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Created 2019-04-30
7,941 commits to master branch, last one a day ago
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292
mit
206
Repository to host tool-specific module files for the Nextflow DSL2 community!
Created 2019-07-26
6,875 commits to master branch, last one 21 hours ago
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mit
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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
Created 2019-04-08
1,612 commits to master branch, last one 2 months ago
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247
mit
150
Python package with helper tools for the nf-core community.
Created 2018-02-13
12,120 commits to main branch, last one 22 days ago
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mit
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Assembly and binning of metagenomes
Created 2018-05-22
2,574 commits to master branch, last one 5 days ago
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206
mit
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ChIP-seq peak-calling, QC and differential analysis pipeline.
Created 2018-04-24
1,835 commits to master branch, last one 4 months ago
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mit
150
ATAC-seq peak-calling and QC analysis pipeline
Created 2018-11-05
1,416 commits to master branch, last one about a year ago
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mit
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Nanopore demultiplexing, QC and alignment pipeline
Created 2019-09-09
1,587 commits to master branch, last one about a year ago
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mit
151
Amplicon sequencing analysis workflow using DADA2 and QIIME2
Created 2018-09-26
2,541 commits to master branch, last one 3 months ago
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mit
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Pipeline to fetch metadata and raw FastQ files from public databases
Created 2021-06-03
1,079 commits to master branch, last one 11 months ago
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mit
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A fully reproducible and state-of-the-art ancient DNA analysis pipeline
Created 2018-06-03
3,271 commits to master branch, last one 7 months ago
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mit
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Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
Created 2018-03-12
1,691 commits to master branch, last one 2 months ago
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150
mit
149
RNA-seq analysis pipeline for detection of gene-fusions
Created 2018-10-05
1,913 commits to master branch, last one about a month ago
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
Created 2022-02-18
2,083 commits to master branch, last one about a month ago
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mit
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Assembly and intrahost/low-frequency variant calling for viral samples
Created 2020-03-30
2,788 commits to master branch, last one about a year ago
Test data to be used for automated testing with the nf-core pipelines
Created 2018-03-12
123 commits to master branch, last one about a year ago
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mit
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Analysis of Chromosome Conformation Capture data (Hi-C)
Created 2019-04-09
471 commits to master branch, last one about a year ago
Call and score variants from WGS/WES of rare disease patients.
Created 2021-06-21
2,927 commits to master branch, last one 6 days ago
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mit
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Config files used to define parameters specific to compute environments at different Institutions
Created 2018-11-23
3,640 commits to master branch, last one 7 days ago
Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes QC, support for spike-ins, IgG controls, peak calling and downstream analysis.
Created 2021-01-14
1,700 commits to master branch, last one about a year ago
Renders a collection of sequences into a pangenome graph. https://doi.org/10.1093/bioinformatics/btae609.
Created 2020-11-08
771 commits to master branch, last one 10 days ago
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mit
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A small-RNA sequencing analysis pipeline
Created 2018-07-11
1,686 commits to master branch, last one 4 months ago
(Meta-)genome screening for functional and natural product gene sequences
Created 2021-12-13
1,606 commits to master branch, last one 5 months ago
Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
Created 2022-10-12
1,105 commits to master branch, last one 9 months ago
Protein 3D structure prediction pipeline
Created 2022-03-03
768 commits to master branch, last one about a month ago
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mit
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Code and files for the main nf-core website.
Created 2018-04-18
10,767 commits to main branch, last one 23 hours ago
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mit
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Simple bacterial assembly and annotation pipeline
Created 2019-01-31
726 commits to master branch, last one 3 months ago
Precision HLA typing from next-generation sequencing data
Created 2018-07-11
430 commits to master branch, last one 2 years ago
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mit
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B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework
Created 2018-12-04
2,509 commits to master branch, last one 2 months ago