Search Results - RepositoryStats

713

949

mit

157

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

rna nf-core rna-seq nextflow pipeline workflow

Created 2018-03-29

5,806 commits to master branch, last one 10 days ago

sarek nf-core

419

414

mit

135

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

Created 2019-04-30

7,940 commits to master branch, last one 18 days ago

modules nf-core

735

287

mit

230

Repository to host tool-specific module files for the Nextflow DSL2 community!

dsl2 modules nf-core nf-test nextflow pipelines workflows

Created 2019-07-26

6,701 commits to master branch, last one 10 days ago

tools nf-core

192

245

mit

150

Python package with helper tools for the nf-core community.

linter python linting nf-core nextflow pipeline workflow bioinformatics

Created 2018-02-13

12,003 commits to main branch, last one 10 days ago

mag nf-core

113

222

mit

161

Assembly and binning of metagenomes

binning nf-core assembly nanopore nextflow pipeline workflow annotation metagenomes metagenomics bioinformatics nanopore-sequencing long-read-sequencing

Created 2018-05-22

2,527 commits to master branch, last one 11 days ago

scrnaseq nf-core

174

220

mit

137

A single-cell RNAseq pipeline for 10X genomics data

alevin nf-core rna-seq bustools kallisto nextflow pipeline workflow star-solo cellranger 10xgenomics single-cell 10x-genomics

Created 2019-04-08

1,612 commits to master branch, last one 20 days ago

chipseq nf-core

150

201

mit

148

ChIP-seq peak-calling, QC and differential analysis pipeline.

chip macs2 nf-core chip-seq nextflow pipeline workflow peak-calling chromatin-immunoprecipitation

Created 2018-04-24

1,835 commits to master branch, last one 2 months ago

atacseq nf-core

122

193

mit

150

ATAC-seq peak-calling and QC analysis pipeline

nf-core atac-seq nextflow pipeline workflow chromatin-accessibiity

Created 2018-11-05

1,416 commits to master branch, last one about a year ago

ampliseq nf-core

124

189

mit

152

Amplicon sequencing analysis workflow using DADA2 and QIIME2

16s 18s its edna rrna pacbio qiime2 nf-core illumina nextflow pipeline workflow iontorrent microbiome metagenomics metabarcoding amplicon-sequencing taxonomic-profiling taxonomic-classification

Created 2018-09-26

2,541 commits to master branch, last one about a month ago

nanoseq nf-core

83

186

mit

140

Nanopore demultiplexing, QC and alignment pipeline

qc nf-core nanopore nextflow pipeline workflow alignment demultiplexing

Created 2019-09-09

1,587 commits to master branch, last one about a year ago

eager nf-core

82

154

mit

160

A fully reproducible and state-of-the-art ancient DNA analysis pipeline

adna genome nf-core nextflow pipeline workflow ancientdna metagenomics bioinformatics pathogen-genomics population-genetics ancient-dna-analysis

Created 2018-06-03

3,271 commits to master branch, last one 6 months ago

fetchngs nf-core

75

154

mit

100

Pipeline to fetch metadata and raw FastQ files from public databases

ena geo sra ddbj fastq nf-core synapse download nextflow pipeline workflow

Created 2021-06-03

1,079 commits to master branch, last one 10 months ago

methylseq nf-core

146

150

mit

151

Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel

pbat rrbs em-seq nf-core nextflow pipeline workflow epigenome methyl-seq epigenomics dna-methylation bisulfite-sequencing

Created 2018-03-12

1,691 commits to master branch, last one 14 days ago

rnafusion nf-core

98

148

mit

150

RNA-seq analysis pipeline for detection of gene-fusions

rna fusion nf-core rna-seq nextflow pipeline workflow gene-fusion fusion-genes

Created 2018-10-05

1,912 commits to master branch, last one 8 months ago

taxprofiler nf-core

38

132

mit

155

Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data

nf-core shotgun illumina nanopore nextflow pathogen pipeline workflow profiling long-reads microbiome metagenomics bioinformatics classification taxonomic-profiling taxonomic-classification

Created 2022-02-18

2,031 commits to master branch, last one about a month ago

viralrecon nf-core

114

128

mit

107

Assembly and intrahost/low-frequency variant calling for viral samples

ont artic viral virus covid19 nf-core amplicon assembly covid-19 illumina nanopore nextflow pipeline workflow sars-cov-2 metagenomics oxford-nanopore variant-calling long-read-sequencing

Created 2020-03-30

2,788 commits to master branch, last one about a year ago

test-datasets nf-core

361

109

mit

147

Test data to be used for automated testing with the nf-core pipelines

nf-core testing nextflow workflow pipelines test-data test-datasets

Created 2018-03-12

123 commits to master branch, last one about a year ago

hic nf-core

56

92

mit

140

Analysis of Chromosome Conformation Capture data (Hi-C)

hi-c nf-core nextflow pipeline workflow chromosome-conformation-capture

Created 2019-04-09

471 commits to master branch, last one about a year ago

raredisease nf-core

36

91

mit

158

Call and score variants from WGS/WES of rare disease patients.

snv wes wgs nf-core nextflow pipeline workflow diagnostics rare-disease variant-calling variant-annotation structural-variants

Created 2021-06-21

2,676 commits to master branch, last one 3 months ago

configs nf-core

277

90

mit

160

Config files used to define parameters specific to compute environments at different Institutions

nf-core nextflow pipelines workflows configuration bioinformatics

Created 2018-11-23

3,514 commits to master branch, last one 6 days ago

cutandrun nf-core

49

86

mit

159

Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes QC, support for spike-ins, IgG controls, peak calling and downstream analysis.

nf-core nextflow pipeline workflow cutandrun cutandtag cutandrun-seq cutandtag-seq

Created 2021-01-14

1,700 commits to master branch, last one 11 months ago

pangenome nf-core

17

78

mit

63

Renders a collection of sequences into a pangenome graph. https://doi.org/10.1093/bioinformatics/btae609.

nf-core nextflow pipeline workflow pangenome

Created 2020-11-08

693 commits to master branch, last one 5 months ago

smrnaseq nf-core

127

76

mit

149

A small-RNA sequencing analysis pipeline

nf-core nextflow pipeline workflow small-rna smrna-seq

Created 2018-07-11

1,686 commits to master branch, last one 2 months ago

funcscan nf-core

22

75

mit

99

(Meta-)genome screening for functional and natural product gene sequences

Created 2021-12-13

1,606 commits to master branch, last one 3 months ago

website nf-core

194

70

mit

153

Code and files for the main nf-core website.

nf-core website nextflow

Created 2018-04-18

10,098 commits to main branch, last one 23 hours ago

differentialabundance nf-core

41

66

mit

150

Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq

gsea limma shiny deseq2 nf-core rna-seq atac-seq chip-seq nextflow pipeline workflow microarray differential-abundance differential-expression

Created 2022-10-12

1,105 commits to master branch, last one 7 months ago

proteinfold nf-core

43

64

mit

163

Protein 3D structure prediction pipeline

nf-core nextflow pipeline workflow alphafold2 protein-folding protein-sequences protein-structure protein-fold-prediction

Created 2022-03-03

767 commits to master branch, last one 5 months ago

bacass nf-core

43

63

mit

151

Simple bacterial assembly and annotation pipeline

denovo nf-core assembly nanopore nextflow pipeline workflow denovo-assembly genome-assembly hybrid-assembly bacterial-genomes nanopore-sequencing

Created 2019-01-31

726 commits to master branch, last one about a month ago

hlatyping nf-core

31

63

mit

157

Precision HLA typing from next-generation sequencing data

dna hla rna nf-core nextflow optitype pipeline workflow hla-typing immunology personalized-medicine

Created 2018-07-11

430 commits to master branch, last one 2 years ago

airrflow nf-core

36

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mit

150

B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework

airr b-cell repseq nf-core nextflow pipeline workflow immcantation immunorepertoire

Created 2018-12-04

2,509 commits to master branch, last one 20 days ago