Nf-core - OmicsDI

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Transcriptomics (810)
Unknown (674)
Genomics (302)
Proteomics (47)
Metabolomics (12)
Other (4)
Multiomics (2)
Models (1)
Methylation profiling (1)

Organisms

Mus musculus (437)
Homo sapiens (406)
Rattus norvegicus (19)
Drosophila melanogaster (19)
Danio rerio (15)
Arabidopsis thaliana (11)
Saccharomyces cerevisiae (9)
Bos taurus (7)
Sus scrofa (5)
Caenorhabditis elegans (3)
Pan troglodytes (2)
Xenopus laevis (2)
Aspergillus fumigatus (2)
Vitis vinifera (2)
Bacillus subtilis (2)
Solanum tuberosum (2)
Gallus gallus (2)
Candida albicans (2)
Oncorhynchus kisutch (1)
Streptomyces avermitilis (1)
Saccharum officinarum (1)
Shewanella oneidensis MR-1 (1)
Bifidobacterium breve UCC2003 (1)
Streptococcus mutans UA159 (1)
Myxococcus xanthus (1)
Taeniopygia guttata (1)
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Brassica napus (1)
Malus domestica (1)
Coturnix japonica (1)

Organisms

Homo sapiens (62)
Mus musculus (45)
Rattus norvegicus (2)
Candidozyma auris (1)
Drosophila melanogaster (1)
Ovis aries (1)
Musculus (1)
Zea mays (1)
freshwater sediment metagenome (1)
Sus scrofa (1)
Danio rerio (1)
Arabidopsis thaliana (1)
Sus scrofa domesticus (1)

Repository

biostudies-arrayexpress (887)
ENA (152)
geo (73)
MassIVE (23)
pride (14)
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IRAK-4 Q293X mutation (1)
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S enteritidis (1)
Neurofibromatosis type 1 (1)
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Lung adenocarcinoma (1)
Melanoma (1)
Leptospirosis (1)

Technology Type

Mass Spectrometry (14)
Mass spectrometry (11)
Bottom-up proteomics (7)
Data-dependent acquisition (4)
Shotgun proteomics (4)
Data-independent acquisition (2)
Mass spectrometry assay (1)
Affinity purification coupled with mass spectrometry proteomics (1)
Chemical cross-linking coupled with mass spectrometry proteomics (1)

Instrument Platform

Illumina NovaSeq 6000 (44)
NextSeq 500 (27)
NextSeq 2000 (12)
Illumina HiSeq 2500 (10)
Illumina HiSeq 2000 (10)
Illumina HiSeq 4000 (10)
Illumina NovaSeq X (6)
DNBSEQ-G400 (4)
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NA (2)
Illumina HiSeq X (2)
Maxwell RSC instrument (1)
Maxwell RSC Instrument (1)
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Chromium Controller, 10x Genomics and Chromium X, 10x Genomics (1)
Cell culture (1)
HPC (1)
NEXTflex small RNA library preparation kit v4; TruSeq exome RNA library preparation kit (Illumina); High Sensitivity DNA ScreenTape D1000 (1)
QIAzol and miRNeasy micro kits; Bioanalyzer TapeStation 2100; Qubit microRNA assay (1)
NEBNext Ultra II RNA Library Prep Kit (1)
NEBNext Globin and rRNA Depletion Kit (1)
PAXgene Blood RNA tubes (1)
DNBSEQ Devices (1)
TriFast (VWR, 30-2010), RNeasy Mini Kit (Qiagen, 74104), DNAse 1 (NEB, M0303); Agilent 2100 Bioanalyzer (1)
HEK-293T cells, Media, PEI, Illumination device (1)
Real-time PCR Thermal Cycler (1)

Publication Date

2010 (122)
2015 (107)
2013 (101)
2014 (87)
2011 (79)
2012 (73)
2008 (68)
2026 (67)
2025 (55)
2009 (43)
2024 (35)
2007 (31)
2016 (30)
2020 (26)
2022 (21)
2021 (21)
2023 (14)
2018 (10)
2006 (10)
2019 (8)
2017 (5)
2004 (4)
2005 (2)

CHEBI ID

CHEBI:42255 (4)
CHEBI:16220 (3)
CHEBI:18152 (3)
CHEBI:75633 (3)
CHEBI:30754 (3)
CHEBI:28327 (3)
CHEBI:38747 (3)
CHEBI:36281 (3)
CHEBI:8113 (3)
CHEBI:16709 (3)
CHEBI:17858 (3)
CHEBI:16856 (3)
CHEBI:15729 (3)
CHEBI:17015 (3)
CHEBI:116314 (3)
CHEBI:30763 (3)
CHEBI:16335 (3)
CHEBI:16857 (3)
CHEBI:16015 (3)
CHEBI:16414 (3)
CHEBI:16643 (3)
CHEBI:17895 (3)
CHEBI:17295 (3)
CHEBI:28716 (3)
CHEBI:15756 (3)
CHEBI:18010 (2)
CHEBI:28647 (2)
CHEBI:982 (2)
CHEBI:40585 (2)
CHEBI:28603 (2)

Metabolite Name

L-Phenylalanine (4)
Coniferin (3)
2'-Deoxyadenosine (3)
Argininosuccinic acid (3)
Nicotinamide (3)
Choline (3)
5-Hydroxytryptophol (3)
4-Hydroxybenzaldehyde (3)
Adenosine (3)
N-Acetylputrescine (3)
Guanine (3)
Riboflavin (3)
L-Valine (3)
(S)-10-Hydroxycamptothecin (2)
NG,NG-Dimethyl-L-arginine (2)
3-Methoxyflavone (2)
3,7-Di-O-methylquercetin (2)
D-Panthenol (2)
L-(+)-Arabinose (2)
Alpha-Tocotrienol (2)
Ustiloxin D (2)
N-Acetyl-D-galactosamine (2)
Epigallocatechin (2)
Syringin (2)
D-Glucosamine (2)
Myricetin (2)
Deoxycorticosterone (2)
Palmitoleic Acid (2)
Calcimycin (2)
Eriosemaone C (2)

IsPrivate

False (1)

First Public Date

2026 (39)
2025 (32)
2020 (19)
2024 (12)
2022 (11)
2021 (10)
2014 (10)
2018 (7)
2023 (4)
2016 (3)
2019 (2)
2015 (2)
2013 (1)

Classification

fungi (1)

Modelling Approach

Ordinary differential equation model (1)

Study type

Transcription profiling by array (513)
RNA-seq of coding RNA (132)
ChIP-seq (114)
ChIP-chip by tiling array (22)
Unknown experiment type (18)
RNA-seq of total RNA (10)
Methylation profiling by array (7)
Comparative genomic hybridization by array (6)
RNA-seq of coding RNA from single cells (6)
ChIP-chip by array (5)
ATAC-seq (5)
Other (5)
Methylation profiling by high throughput sequencing (5)
RNA-seq of non coding RNA (5)
High-throughput sequencing (4)
DNA-seq (4)
CUT&RUN (4)
Cell line - High-throughput sequencing (3)
Transcription profiling by SAGE (2)
Animal - High-throughput sequencing (2)
RNAi profiling by array (2)
CLIP-seq (2)
CUT&Tag (1)
Human - Single-cell sequencing (1)
Transcription profiling by tiling array (1)
Genotyping by array (1)
Transcription profiling by RT-PCR (1)
MicroRNA profiling by high throughput sequencing (1)
4C (1)
Hi-C (1)

Release Date

2025 (148)
2010 (125)
2013 (117)
2015 (116)
2022 (96)
2023 (94)
2024 (93)
2014 (92)
2011 (87)
2021 (86)
2012 (84)
2008 (72)
2026 (65)
2009 (50)
2016 (49)
2020 (46)
2018 (35)
2007 (32)
2019 (26)
2017 (18)
2006 (14)
2005 (5)
2004 (4)
2003 (2)
2000 (2)
2001 (1)
1999 (1)
1998 (1)

Lab affiliation

Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece (3)
EMBL-EBI (2)
Quantitative Biology Center (QBiC), University of Tübingen, Germany. (1)
Department of Peptide-based Immunotherapy (1)
Department of Peptide-based Immunotherapy, University and University Hospital Tuebingen, Germany (1)
Institute for Cell Biology, Dept. Immunology Auf der Morgenstelle 15, 72076 Tübingen, Germany Partner Site of the German Cancer Consortium (1)
INCLIVA Biomedical Research Institute (1)
Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, Austria (1)
Eco-Biotechnology & Drug Development Group, Laboratory for Microbial Molecular Genetics and Ecology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11000, Belgrade, Serbia (1)
National Institute of Animal Biotechnology, Hyderabad, India (1)
Oregon State University (1)

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nf-core/taxprofiler and nf-core/createtaxdb provide scalable and reproducible metagenomic multi-classifier database construction and taxonomic profiling

PRJEB113439 | ENA

Deep mutational scanning by nicking, shotgun sequencing and nf-core/deepmutscan

PRJEB110196 | ENA

nf-core/airrflow: An adaptive immune receptor repertoire analysis workflow employing the Immcantation framework.

Not available

S-EPMC11305553 | biostudies-literature

nf-core/crisprseq: a versatile pipeline for comprehensive analysis of CRISPR gene editing and screening assays.

Not available

S-EPMC12805889 | biostudies-literature

Cluster-efficient pangenome graph construction with nf-core/pangenome.

Not available

S-EPMC11568064 | biostudies-literature

3' sequencing of nuclear and cytoplasmic fractions following treatment with a CLK inhibitor

CLK kinases phosphorylate the SR domains of SR proteins. The phosphorylation state controls the localisation of SR proteins, with hypo-phosphorylated SR proteins being more enriched in nuclear speckles. We identified a set of mRNAs that are bound by SR proteins in the nucleus, and we wondered whethe...

ORGANISM(S): Homo sapiens

2025-07-29 | E-MTAB-13328 | biostudies-arrayexpress

Empowering bioinformatics communities with Nextflow and nf-core.

Not available

S-EPMC12309086 | biostudies-literature

scnanoseq: an nf-core pipeline for Oxford Nanopore single-cell RNA-sequencing.

Not available

S-EPMC12449243 | biostudies-literature

nf-core/detaxizer: a benchmarking study for decontamination from human sequences.

Not available

S-EPMC12455401 | biostudies-literature

nf-core/mag: a best-practice pipeline for metagenome hybrid assembly and binning.