Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: pypi: nf-core

https://packages.ecosyste.ms/registries/pypi.org/packages/nf-core

Helper tools for use with nf-core Nextflow pipelines.
40 versions
Latest release: about 1 year ago
1 dependent package
6,674 downloads last month

Papers Mentioning nf-core 18

Interpretations of Environmental Microbial Community Studies Are Biased by the Selected 16S rRNA (Gene) Amplicon Sequencing Pipeline
Cited by: 91
Author(s): Daniel Straub, Nia Blackwell, Adrian Langarica‐Fuentes, Alexander Peltzer, Sven Nahnsen, Sara Kleindienst
Software Mentions: 22
Published: about 4 years ago

10.3389/fimmu.2020.585168

Distinct Age-Related Epigenetic Signatures in CD4 and CD8 T Cells
Cited by: 40
Author(s): Bin Hu, Rohit R. Jadhav, Claire E. Gustafson, Sabine Le Saux, Zhongde Ye, Xuanying Li, Lu Tian, Cornelia M. Weyand, Jörg J. Goronzy
Software Mentions: 7
Published: almost 4 years ago

10.3390/genes11121487

RNAflow: An Effective and Simple RNA-Seq Differential Gene Expression Pipeline Using Nextflow
Cited by: 13
Author(s): Marie Lataretu, Martin Hölzer
Software Mentions: 6
Published: almost 4 years ago

10.1186/s12864-020-6714-x

DolphinNext: a distributed data processing platform for high throughput genomics
Cited by: 61
Author(s): Onur Yukselen, Osman Turkyilmaz, Ahmet Öztürk, Manuel Garber, Alper Küçükural
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pcbi.1008622

Using prototyping to choose a bioinformatics workflow management system
Cited by: 20
Author(s): Michael Jackson, Kostas Kavoussanakis, Eric Wallace
Software Mentions: 5
Published: over 3 years ago

10.1186/s12864-020-06886-3

MethylStar: A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing data
Cited by: 8
Author(s): Yadollah Shahryary, Rashmi R. Hazarika, Frank Johannes
Software Mentions: 4
Published: over 4 years ago

10.7554/eLife.68203

Genetic variant in 3’ untranslated region of the mouse pycard gene regulates inflammasome activity
Cited by: 11
Author(s): Brian Ritchey, Qimin Hai, Juying Han, John Barnard, Jonathan Smith
Software Mentions: 4
Published: over 3 years ago

10.7717/peerj.10947

Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager
Cited by: 34
Author(s): James A. Fellows Yates, Thiseas Christos Lamnidis, Maxime Borry, Aida Andrades Valtueña, Zandra Fagernäs, Stephen Clayton, Maxime Garcia, Judith Neukamm, Alexander Peltzer
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0237055

Genome-wide binding analysis of 195 DNA binding proteins reveals “reservoir” promoters and human specific SVA-repeat family regulation
Cited by: 1
Author(s): Michael J. Smallegan, Soraya I. Shehata, Savannah Spradlin, Alison R. Swearingen, Graycen E. Wheeler, Arpan Das, Giulia A Corbet, Benjamin Nebenfuehr, Daniel Ahrens, Devin Tauber, Shelby R. Lennon, Kevin Choi, Thao Ngoc Huynh, Tom Wieser, Kristen Schneider, Michael S. Bradshaw, Joel Basken, Maria Eliana Lai, Timothy D. Read, Matt Hynes-Grace, Dan Timmons, Jon Demasi, John L. Rinn
Software Mentions: 3
Published: over 3 years ago

10.3390/ijms22042136

Extensive Placental Methylation Profiling in Normal Pregnancies
Cited by: 8
Author(s): Ornella Rondinone, Alessio Murgia, Jole Costanza, Silvia Tabano, Margherita Camanni, Luigi Corsaro, Laura Fontana, Patrizia Colapietro, Luciano Calzari, S. Motta, Carlo Santaniello, Tatjana Radaelli, Enrico Ferrazzi, Silvano Bòsari, Davide Gentilini, Silvia Maria Sirchia, Monica Miozzo
Software Mentions: 3
Published: over 3 years ago

10.1038/s10038-020-00862-1

Practical guide for managing large-scale human genome data in research
Cited by: 26
Author(s): Tomoya Tanjo, Yosuke Kawai, Katsushi Tokunaga, Osamu Ogasawara, Masao Nagasaki
Software Mentions: 3
Published: about 4 years ago

10.3390/cancers13061263

Harnessing the IL-21-BATF Pathway in the CD8+ T Cell Anti-Tumor Response
Cited by: 14
Author(s): Paytsar Topchyan, Gang Xu, Yao Chen, Shikan Zheng, Robert T. Burns, Jian Shen, Moujtaba Y. Kasmani, Matthew R. Kudek, Na Yang, Weiguo Cui
Software Mentions: 3
Published: over 3 years ago

10.1128/JVI.01583-20

A Founder Effect Led Early SARS-CoV-2 Transmission in Spain
Cited by: 49
Author(s): Francisco Díez-Fuertes, María Iglesias-Caballero, Javier García-Pérez, Sara Monzón, Pilar Jiménez, Sarai Varona, Isabel Cuesta, Ángel Zaballos, Mercedes Jiménez, Laura Checa, Francisco Pozo, Mayte Pérez‐Olmeda, Michael M. Thomson, José Alcamı́, Inmaculada Casas
Software Mentions: 2
Published: almost 4 years ago

10.7717/peerj.9001

CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content
Cited by: 30
Author(s): Maxime Borry, Bryan Cordova, Angela R. Perri, Marsha C. Wibowo, Tanvi P. Honap, Jada Ko, Jie Yu, Kate Britton, Linus Girdland-Flink, Robert C. Power, Ingelise Stuijts, Domingo C. Salazar‐García, Courtney A. Hofman, Richard Hagan, Thérèse Kagoné, Nicolas Méda, Hélène Carabin, David P. Jacobson, Karl J. Reinhard, Cecil M. Lewis, Aleksandar D. Kostic, Choongwon Jeong, Alexander Herbig, Alexander Hübner, Christina Warinner
Software Mentions: 2
Published: over 4 years ago

10.1186/s13148-021-01097-3

Ultralow amounts of DNA from long-term archived serum samples produce high-quality methylomes
Cited by: 0
Author(s): Marcin W. Wojewodzic, Magnus Leithaug, Marianne Lauritzen, Robert Lyle, Sofia Haglund, Carl-Johan Rubin, Philip Ewels, Tom Grotmol, Trine B. Rounge
Software Mentions: 2
Published: over 3 years ago

10.1097/HS9.0000000000000522

Performances of Targeted RNA Sequencing for the Analysis of Fusion Transcripts, Gene Mutation, and Expression in Hematological Malignancies
Cited by: 2
Author(s): Sandrine Hayette, Béatrice Grange, Maxime Vallée, Claire Bardel, Sarah Huet, Isabelle Mosnier, Kaddour Chabane, Thomas Simonet, Marie Balsat, Maël Heiblig, Isabelle Tigaud, Franck E. Nicolini, Sylvain Mareschal, Gilles Salles, Pierre Sujobert
Software Mentions: 2
Published: almost 4 years ago

10.12688/f1000research.16665.2

Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants
Cited by: 70
Author(s): Manon Garcia, Szilveszter Juhos, Malin Larsson, Pall I. Olason, Marcel Martin, Jesper Eisfeldt, Sebastian DiLorenzo, Johanna Sandgren, Teresita Díaz de Ståhl, Philip Ewels, Valtteri Wirta, Monica Nistér, Max Käller, Björn Nystedt
Software Mentions: 1
Published: about 4 years ago

10.1371/journal.pcbi.1008260

Ten simple rules for annotating sequencing experiments
Cited by: 11
Author(s): Irene Stevens, Abdul Kadir Mukarram, Matthias Hörtenhuber, Terrence F. Meehan, Johan Rung, Carsten O. Daub
Software Mentions: 1
Published: about 4 years ago