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: bioconductor: SRAdb

https://packages.ecosyste.ms/registries/bioconductor.org/packages/SRAdb

A compilation of metadata from NCBI SRA and tools
1 version
Latest release: about 1 year ago
107,841 downloads total

Papers Mentioning SRAdb 20

10.1002/pmic.201400392

Visualization of proteomics data using R and Bioconductor
Cited by: 46
Author(s): Laurent Gatto, Lisa M. Breckels, Thomas Naake, Sebastian Gibb
Software Mentions: 62
Published: over 9 years ago

BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests
Cited by: 20
Author(s): Andrea Komljenović, Julien Roux, Julien Wollbrett, Marc Robinson‐Rechavi, Frederic Bastian
Software Mentions: 33
Published: over 6 years ago

10.1371/journal.pcbi.1006242

Phylogeny-corrected identification of microbial gene families relevant to human gut colonization
Cited by: 29
Author(s): Patrick H. Bradley, Stephen Nayfach, Katherine S. Pollard
Software Mentions: 27
Published: over 6 years ago

10.12688/f1000research.12223.1

recount workflow: Accessing over 70,000 human RNA-seq samples with Bioconductor
Cited by: 47
Author(s): Leonardo Collado‐Torres, Abhinav Nellore, Andrew E. Jaffe
Software Mentions: 14
Published: about 7 years ago

10.1038/s41598-020-57716-1

Ontology-driven integrative analysis of omics data through Onassis
Cited by: 9
Author(s): Eugenia Galeota, Kamal Kishore, Mattia Pelizzola
Software Mentions: 6
Published: almost 5 years ago

10.1186/s12859-019-2643-6

First step toward gene expression data integration: transcriptomic data acquisition with COMMAND>_
Cited by: 8
Author(s): Marco Moretto, Paolo Sonego, Ana B. Villasenõr-Altamirano, Kristof Engelen
Software Mentions: 6
Published: almost 6 years ago

10.3389/fimmu.2018.01286

seq-ImmuCC: Cell-Centric View of Tissue Transcriptome Measuring Cellular Compositions of Immune Microenvironment From Mouse RNA-Seq Data
Cited by: 61
Author(s): Ziyi Chen, Lijun Quan, Anfei Huang, Qiang Zhao, Yuan Yao, Xuye Yuan, Qin Shen, Jingzhe Shang, Yinyin Ben, F. Xiao-Feng Qin, Aiping Wu
Software Mentions: 5
Published: over 6 years ago

10.1186/s13059-015-0611-7

Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome
Cited by: 206
Author(s): Stephen Nayfach, Katherine S. Pollard
Software Mentions: 4
Published: over 9 years ago

10.1128/mSystems.00332-18

A Metagenomic Meta-analysis Reveals Functional Signatures of Health and Disease in the Human Gut Microbiome
Cited by: 110
Author(s): Courtney R. Armour, Stephen Nayfach, Katherine S. Pollard, Thomas J. Sharpton
Software Mentions: 4
Published: about 5 years ago

10.12688/f1000research.18676.1

pysradb: A Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive
Cited by: 23
Author(s): Saket Choudhary
Software Mentions: 4
Published: over 5 years ago

10.3390/genes10090714

NCBI’s Virus Discovery Hackathon: Engaging Research Communities to Identify Cloud Infrastructure Requirements
Cited by: 13
Author(s): Ryan Connor, Rodney Brister, Jan P. Buchmann, Ward Deboutte, Robert A. Edwards, Joan Martí-Carreras, Michael J. Tisza, Vadim Zalunin, Juan S. Andrade-Martínez, Adrian Cantu, Michael D’Amour, Alexandre Efremov, Lydia Fleischmann, Laura Milena Forero‐Junco, Sanzhima Garmaeva, Melissa Giluso, Cody Glickman, Margaret Henderson, Benjamin P. Kellman, David M. Kristensen, Carl Leubsdorf, Kyle Levi, Shane Levi, Suman B. Pakala, Vikas Peddu, Alise J. Ponsero, Eldred A. Ribeiro, Farrah Roy, Lindsay Rutter, Surya Saha, Migun Shakya, Ryan C. Shean, Matthew Miller, Benjamin J. Tully, Christopher J R Turkington, Ken Youens‐Clark, Bert Vanmechelen, Ben Busby
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-019-45934-1

Single-cell RNA-seq variant analysis for exploration of genetic heterogeneity in cancer
Cited by: 20
Author(s): Erik Fasterius, Mathias Uhlén, Cristina Al‐Khalili Szigyarto
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2105-14-S14-S17

mirCoX: a database of miRNA-mRNA expression correlations derived from RNA-seq meta-analysis
Cited by: 17
Author(s): Cory B. Giles, G. Reshmi, Mikhail G. Dozmorov, Jonathan D. Wren
Software Mentions: 3
Published: about 11 years ago

10.1099/mgen.0.000116

SNVPhyl: a single nucleotide variant phylogenomics pipeline for microbial genomic epidemiology
Cited by: 86
Author(s): A. Petkau, Philip Mabon, Cameron Sieffert, Natalie Knox, Jennifer Cabral, Mariam Iskander, Mark Iskander, Kelly Weedmark, Rahat Zaheer, Lee S. Katz, Céline Nadon, Aleisha Reimer, Eduardo N. Taboada, Robert G. Beiko, William W. L. Hsiao, Fiona S. L. Brinkman, Morag Graham, Gary Van Domselaar
Software Mentions: 3
Published: over 7 years ago

10.1515/jib-2019-0046

Fungal metabarcoding data integration framework for the MycoDiversity DataBase (MDDB)
Cited by: 6
Author(s): Irene Martorelli, Leon S. Helwerda, Jesse Kerkvliet, Sofia I. F. Gomes, Jorinde Nuytinck, Chivany R. A. van der Werff, Guus J. Ramackers, Alexander P. Gultyaev, Vincent Merckx, Fons J. Verbeek
Software Mentions: 2
Published: over 4 years ago