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: iSEE

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

Interactive SummarizedExperiment Explorer
2 versions
Latest release: about 1 year ago
7 dependent packages
28,261 downloads total

Papers Mentioning iSEE 13

10.1371/journal.pcbi.1007912

bigPint: A Bioconductor visualization package that makes big data pint-sized
Cited by: 3
Author(s): Lindsay Rutter, Dianne Cook
Software Mentions: 47
Published: over 4 years ago

10.15252/msb.20188746

Current best practices in single‐cell RNA‐seq analysis: a tutorial
Cited by: 1,173
Author(s): Malte D. Luecken, Fabian J. Theis
Software Mentions: 20
Published: over 5 years ago

10.1186/s12859-020-03819-5

ideal: an R/Bioconductor package for interactive differential expression analysis
Cited by: 18
Author(s): Fédérico Marini, Jan Linke, Harald Binder
Software Mentions: 17
Published: almost 4 years ago

PiGx: reproducible genomics analysis pipelines with GNU Guix
Cited by: 51
Author(s): Ricardo Wurmus, Bora Uyar, Brendan Osberg, Vedran Franke, Alexander Gosdschan, Katarzyna Wreczycka, Jonathan Ronen, Altuna Akalin
Software Mentions: 15
Published: about 6 years ago

10.1186/s12859-021-04142-3

SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses
Cited by: 11
Author(s): Nicholas J. Eagles, Emily E. Burke, Jacob Leonard, Brianna K. Barry, Joshua M. Stolz, Louise A Huuki, BaDoi N. Phan, Violeta Larios Serrato, Everardo Gutiérrez-Millán, Israel Aguilar-Ordóñez, Andrew E. Jaffe, Leonardo Collado‐Torres
Software Mentions: 13
Published: over 3 years ago

10.1038/s42003-019-0415-5

diffcyt: Differential discovery in high-dimensional cytometry via high-resolution clustering
Cited by: 137
Author(s): Lukas M. Weber, Małgorzata Nowicka, Charlotte Soneson, Mark D. Robinson
Software Mentions: 12
Published: over 5 years ago

10.12688/f1000research.14966.1

iSEE: Interactive SummarizedExperiment Explorer
Cited by: 68
Author(s): Kévin Rue-Albrecht, Fédérico Marini, Charlotte Soneson, Aaron T. L. Lun
Software Mentions: 9
Published: over 6 years ago

10.1534/g3.119.400185

ARMOR: An Automated Reproducible MOdular Workflow for Preprocessing and Differential Analysis of RNA-seq Data
Cited by: 35
Author(s): Stephany Orjuela, Ronald Huang, Katharina Hembach, Mark D. Robinson, Charlotte Soneson
Software Mentions: 8
Published: over 5 years ago

10.1371/journal.pone.0240573

Assessment of software methods for estimating protein-protein relative binding affinities
Cited by: 10
Author(s): Tawny R Gonzalez, Kyle Martin, Jonathan E. Barnes, Jagdish Suresh Patel, F. Marty Ytreberg
Software Mentions: 7
Published: almost 4 years ago

10.1093/bib/bbaa150

Recent advances in user-friendly computational tools to engineer protein function
Cited by: 30
Author(s): Carlos Sequeiros-Borja, Bartłomiej Surpeta, Jan Brezovský
Software Mentions: 5
Published: over 4 years ago

10.3390/ijms21072563

SAAMBE-3D: Predicting Effect of Mutations on Protein–Protein Interactions
Cited by: 60
Author(s): Swagata Pahari, Gen Li, Adithya Krishna Murthy, Siqi Liang, Robert Fragoza, Haiyuan Yu, Emil Alexov
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0049417

Implementation of Web-Based Respondent-Driven Sampling among Men Who Have Sex with Men in Vietnam
Cited by: 52
Author(s): Linus Bengtsson, Xin Lu, Quoc Cuong Nguyen, Martin Camitz, Nguyen Le Hoang, Tuan Anh Nguyen, Fredrik Liljeros, Anna Thorson
Software Mentions: 1
Published: about 12 years ago

10.3389/fpls.2019.00889

Modeling Top-Down and Bottom-Up Drivers of a Regime Shift in Invasive Aquatic Plant Stable States
Cited by: 15
Author(s): Emily Strange, Pietro Landi, Jaclyn M. Hill, Julie A. Coetzee
Software Mentions: 1
Published: over 5 years ago