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: cran: matrixStats
https://packages.ecosyste.ms/registries/cran.r-project.org/packages/matrixStats
Functions that Apply to Rows and Columns of Matrices (and to
Vectors)
53 versions
Latest release: over 1 year ago
276 dependent packages
181,748 downloads last month
Papers Mentioning matrixStats 46
10.12688/f1000research.17824.2
Enhancing gene set enrichment using networksCited by: 2
Author(s): Michael Prummer
Software Mentions: 51
Published: over 5 years ago
10.12688/f1000research.22259.1
Fluent genomics with plyranges and tximetaCited by: 2
Author(s): Stuart Lee, Michael C. Lawrence, Michael I. Love
Software Mentions: 35
Published: over 4 years ago
10.12688/f1000research.9973.2
BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment testsCited by: 20
Author(s): Andrea Komljenović, Julien Roux, Julien Wollbrett, Marc Robinson‐Rechavi, Frederic Bastian
Software Mentions: 33
Published: about 6 years ago
10.1371/journal.pcbi.1005752
mixOmics: An R package for ‘omics feature selection and multiple data integrationCited by: 1,902
Author(s): Florian Rohart, Benoît Gautier, Amrit Singh, Kim‐Anh Lê Cao
Software Mentions: 29
Published: about 7 years ago
10.3389/fmolb.2020.570702
Prognostic Prediction Using a Stemness Index-Related Signature in a Cohort of Gastric CancerCited by: 27
Author(s): Xiaowei Chen, Dawei Zhang, Fei Jiang, Yan Shen, Xin Li, Xin Hu, Pingmin Wei, Xiaobing Shen
Software Mentions: 24
Published: about 4 years ago
10.3389/fimmu.2021.701085
A Single-Cell Atlas of Lymphocyte Adaptive Immune Repertoires and Transcriptomes Reveals Age-Related Differences in Convalescent COVID-19 PatientsCited by: 29
Author(s): Florian Bieberich, Rodrigo Vazquez-Lombardi, Alexander Yermanos, Roy Ehling, Derek M Mason, Bastian Wagner, Edo Kapetanovic, Raphaël Brisset Di Roberto, Cédric R. Weber, Miodrag Savic, Fabian Rudolf, Sai T. Reddy
Software Mentions: 23
Published: over 3 years ago
10.3389/fimmu.2021.632333
Immunological Feature and Transcriptional Signaling of Ly6C Monocyte Subsets From Transcriptome Analysis in Control and Hyperhomocysteinemic MiceCited by: 7
Author(s): Panpan Yang, Lu Liu, Lili Sun, Fang Pu, Nathaniel W. Snyder, Jason Saredy, Yong Ji, Wen Shen, Xuebin Qin, Qinghua Wu, Xiaofeng Yang, Hong Wang
Software Mentions: 21
Published: over 3 years ago
10.3390/genes11030257
mRNAsi Index: Machine Learning in Mining Lung Adenocarcinoma Stem Cell BiomarkersCited by: 61
Author(s): Yitong Zhang, Joseph T. Tseng, I-Chia Lien, Fenglan Li, Wei Wu, Hui Li
Software Mentions: 20
Published: over 4 years ago
10.18632/aging.203108
Cognitive dedifferentiation as a function of cognitive impairment in the ADNI and MemClin cohortsCited by: 2
Author(s): John Wallert, Anna Rennie, Daniel Ferreira, J‐Sebastian Muehlboeck, Lars‐Olof Wahlund, Eric Westman, Urban Ekman
Software Mentions: 20
Published: over 3 years ago
10.3390/cancers12040948
Reconstruction of Ewing Sarcoma Developmental Context from Mass-Scale Transcriptomics Reveals Characteristics of EWSR1-FLI1 PermissibilityCited by: 23
Author(s): Henry E. Miller, Aparna Gorthi, Nicklas Bassani, Liesl A. Lawrence, Brian S. Iskra, Alexander J.R. Bishop
Software Mentions: 19
Published: over 4 years ago
10.3390/genes12030413
Spt4 Promotes Pol I Processivity and Transcription ElongationCited by: 5
Author(s): Abigail K. Huffines, Yvonne J. K. Edwards, David A. Schneider
Software Mentions: 18
Published: over 3 years ago
10.7554/eLife.21883
Layer-specific chromatin accessibility landscapes reveal regulatory networks in adult mouse visual cortexCited by: 72
Author(s): Lucas T. Gray, Zizhen Yao, Thuc Nghi Nguyen, Tae Kyung Kim, Hongkui Zeng, Bosiljka Tasic
Software Mentions: 16
Published: almost 8 years ago
10.1007/s00204-021-03031-1
Functional alterations by a subgroup of neonicotinoid pesticides in human dopaminergic neuronsCited by: 26
Author(s): Dominik Loser, María G. Hinojosa, John D. Blum, Jasmin Schaefer, Markus Brüll, Ylva Johansson, Ilinca Suciu, Karin Grillberger, Timm Danker, Clemens Möller, Iain Gardner, Gerhard Ecker, Susanne Hougaard Bennekou, Anna Forsby, Udo Kraushaar, Marcel Leist
Software Mentions: 15
Published: over 3 years ago
10.1186/s40168-020-00961-3
Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approachCited by: 30
Author(s): Wang Ya, Yan Yan, Kelsey N. Thompson, Sena Bae, Emma K. Accorsi, Yancong Zhang, Jiaxian Shen, Hera Vlamakis, Erica M. Hartmann, Curtis Huttenhower
Software Mentions: 15
Published: almost 4 years ago
10.3390/cancers13174348
Histological Grade of Endometrioid Endometrial Cancer and Relapse Risk Can Be Predicted with Machine Learning from Gene Expression DataCited by: 4
Author(s): Péter Gargya, Bálint László Bálint
Software Mentions: 14
Published: about 3 years ago
10.1007/s00204-020-02956-3
Human neuronal signaling and communication assays to assess functional neurotoxicityCited by: 13
Author(s): Dominik Loser, Jasmin Schaefer, Timm Danker, Clemens Möller, Markus Brüll, Ilinca Suciu, Anna‐Katharina Ückert, Stefanie Klima, Marcel Leist, Udo Kraushaar
Software Mentions: 14
Published: almost 4 years ago
10.3389/fonc.2020.01767
Ovarian Blood Sampling Identifies Junction Plakoglobin as a Novel Biomarker of Early Ovarian CancerCited by: 6
Author(s): Florian Weiland, Noor A. Lokman, Manuela Klingler‐Hoffmann, Thomas W. Jobling, Andrew N. Stephens, Karin Sundfeldt, Peter Hoffmann, Martin K. Oehler
Software Mentions: 13
Published: about 4 years ago
10.7554/eLife.61980
Metabolomic profiling of rare cell populations isolated by flow cytometry from tissuesCited by: 43
Author(s): Andrew W. DeVilbiss, Zhiyu Zhao, Misty S. Martin-Sandoval, Jessalyn M. Ubellacker, Alpaslan Tasdogan, Michalis Agathocleous, Thomas P. Mathews, Sean J. Morrison
Software Mentions: 13
Published: almost 4 years ago
10.12688/f1000research.8839.3
A cross-package Bioconductor workflow for analysing methylation array dataCited by: 80
Author(s): Jovana Maksimovic, Belinda Phipson, Alicia Oshlack
Software Mentions: 12
Published: over 7 years ago
10.1038/s41598-019-46850-0
Deep Learning using Convolutional LSTM estimates Biological Age from Physical ActivityCited by: 56
Author(s): Syed Ashiqur Rahman, Donald A. Adjeroh
Software Mentions: 11
Published: about 5 years ago
10.3389/fpsyg.2019.01529
Social Support and Emotional Intelligence as Protective Resources for Well-Being in Moroccan AdolescentsCited by: 33
Author(s): Esther López-Zafra, Manuel M. Ramos‐Álvarez, Karima El Ghoudani, Octavio Luque-Reca, José María Augusto Landa, Benaissa Zarhbouch, Smail Alaoui, Daniel Cortés-Denia, Manuel Pulido-Martos
Software Mentions: 11
Published: over 5 years ago
10.1038/s41598-020-58111-6
Projected distribution and climate refugia of endangered Kashmir musk deer Moschus cupreus in greater Himalaya, South AsiaCited by: 19
Author(s): Paras B. Singh, Kumar P. Mainali, Zhigang Jiang, Arjun Thapa, Naresh Subedi, Muhammad Naeem Awan, Orus Ilyas, Himal Luitel, Zhixin Zhou, Huijian Hu
Software Mentions: 11
Published: almost 5 years ago
10.3389/fonc.2014.00147
An Integrative Analysis of Meningioma Tumors Reveals the Determinant Genes and Pathways of Malignant TransformationCited by: 7
Author(s): José Carlos Iglesias Gómez, Adrián Mosquera Orgueira
Software Mentions: 11
Published: over 10 years ago
10.1186/s12859-017-1847-x
Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse dataCited by: 42
Author(s): Joseph N. Paulson, Cho-Yi Chen, Camila M. Lopes‐Ramos, Marieke L. Kuijjer, John Platig, Abhijeet R. Sonawane, Maud Fagny, Kimberly Glass, John Quackenbush
Software Mentions: 10
Published: about 7 years ago
10.1186/s13148-020-0824-9
Maternal diabetes and obesity influence the fetal epigenome in a largely Hispanic populationCited by: 18
Author(s): Heather E. Rizzo, Elia N. Escaname, Nicholas B. Alana, Elizabeth Lavender, Jonathan Gelfond, Roman Fernandez, Matthew A. Hibbs, Julie King, Nicholas Carr, Cynthia L. Blanco
Software Mentions: 9
Published: over 4 years ago
10.1371/journal.pone.0123483
Wiki Surveys: Open and Quantifiable Social Data CollectionCited by: 89
Author(s): Matthew J. Salganik, Karen Levy
Software Mentions: 9
Published: over 9 years ago
10.1186/s12864-020-06977-1
Integrating binding and expression data to predict transcription factors combined functionCited by: 9
Author(s): Mahmoud Ahmed, Do Sik Min, Deok Ryong Kim
Software Mentions: 8
Published: about 4 years ago
10.3390/metabo10120494
Metabolic Drug Response Phenotyping in Colorectal Cancer Organoids by LC-QTOF-MSCited by: 17
Author(s): Sylvia K. Neef, Nicole Janssen, Stefan Winter, Svenja K. Wallisch, Ute Hofmann, Marc H. Dahlke, Matthias Schwab, Thomas E. Mürdter, Mathias Haag
Software Mentions: 8
Published: almost 4 years ago
10.1038/srep42719
A pan-cancer analysis of secreted Frizzled-related proteins: re-examining their proposed tumour suppressive functionCited by: 37
Author(s): Krista Vincent, Lynne-Marie Postovit
Software Mentions: 8
Published: over 7 years ago
10.1186/s12859-021-04130-7
Correlation AnalyzeR: functional predictions from gene co-expression correlationsCited by: 35
Author(s): Henry E. Miller, Alexander J.R. Bishop
Software Mentions: 8
Published: over 3 years ago
10.7554/eLife.12845
Two FGFRL-Wnt circuits organize the planarian anteroposterior axisCited by: 90
Author(s): M. Lucila Scimone, Lauren E. Cote, Travis Rogers, Peter W. Reddien
Software Mentions: 7
Published: over 8 years ago
10.3389/fimmu.2020.01166
Non-sterilizing, Infection-Permissive Vaccination With Inactivated Influenza Virus Vaccine Reshapes Subsequent Virus Infection-Induced Protective Heterosubtypic Immunity From Cellular to Humoral Cross-Reactive Immune ResponsesCited by: 6
Author(s): Angela Choi, Lorena Itatí Ibáñez, Shirin Strohmeier, Florian Krammer, Adolfo Garcı́a-Sastre, Michael Schotsaert
Software Mentions: 7
Published: over 4 years ago
10.1186/s12859-019-2990-3
Analysis of networks of host proteins in the early time points following HIV transductionCited by: 8
Author(s): Éva Csősz, Ferenc Tóth, Mohamed Mahdi, George Tsaprailis, Miklós Emri, József Tözsér
Software Mentions: 7
Published: over 5 years ago
10.1186/s13148-020-0821-z
DNA methylation-driven EMT is a common mechanism of resistance to various therapeutic agents in cancerCited by: 49
Author(s): Eva Galle, Bernard Thienpont, Sarah Cappuyns, Tom Venken, Pieter Busschaert, Matthias Van Haele, Éric Van Cutsem, Tania Roskams, Jos van Pelt, Chris Verslype, Jeroen Dekervel, Diether Lambrechts
Software Mentions: 7
Published: over 4 years ago
10.3390/vaccines7030113
TIV Vaccination Modulates Host Responses to Influenza Virus Infection that Correlate with Protection against Bacterial SuperinfectionCited by: 5
Author(s): Angela Choi, Ioanna Christopoulou, Xavier Saelens, Adolfo Garcı́a-Sastre, Michael Schotsaert
Software Mentions: 7
Published: about 5 years ago
10.3389/fcell.2019.00141
Single Cell Imaging of Nuclear Architecture ChangesCited by: 17
Author(s): Rikke Morrish, Michael Hermes, Jeremy Metz, Edwin M. Stone, Stefano Pagliara, Richard Chahwan, Francesca Palombo
Software Mentions: 6
Published: over 5 years ago
10.1038/s41437-018-0143-5
Power law fitness landscapes and their ability to predict fitnessCited by: 3
Author(s): Diogo Passagem-Santos, Simone Zacarias, Lília Perfeito
Software Mentions: 6
Published: about 6 years ago
10.3389/fcell.2014.00040
Quantifying periodicity in omics dataCited by: 7
Author(s): Cornelia Amariei, Masaru Tomita, Douglas B. Murray
Software Mentions: 5
Published: about 10 years ago
10.1371/journal.pone.0112909
Gene Expression Analyses of the Spatio-Temporal Relationships of Human Medulloblastoma Subgroups during Early Human NeurogenesisCited by: 24
Author(s): Cornelia M. Hooper, Susan Melanie Hawes, Ursula R. Kees, Nicholas G. Gottardo, Peter B. Dallas
Software Mentions: 5
Published: almost 10 years ago
10.1038/sdata.2018.245
Brain metastasis DNA methylomes, a novel resource for the identification of biological and clinical featuresCited by: 18
Author(s): Matthew P. Salomon, Javier I. J. Orozco, James S. Wilmott, Parvinder Hothi, Ayla O. Manughian-Peter, Charles S. Cobbs, Richard A. Scolyer, Dave S.B. Hoon, Diego M. Marzese
Software Mentions: 4
Published: almost 6 years ago
10.1093/jxb/eraa036
The contribution of cis- and trans-acting variants to gene regulation in wild and domesticated barley under cold stress and control conditionsCited by: 14
Author(s): Matthew Haas, Axel Himmelbach, Martin Mascher
Software Mentions: 4
Published: almost 5 years ago
10.1371/journal.pone.0206855
Workload measurement for molecular genetics laboratory: A survey studyCited by: 6
Author(s): Enrico Tagliafico, Isabella Bernardis, Marina Grasso, Maria Rosaria D’Apice, Cristina Lapucci, Annalisa Botta, Daniela Giachino, Maria Marinelli, Paola Primignani, Silvia Russo, Ilaria Sani, Manuela Seia, Sergio Fini, Paola Rimessi, Elena Tenedini, Anna Ravani, Maurizio Genuardi, Alessandra Ferlini
Software Mentions: 3
Published: almost 6 years ago
10.3389/fpls.2021.656683
Membrane-Enriched Proteomics Link Ribosome Accumulation and Proteome Reprogramming With Cold Acclimation in Barley Root MeristemsCited by: 15
Author(s): Federico Martinez‐Seidel, Pipob Suwanchaikasem, Shuai Nie, Michael G. Leeming, Alexandre Augusto Pereira Firmino, Nicholas A. Williamson, Joachim Kopka, Ute Roessner, Berin A. Boughton
Software Mentions: 3
Published: over 3 years ago
10.1371/journal.pone.0235413
RNA from stabilized whole blood enables more comprehensive immune gene expression profiling compared to RNA from peripheral blood mononuclear cellsCited by: 13
Author(s): Fleur van der Sijde, Yunlei Li, Rick Schraauwen, Willem de Koning, Casper H.J. van Eijck, Dana A. M. Mustafa
Software Mentions: 2
Published: over 4 years ago
10.1186/s12864-018-4637-6
Comparison of normalization methods for the analysis of metagenomic gene abundance dataCited by: 98
Author(s): Mariana Buongermino Pereira, Mikael Wallroth, Viktor Jönsson, Erik Kristiansson
Software Mentions: 2
Published: over 6 years ago
10.1038/s41598-018-32221-8
The human gut pan-microbiome presents a compositional core formed by discrete phylogenetic unitsCited by: 25
Author(s): Daniel Aguirre de Cárcer
Software Mentions: 2
Published: about 6 years ago