bioconductor: PROPER | Projects | Ecosyste.ms: Papers

10.1186/s12859-016-0994-9

Sample size calculation while controlling false discovery rate for differential expression analysis with RNA-sequencing experiments
Cited by: 79
Author(s): Ran Bi, Peng Liu
Software Mentions: 9
Published: over 8 years ago

10.1177/2515841419835460

RNA-sequencing in ophthalmology research: considerations for experimental design and analysis
Cited by: 6
Author(s): Nicholas Owen, Mariya Moosajee
Software Mentions: 9
Published: almost 6 years ago

10.1007/s00018-018-2898-5

Celiac disease biomarkers identified by transcriptome analysis of small intestinal biopsies
Cited by: 32
Author(s): Hanna Bragde, Ulf Jansson, Mats Fredrikson, Ewa Grodzinsky, Jan Söderman
Software Mentions: 8
Published: over 6 years ago

10.1186/s13059-019-1730-3

Current status and applications of genome-scale metabolic models
Cited by: 406
Author(s): Changdai Gu, Gi Bae Kim, Won Jun Kim, Hyun Uk Kim, Sang Yup Lee
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.ppat.1008986

Qualitative Differences Between the IFNα subtypes and IFNβ Influence Chronic Mucosal HIV-1 Pathogenesis
Cited by: 21
Author(s): Kejun Guo, Guannan Shen, Jon Kibbie, Tanía González, Stephanie M. Dillon, Harry A. Smith, Emily Cooper, Kerry J. Lavender, Kim J. Hasenkrug, Kathrin Sutter, Ulf Dittmer, Miranda Kroehl, Katerina Kechris, Cara C. Wilson, Mario L. Santiago
Software Mentions: 5
Published: about 4 years ago

10.1186/s12859-018-2191-5

RnaSeqSampleSize: real data based sample size estimation for RNA sequencing
Cited by: 54
Author(s): Shilin Zhao, Chung I. Li, Yan Guo, Quanhu Sheng, Yu Shyr
Software Mentions: 4
Published: over 6 years ago

10.1186/s12859-017-1648-2

Power analysis for RNA-Seq differential expression studies
Cited by: 27
Author(s): Lianbo Yu, Soledad Fernández, Guy Brock
Software Mentions: 4
Published: over 7 years ago

10.3389/fgene.2016.00225

Extending the R Library PROPER to Enable Power Calculations for Isoform-Level Analysis with EBSeq
Cited by: 2
Author(s): Amadou Thierno Gaye
Software Mentions: 4
Published: almost 8 years ago

10.1186/s12859-019-2804-7

pwrEWAS: a user-friendly tool for comprehensive power estimation for epigenome wide association studies (EWAS)
Cited by: 40
Author(s): Stefan Graw, Rosalyn Henn, Jeffrey Thompson, Devin C. Koestler
Software Mentions: 4
Published: over 5 years ago

10.1107/S1600577517007032

Numerical simulations of the hard X-ray pulse intensity distribution at the Linac Coherent Light Source
Cited by: 6
Author(s): T. Pardini, Andrew Aquila, Sébastien Boutet, Daniele Cocco, Stefan P. Hau‐Riege
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2105-6-S1-S4

BioCreAtIvE Task1A: entity identification with a stochastic tagger
Cited by: 26
Author(s): Shuhei Kinoshita, K. Bretonnel Cohen, Philip V. Ogren, Lawrence Hunter
Software Mentions: 2
Published: over 19 years ago

10.1371/journal.pcbi.1004705

Systems-Wide Prediction of Enzyme Promiscuity Reveals a New Underground Alternative Route for Pyridoxal 5’-Phosphate Production in E. coli
Cited by: 19
Author(s): Matthew Oberhardt, Raphy Zarecki, Lea Reshef, Fangfang Xia, Miquel Duran‐Frigola, Rachel Schreiber, Christopher S. Henry, Nir Ben‐Tal, Daniel J. Dwyer, Uri Gophna, Eytan Ruppin
Software Mentions: 2
Published: almost 9 years ago

10.3390/ijms20071637

Prediction Medicine: Biomarkers, Risk Calculators and Magnetic Resonance Imaging as Risk Stratification Tools in Prostate Cancer Diagnosis
Cited by: 72
Author(s): Daniël F. Osses, Monique J. Roobol, Ivo G. Schoots
Software Mentions: 1
Published: over 5 years ago

10.1186/s12889-020-09042-4

A comparative impact evaluation of two human resource models for community-based active tuberculosis case finding in Ho Chi Minh City, Viet Nam
Cited by: 20
Author(s): Luan Nguyen Quang Vo, Rachel Jeanette Forse, Andrew James Codlin, Thanh Tung Vu, Giang Truong Le, Giang Chau, Vinh Van Truong, Ha Dang, Lan Huu Nguyen, Hoa B. Nguyen, Nhung Viet Nguyen, Jens Levy, S. Bertel Squire, Knut Lönnroth, Maxine Caws
Software Mentions: 1
Published: over 4 years ago

10.1186/s12859-020-03827-5

SAlign–a structure aware method for global PPI network alignment
Cited by: 8
Author(s): Umair Ayub, Imran Haider, Hammad Naveed
Software Mentions: 1
Published: about 4 years ago

10.1186/s12859-016-1395-9

PROPER: global protein interaction network alignment through percolation matching
Cited by: 32
Author(s): Ehsan Kazemi, Hamed Hassani, Matthias Grossglauser, Hassan Pezeshgi Modarres
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12864-019-6271-3

LePrimAlign: local entropy-based alignment of PPI networks to predict conserved modules
Cited by: 2
Author(s): Sawal Maskey, Young-Rae Cho
Software Mentions: 1
Published: almost 5 years ago

10.1186/1471-244X-13-307

PROPER I: frequency and appropriateness of psychotropic drugs use in nursing home patients and its associations: a study protocol
Cited by: 20
Author(s): Klaas van der Spek, Debby L. Gerritsen, Martin Smalbrugge, Marjorie Nelissen-Vrancken, Roland B Wetzels, Claudia H. W. Smeets, Sytse U. Zuidema, Raymond T.C.M. Koopmans
Software Mentions: 1
Published: about 11 years ago

10.1186/s12888-019-2291-4

Reducing inappropriate psychotropic drug use in nursing home residents with dementia: protocol for participatory action research in a stepped-wedge cluster randomized trial
Cited by: 12
Author(s): Claudia M. Groot Kormelinck, Charlotte Frederike van Teunenbroek, Boudewijn J. Kollen, Margreet Reitsma, Debby L. Gerritsen, Martin Smalbrugge, Sytse U. Zuidema
Software Mentions: 1
Published: about 5 years ago

10.1186/1471-244X-13-280

Improving psychotropic drug prescription in nursing home patients with dementia: design of a cluster randomized controlled trial
Cited by: 18
Author(s): Claudia H. W. Smeets, Martin Smalbrugge, Debby L. Gerritsen, Marjorie Nelissen-Vrancken, Roland B Wetzels, Klaas van der Spek, Sytse U. Zuidema, Raymond T.C.M. Koopmans
Software Mentions: 1
Published: about 11 years ago

10.1186/1471-2105-7-S5-S11

NERBio: using selected word conjunctions, term normalization, and global patterns to improve biomedical named entity recognition
Cited by: 103
Author(s): Richard Tzong-Han Tsai, Cheng Lung Sung, Hong Jie Dai, Hsieh Chuan Hung, Ting Yi Sung, Wen Lian Hsu
Software Mentions: 1
Published: almost 18 years ago

10.12688/f1000research.22432.6

Does standard cosmology really predict the cosmic microwave background?
Cited by: 1
Author(s): Hartmut Traunmüller
Software Mentions: 1
Published: about 3 years ago

10.1038/s41598-021-94638-y

Target position and avoidance margin effects on path planning in obstacle avoidance
Cited by: 2
Author(s): Mohammad R. Saeedpour-Parizi, Shirin E. Hassan, Ariful Azad, Kelly J. Baute, Tayebeh Baniasadi, John B. Shea
Software Mentions: 1
Published: over 3 years ago

10.1186/s13029-015-0047-1

PROPER: Performance visualization for optimizing and comparing ranking classifiers in MATLAB
Cited by: 2
Author(s): Samad Jahandideh, Fatemeh Sharifi, Lukasz Jaroszewski, Adam Godzik
Software Mentions: 1
Published: almost 9 years ago

10.1186/s13063-015-1049-7

PERC rule to exclude the diagnosis of pulmonary embolism in emergency low-risk patients: study protocol for the PROPER randomized controlled study
Cited by: 12
Author(s): Yonathan Freund, Alexandra Rousseau, Yann-Érick Claessens, Olivier Hügli, Olivier Sanchez, Tabassome Simon, Bruno Riou
Software Mentions: 1
Published: almost 9 years ago

Ecosyste.ms: Papers

Projects: bioconductor: PROPER

Papers Mentioning PROPER 25