cran: locfdr | Projects | Ecosyste.ms: Papers

10.1186/s13059-019-1716-1

A practical guide to methods controlling false discoveries in computational biology
Cited by: 178
Author(s): Keegan Korthauer, Patrick K. Kimes, Claire Duvallet, Alejandro Reyes, Ayshwarya Subramanian, Mingxiang Teng, Chinmay Shukla, Eric J. Alm, Stephanie C. Hicks
Software Mentions: 11
Published: over 5 years ago

10.1016/j.celrep.2020.108629

VELCRO-IP RNA-seq reveals ribosome expansion segment function in translation genome-wide
Cited by: 10
Author(s): Kathrin Leppek, Gun Woo Byeon, Kotaro Fujii, Maria Barna
Software Mentions: 6
Published: over 3 years ago

10.1186/1471-2105-9-303

A unified approach to false discovery rate estimation
Cited by: 343
Author(s): Korbinian Strimmer
Software Mentions: 5
Published: about 16 years ago

10.1371/journal.pgen.1000302

The Chromosomal High-Affinity Binding Sites for the Drosophila Dosage Compensation Complex
Cited by: 171
Author(s): Tobias Straub, Charlotte Grimaud, Gregor D. Gilfillan, Angelika Mitterweger, Peter B. Becker
Software Mentions: 5
Published: almost 16 years ago

10.1007/s00251-014-0819-9

Different binding motifs of the celiac disease-associated HLA molecules DQ2.5, DQ2.2, and DQ7.5 revealed by relative quantitative proteomics of endogenous peptide repertoires
Cited by: 79
Author(s): Elin Bergseng, Siri Dørum, Magnus Ø. Arntzen, Morten Nielsen, Ståle Nygård, Søren Buus, Gustavo Souza, Ludvig M. Sollid
Software Mentions: 4
Published: almost 10 years ago

10.1371/journal.pone.0187287

EAMA: Empirically adjusted meta-analysis for large-scale simultaneous hypothesis testing in genomic experiments
Cited by: 3
Author(s): Sinjini Sikdar, Somnath Datta, Susmita Datta
Software Mentions: 4
Published: almost 7 years ago

10.3390/cancers12123786

Stroma Transcriptomic and Proteomic Profile of Prostate Cancer Metastasis Xenograft Models Reveals Prognostic Value of Stroma Signatures
Cited by: 9
Author(s): Sofia Karkampouna, Maria Rosaria De Filippo, Charlotte K.Y. Ng, Irena Klima, Eugenio Zoni, Martin Spahn, Frank Stein, Per Haberkant, George N. Thalmann, Marianna Kruithof-de Julio
Software Mentions: 4
Published: almost 4 years ago

10.1093/biostatistics/kxw041

False discovery rates: a new deal
Cited by: 474
Author(s): Matthew Stephens
Software Mentions: 4
Published: almost 8 years ago

10.1371/journal.pcbi.1005700

Extracting replicable associations across multiple studies: Empirical Bayes algorithms for controlling the false discovery rate
Cited by: 15
Author(s): David Amar, Ron Shamir, Daniel Yekutieli
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pgen.1003188

Suv4-20h Histone Methyltransferases Promote Neuroectodermal Differentiation by Silencing the Pluripotency-Associated Oct-25 Gene
Cited by: 29
Author(s): Dario Nicetto, Matthias Hahn, Julia Jeannine Jung, Tobias D. Schneider, Tobias Straub, Róbert Dávid, Gunnar Schotta, Ralph A.W. Rupp
Software Mentions: 4
Published: over 11 years ago

10.1186/1471-2164-15-1162

Simultaneous analysis of large-scale RNAi screens for pathogen entry
Cited by: 37
Author(s): Pauli Rämö, Anna Drewek, Cécile Arrieumerlou, Niko Beerenwinkel, Houchaïma Ben-Tekaya, Bettina Cardel, Alain Casanova, Raquel Conde-Álvarez, Pascale Cossart, Gábor Csúcs, Simone Eicher, Mario Emmenlauer, Urs F. Greber, Wolf‐Dietrich Hardt, Ari Helenius, Christoph Kasper, Andreas M. Kaufmann, Saskia Kreibich, Andreas Kühbacher, Péter Z. Kunszt, Shyan Huey Low, Jason Mercer, Daria Mudrak, Simone Muntwiler, Lucas Pelkmans, Javier Pizarro‐Cerdá, Michael Podvinec, Eva Pujadas, Bernd Rinn, Vincent Rouilly, Fabian Schmich, Juliane Siebourg‐Polster, Berend Snijder, Michael Stebler, Gabriel Studer, Ewa Szczurek, Matthias C. Truttmann, Christian von Mering, Andreas Vonderheit, Artur Yakimovich, Peter Bühlmann, Christoph Dehio
Software Mentions: 3
Published: almost 10 years ago

10.1186/s12864-020-07241-2

Comprehensive network modeling from single cell RNA sequencing of human and mouse reveals well conserved transcription regulation of hematopoiesis
Cited by: 8
Author(s): Shaojian Gao, Zhijie Wu, Xingmin Feng, Sachiko Kajigaya, Xujing Wang, Neal S. Young
Software Mentions: 3
Published: almost 4 years ago

10.3389/fgene.2013.00270

Evaluation of the lasso and the elastic net in genome-wide association studies
Cited by: 154
Author(s): Patrik Waldmann, Gábor Mészáros, Birgit Gredler, Christian Fuerst, Johann Sölkner
Software Mentions: 3
Published: over 11 years ago

10.1186/1471-2105-6-199

Cited by: 84
Author(s): Per Broberg
Software Mentions: 3
Published: over 19 years ago

10.1186/1471-2105-11-63

Validation of differential gene expression algorithms: Application comparing fold-change estimation to hypothesis testing
Cited by: 14
Author(s): Corey Yanofsky, David R. Bickel
Software Mentions: 3
Published: over 14 years ago

10.6064/2012/519394

A Comparison of Two Classes of Methods for Estimating False Discovery Rates in Microarray Studies
Cited by: 3
Author(s): Emily Hansen, Kathleen F. Kerr
Software Mentions: 2
Published: over 12 years ago

10.1186/1471-2164-16-S5-S5

Memory acquisition and retrieval impact different epigenetic processes that regulate gene expression
Cited by: 44
Author(s): Lucı́a Peixoto, Mathieu E. Wimmer, Shane G. Poplawski, Jennifer C Tudor, Charles A. Kenworthy, Shichong Liu, Keiko Mizuno, Benjamin A. Garcia, Nancy R. Zhang, K. Peter Giese, Ted Abel
Software Mentions: 2
Published: over 9 years ago

10.1186/s13040-018-0163-y

A novel joint analysis framework improves identification of differentially expressed genes in cross disease transcriptomic analysis
Cited by: 6
Author(s): Wenyi Qin, Hui Liu
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0071334

Expansion of Multipotent Stem Cells from the Adult Human Brain
Cited by: 38
Author(s): Wayne Murrell, Emily Palmero, John Bianco, Biljana Stangeland, Mrinal Joel, Linda Paulson, Bernd Thiede, Zanina Grieg, Ingunn Ramsnes, Håvard Kjesbu Skjellegrind, Ståle Nygård, Petter Brandal, Cecilie Sandberg, Einar O. Vik-Mo, Sheryl Palmero, Iver A. Langmoen
Software Mentions: 2
Published: about 11 years ago

10.1186/s13059-014-0489-9

MSEA: detection and quantification of mutation hotspots through mutation set enrichment analysis
Cited by: 48
Author(s): Peilin Jia, Quan Wang, Qingxia Chen, Katherine E. Hutchinson, William Pao, Zhongming Zhao
Software Mentions: 2
Published: almost 10 years ago

10.1038/srep17221

Local false discovery rate estimation using feature reliability in LC/MS metabolomics data
Cited by: 23
Author(s): Elizabeth Chong, Yijian Huang, Hao Wu, Nima Ghasemzadeh, Karan Uppal, Arshed A Quyyumi, Dean P. Jones, Tianwei Yu
Software Mentions: 2
Published: almost 9 years ago

10.1038/srep41262

Improving polygenic risk prediction from summary statistics by an empirical Bayes approach
Cited by: 43
Author(s): Hon‐Cheong So, Pak C. Sham
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2105-8-229

A constrained polynomial regression procedure for estimating the local False Discovery Rate
Cited by: 10
Author(s): Cyril Dalmasso, Avner Bar-Hen, Philippe Broët
Software Mentions: 1
Published: about 17 years ago

10.1371/journal.pone.0013898

Estimating the Total Number of Susceptibility Variants Underlying Complex Diseases from Genome-Wide Association Studies
Cited by: 16
Author(s): Hon‐Cheong So, Benjamin Hon Kei Yip, Pak C. Sham
Software Mentions: 1
Published: almost 14 years ago

10.1186/1471-2164-13-S4-S9

Domain landscapes of somatic mutations in cancer
Cited by: 48
Author(s): Nathan L. Nehrt, Thomas Peterson, DoHwan Park, Maricel G. Kann
Software Mentions: 1
Published: over 12 years ago

10.1186/s13336-015-0016-6

K-core decomposition of a protein domain co-occurrence network reveals lower cancer mutation rates for interior cores
Cited by: 9
Author(s): Arnold I Emerson, Simeon Andrews, Ikhlak Ahmed, Thasni Ka Azis, Joel A. Malek
Software Mentions: 1
Published: over 9 years ago

10.1038/srep07097

Potential microRNA-mediated oncogenic intercellular communication revealed by pan-cancer analysis
Cited by: 17
Author(s): Yue Li, Zhaolei Zhang
Software Mentions: 1
Published: almost 10 years ago

10.1111/dom.13460

The effects of kisspeptin on β‐cell function, serum metabolites and appetite in humans
Cited by: 69
Author(s): Chioma Izzi‐Engbeaya, Alexander Comninos, Sophie Clarke, Anne Jomard, Lisa Yang, SE Jones, Ali Abbara, Shakunthala Narayanaswamy, Pei Chia Eng, Deborah Papadopoulou, Julia Prague, Paul Bech, Ian F. Godsland, Paul Bassett, Caroline Sands, Stéphane Camuzeaux, María José Gómez-Romero, Jake T M Pearce, Matthew R. Lewis, Elaine Holmes, Jeremy K. Nicholson, Tricia Tan, Risheka Ratnasabapathy, Ming Hu, Gaëlle Carrat, Lorenzo Piemonti, Marco Bugliani, Piero Marchetti, Paul Johnson, Stephen J. Hughes, A. M. James Shapiro, Guy A. Rutter, Waljit S. Dhillo
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0133404

Network-Based Analysis of Schizophrenia Genome-Wide Association Data to Detect the Joint Functional Association Signals
Cited by: 31
Author(s): Suhua Chang, Kechi Fang, Kunlin Zhang, Jing Wang
Software Mentions: 1
Published: about 9 years ago

10.3389/fnins.2015.00316

An empirical Bayes normalization method for connectivity metrics in resting state fMRI
Cited by: 17
Author(s): Shuo Chen, Jian Kang, Guoqing Wang
Software Mentions: 1
Published: about 9 years ago

Ecosyste.ms: Papers

Projects: cran: locfdr

Papers Mentioning locfdr 30