bioconductor: BiocParallel | Projects

10.12688/f1000research.17824.2

Enhancing gene set enrichment using networks
Cited by: 2
Author(s): Michael Prummer
Software Mentions: 51
Published: over 5 years ago

10.12688/f1000research.22259.1

Fluent genomics with plyranges and tximeta
Cited by: 2
Author(s): Stuart Lee, Michael C. Lawrence, Michael I. Love
Software Mentions: 35
Published: almost 5 years ago

10.3390/ijms22063251

Untargeted In Silico Compound Classification—A Novel Metabolomics Method to Assess the Chemodiversity in Bryophytes
Cited by: 11
Author(s): Kristian Peters, Gerd Ulrich Balcke, Niklas Kleinenkuhnen, Hendrik Treutler, Steffen Neumann
Software Mentions: 31
Published: over 3 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 Patients
Cited 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

10.1016/j.patter.2021.100322

The role of metadata in reproducible computational research
Cited by: 38
Author(s): Jeremy Leipzig, Daniel Nüst, Charles Tapley Hoyt, Karthik Ram, Jane Greenberg
Software Mentions: 21
Published: over 3 years ago

10.1186/s12859-016-1241-0

systemPipeR: NGS workflow and report generation environment
Cited by: 148
Author(s): Tyler W. H. Backman, Thomas Girke
Software Mentions: 19
Published: over 8 years ago

10.1186/s13059-019-1805-1

Divergent neuronal DNA methylation patterns across human cortical development reveal critical periods and a unique role of CpH methylation
Cited by: 65
Author(s): Amanda J. Price, Leonardo Collado‐Torres, Н. А. Иванов, Wei Xia, Emily E. Burke, Joo Heon Shin, Ran Tao, Liang Ma, Yankai Jia, Thomas M. Hyde, Joel E. Kleinman, Daniel R. Weinberger, Andrew E. Jaffe
Software Mentions: 18
Published: about 5 years ago

10.1186/s12859-020-03577-4

NASQAR: a web-based platform for high-throughput sequencing data analysis and visualization
Cited by: 38
Author(s): Ayman Yousif, Nizar Drou, Jillian Rowe, Mohammed Khalfan, Kristin C. Gunsalus
Software Mentions: 17
Published: over 4 years ago

10.1093/bib/bbv080

Public data and open source tools for multi-assay genomic investigation of disease
Cited by: 47
Author(s): Lavanya Kannan, Marcel Ramos, Angela Re, Nehmé El-Hachem, Zhaleh Safikhani, Deena M.A. Gendoo, Sean Davis, David Gomez-Cabrero, Robert Castelo, Kasper D. Hansen, Vincent J. Carey, Martin Morgan, Aedín C. Culhane, Benjamin Haibe‐Kains, Levi Waldron
Software Mentions: 15
Published: about 9 years ago

10.3390/biomedicines9020144

Dietary Rice Bran-Modified Human Gut Microbial Consortia Confers Protection against Colon Carcinogenesis Following Fecal Transfaunation
Cited by: 19
Author(s): Kristopher D. Parker, Akhilendra Kumar Maurya, Hend Ibrahim, Sangeeta Rao, Petronella R. Hove, Dileep Kumar, Rama Kant, B. L. Raina, Rajesh Agarwal, Kristine A. Kuhn, Komal Raina, Elizabeth P. Ryan
Software Mentions: 15
Published: almost 4 years ago

10.26508/lsa.202000766

Egr2 and 3 control inflammation, but maintain homeostasis, of PD-1<sup>high</sup> memory phenotype CD4 T cells
Cited by: 6
Author(s): Alistair L. J. Symonds, Wei Zheng, Tizong Miao, Ang Li, Tieshang Wang, Ruth Kiome, Xiaofeng Hou, Suling Li, Ping Wang
Software Mentions: 15
Published: over 4 years ago

10.3390/cancers13174348

Histological Grade of Endometrioid Endometrial Cancer and Relapse Risk Can Be Predicted with Machine Learning from Gene Expression Data
Cited by: 4
Author(s): Péter Gargya, Bálint László Bálint
Software Mentions: 14
Published: over 3 years ago

10.1038/s41598-020-69239-w

Neural innervation as a potential trigger of morphological color change and sexual dimorphism in cichlid fish
Cited by: 14
Author(s): Yipeng Liang, Axel Meyer, Claudius F. Kratochwil
Software Mentions: 12
Published: over 4 years ago

10.1084/jem.20160553

Egr2 and 3 control adaptive immune responses by temporally uncoupling expansion from T cell differentiation
Cited by: 46
Author(s): Tizong Miao, Alistair L. J. Symonds, Randeep Singh, Janine D. Symonds, Ane Ogbe, Becky Omodho, Bo Zhu, Suling Li, Ping Wang
Software Mentions: 12
Published: over 7 years ago

10.7554/eLife.34409

General decapping activators target different subsets of inefficiently translated mRNAs
Cited by: 40
Author(s): Feng He, Alper Çelik, Chan Wu, Allan Jacobson
Software Mentions: 12
Published: about 6 years ago

10.1155/2016/7972351

Advancements in RNASeqGUI towards a Reproducible Analysis of RNA-Seq Experiments
Cited by: 11
Author(s): Francesco Russo, Dario Righelli, Claudia Angelini
Software Mentions: 11
Published: almost 9 years ago

10.1186/s12859-019-2797-2

scruff: an R/Bioconductor package for preprocessing single-cell RNA-sequencing data
Cited by: 19
Author(s): Zhe Wang, Junming Hu, W. Evan Johnson, Joshua D. Campbell
Software Mentions: 10
Published: over 5 years ago

10.3389/fgene.2021.616686

Identifying Differentially Expressed Genes of Zero Inflated Single Cell RNA Sequencing Data Using Mixed Model Score Tests
Cited by: 2
Author(s): Zhiqiang He, Yueyun Pan, Fang Shao, Hui Wang
Software Mentions: 10
Published: almost 4 years ago

10.1371/journal.pone.0186275

Identification of two types of GGAA-microsatellites and their roles in EWS/FLI binding and gene regulation in Ewing sarcoma
Cited by: 38
Author(s): Kirsten M. Johnson, Cenny Taslim, Ranajeet S. Saund, Stephen L. Lessnick
Software Mentions: 10
Published: about 7 years ago

10.1097/j.pain.0000000000001416

Comprehensive analysis of long noncoding RNA expression in dorsal root ganglion reveals cell-type specificity and dysregulation after nerve injury
Cited by: 41
Author(s): Georgios Baskozos, J. D. K. Dawes, Jean-Sébastien Austin, Ana Antunes-Martins, Lucy A. McDermott, Alex Clark, Teodora Trendafilova, Jon Lees, Stephen B. McMahon, Jeffrey S. Mogil, Christine Orengo, David L.H. Bennett
Software Mentions: 7
Published: about 6 years ago

10.1186/s12859-018-2353-5

XenofilteR: computational deconvolution of mouse and human reads in tumor xenograft sequence data
Cited by: 81
Author(s): Roelof J.C. Kluin, Kristel Kemper, Thomas Kuilman, Julian R. de Ruiter, Vivek Iyer, Josep V. Forment, Paulien Cornelissen-Steijger, Iris de Rink, Petra ter Brugge, Ji‐Ying Song, Sjoerd Klarenbeek, Ultan McDermott, Jos Jonkers, Arno Velds, David J. Adams, Daniel S. Peeper, Oscar Krijgsman
Software Mentions: 7
Published: about 6 years ago

10.3390/ijms20061321

Cellular Gene Expression during Hepatitis C Virus Replication as Revealed by Ribosome Profiling
Cited by: 14
Author(s): Gesche K. Gerresheim, Jochen Bathke, Audrey M. Michel, Dmitry E. Andreev, Lyudmila Shalamova, Oliver Roßbach, Pan Hu, Dieter Glebe, Markus Fricke, Manja Marz, Alexander Goesmann, Stephen J Kiniry, Pavel V. Baranov, Ivan N. Shatsky, Michael Niepmann
Software Mentions: 6
Published: almost 6 years ago

10.3389/fmicb.2020.00390

Response of Tomato Rhizosphere Bacteria to Root-Knot Nematodes, Fenamiphos and Sampling Time Shows Differential Effects on Low Level Taxa
Cited by: 3
Author(s): Mariantonietta Colagiero, Laura Cristina Rosso, Domenico Catalano, Leonardo Schena, Aurelio Ciancio
Software Mentions: 6
Published: almost 5 years ago

10.1186/1471-2105-14-75

virtualArray: a R/bioconductor package to merge raw data from different microarray platforms
Cited by: 51
Author(s): Andreas Heider, Rüdiger Alt
Software Mentions: 5
Published: almost 12 years ago

10.1093/bioinformatics/btz284

clustermq enables efficient parallelization of genomic analyses
Cited by: 5
Author(s): Michaël Schubert
Software Mentions: 5
Published: over 5 years ago

10.12688/f1000research.8288.1

MetaNetVar: Pipeline for applying network analysis tools for genomic variants analysis
Cited by: 3
Author(s): Eric Moyer, Megan Hastings Hagenauer, Matthew Lesko, Felix Francis, Oscar J Rodriguez, Vijayaraj Nagarajan, Vojtech Huser, Ben Busby
Software Mentions: 5
Published: over 8 years ago

10.12688/f1000research.51143.1

periodicDNA: an R/Bioconductor package to investigate k-mer periodicity in DNA
Cited by: 5
Author(s): Jacques Serizay, Julie Ahringer
Software Mentions: 4
Published: almost 4 years ago

10.1186/s12864-019-6313-x

Secretory RING finger proteins function as effectors in a grapevine galling insect
Cited by: 13
Author(s): Chaoyang Zhao, Claude Rispe, Paul D. Nabity
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-018-25428-2

Tissue storage affects lipidome profiling in comparison to in vivo microsampling approach
Cited by: 32
Author(s): Anna Roszkowska, Mengxiao Yu, Vincent Bessonneau, Leslie M. Bragg, Mark R. Servos, Janusz Pawliszyn
Software Mentions: 2
Published: over 6 years ago

10.1038/s42003-018-0091-x

The HTPmod Shiny application enables modeling and visualization of large-scale biological data
Cited by: 11
Author(s): Dijun Chen, Liang-Yu Fu, Dahui Hu, Christian Klukas, Ming Chen, Kerstin Kaufmann
Software Mentions: 1
Published: over 6 years ago

Ecosyste.ms: Papers

Projects: bioconductor: BiocParallel

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