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: BiocParallel
https://packages.ecosyste.ms/registries/bioconductor.org/packages/BiocParallel
Bioconductor facilities for parallel evaluation
2 versions
Latest release: about 1 year ago
354 dependent packages
4,902,168 downloads total
Papers Mentioning BiocParallel 30
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: almost 5 years ago
10.3390/ijms22063251
Untargeted In Silico Compound Classification—A Novel Metabolomics Method to Assess the Chemodiversity in BryophytesCited 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 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
10.1016/j.patter.2021.100322
The role of metadata in reproducible computational researchCited by: 38
Author(s): Jeremy Leipzig, Daniel Nüst, Charles Tapley Hoyt, Karthik Ram, Jane Greenberg
Software Mentions: 21
Published: about 3 years ago
10.1186/s12859-016-1241-0
systemPipeR: NGS workflow and report generation environmentCited by: 148
Author(s): Tyler W. H. Backman, Thomas Girke
Software Mentions: 19
Published: about 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 methylationCited 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 visualizationCited 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 diseaseCited 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 TransfaunationCited 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 cellsCited 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 DataCited by: 4
Author(s): Péter Gargya, Bálint László Bálint
Software Mentions: 14
Published: about 3 years ago
10.1038/s41598-020-69239-w
Neural innervation as a potential trigger of morphological color change and sexual dimorphism in cichlid fishCited 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 differentiationCited 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 mRNAsCited by: 40
Author(s): Feng He, Alper Çelik, Chan Wu, Allan Jacobson
Software Mentions: 12
Published: almost 6 years ago
10.1155/2016/7972351
Advancements in RNASeqGUI towards a Reproducible Analysis of RNA-Seq ExperimentsCited 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 dataCited 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 TestsCited 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 sarcomaCited 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 injuryCited 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 dataCited 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 ProfilingCited 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: over 5 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 TaxaCited by: 3
Author(s): Mariantonietta Colagiero, Laura Cristina Rosso, Domenico Catalano, Leonardo Schena, Aurelio Ciancio
Software Mentions: 6
Published: over 4 years ago
10.1186/1471-2105-14-75
virtualArray: a R/bioconductor package to merge raw data from different microarray platformsCited by: 51
Author(s): Andreas Heider, Rüdiger Alt
Software Mentions: 5
Published: over 11 years ago
10.1093/bioinformatics/btz284
clustermq enables efficient parallelization of genomic analysesCited 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 analysisCited 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 DNACited by: 5
Author(s): Jacques Serizay, Julie Ahringer
Software Mentions: 4
Published: over 3 years ago
10.1186/s12864-019-6313-x
Secretory RING finger proteins function as effectors in a grapevine galling insectCited by: 13
Author(s): Chaoyang Zhao, Claude Rispe, Paul D. Nabity
Software Mentions: 3
Published: almost 5 years ago
10.1038/s41598-018-25428-2
Tissue storage affects lipidome profiling in comparison to in vivo microsampling approachCited 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 dataCited 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