Works matching DE "BIOCONDUCTOR (Computer software)"

Results: 136

chromDraw: an R package for visualization of linear and circular karyotypes.

Published in:

Chromosome Research, 2016, v. 24, n. 2, p. 217, doi. 10.1007/s10577-015-9513-5

By:

Janečka, Jan;
Lysak, Martin

Publication type:

Article

Expression analysis of the estrogen receptor target genes in renal cell carcinoma.

Published in:

Molecular Medicine Reports, 2015, v. 11, n. 1, p. 75, doi. 10.3892/mmr.2014.2766

By:

ZHIHONG LIU;
YOU LU;
ZONGHAI HE;
LIBO CHEN;
YIPING LU

Publication type:

Article

Explore the mechanism of Danshen on coronary heart disease based on network pharmacology.

Published in:

Journal of Hainan Medical University, 2020, v. 26, n. 5, p. 16

By:

Bing-He Su

Publication type:

Article

Analysing time course microarray data using Bioconductor: a case study using yeast2 Affymetrix arrays.

Published in:

2010

By:

Gillespie, Colin S.;
Guiyuan Lei;
Boys, Richard J.;
Greenall, Amanda;
Wilkinson, Darren J.

Publication type:

Case Study

A collection of bioconductor methods to visualizegene-list annotations.

Published in:

BMC Research Notes, 2010, v. 3, p. 10, doi. 10.1186/1756-0500-3-10

By:

Gang Feng;
Pan Du;
Krett, Nancy L.;
Tessel, Michael;
Rosen, Steven;
Kibbe, Warren A.;
Lin, Simon M.

Publication type:

Article

BeadDataPackR: A Tool to Facilitate the Sharing of Raw Data from Illumina BeadArray Studies.

Published in:

Cancer Informatics, 2010, n. 8, p. 217

By:

Smith, Mike L.;
Lynch, Andy G.

Publication type:

Article

Dual KS: Defining Gene Sets with Tissue Set Enrichment Analysis.

Published in:

Cancer Informatics, 2010, n. 8, p. 1

By:

Yarong Yang;
Kort, Eric J.;
Ebrahimi, Nader;
Zhongfa Zhang;
Teh, Bin T.

Publication type:

Article

A Review of Meta-Analysis Packages in R.

Published in:

Journal of Educational & Behavioral Statistics, 2017, v. 42, n. 2, p. 206, doi. 10.3102/1076998616674315

By:

Polanin, Joshua R.;
Hennessy, Emily A.;
Tanner-Smith, Emily E.

Publication type:

Article

GGtools: analysis of genetics of gene expression in bioconductor.

Published in:

Bioinformatics, 2007, v. 23, n. 4, p. 522, doi. 10.1093/bioinformatics/btl628

By:

Vincent J. Carey;
Martin Morgan;
Seth Falcon;
Ross Lazarus;
Robert Gentleman

Publication type:

Article

TCC-GUI: a Shiny-based application for differential expression analysis of RNA-Seq count data.

Published in:

BMC Research Notes, 2019, v. 12, n. 1, p. N.PAG, doi. 10.1186/s13104-019-4179-2

By:

Su, Wei;
Sun, Jianqiang;
Shimizu, Kentaro;
Kadota, Koji

Publication type:

Article

BEclear: Batch Effect Detection and Adjustment in DNA Methylation Data.

Published in:

PLoS ONE, 2016, v. 11, n. 8, p. 1, doi. 10.1371/journal.pone.0159921

By:

Akulenko, Ruslan;
Merl, Markus;
Helms, Volkhard

Publication type:

Article

Prediction and Quantification of Splice Events from RNA-Seq Data.

Published in:

PLoS ONE, 2016, v. 11, n. 5, p. 1, doi. 10.1371/journal.pone.0156132

By:

Goldstein, Leonard D.;
Cao, Yi;
Pau, Gregoire;
Lawrence, Michael;
Wu, Thomas D.;
Seshagiri, Somasekar;
Gentleman, Robert

Publication type:

Article

SWATH2stats: An R/Bioconductor Package to Process and Convert Quantitative SWATH-MS Proteomics Data for Downstream Analysis Tools.

Published in:

PLoS ONE, 2016, v. 11, n. 4, p. 1, doi. 10.1371/journal.pone.0153160

By:

Blattmann, Peter;
Heusel, Moritz;
Aebersold, Ruedi

Publication type:

Article

IMMAN: an R/Bioconductor package for Interolog protein network reconstruction, mapping and mining analysis.

Published in:

BMC Bioinformatics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12859-019-2659-y

By:

Ashtiani, Minoo;
Nickchi, Payman;
Jahangiri-Tazehkand, Soheil;
Safari, Abdollah;
Mirzaie, Mehdi;
Jafari, Mohieddin

Publication type:

Article

miRBaseConverter: an R/Bioconductor package for converting and retrieving miRNA name, accession, sequence and family information in different versions of miRBase.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 19, p. 179, doi. 10.1186/s12859-018-2531-5

By:

Xu, Taosheng;
Su, Ning;
Liu, Lin;
Zhang, Junpeng;
Wang, Hongqiang;
Zhang, Weijia;
Gui, Jie;
Yu, Kui;
Li, Jiuyong;
Le, Thuc Duy

Publication type:

Article

Trendy: segmented regression analysis of expression dynamics in high-throughput ordered profiling experiments.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12859-018-2405-x

By:

Bacher, Rhonda;
Leng, Ning;
Chu, Li-Fang;
Ni, Zijian;
Thomson, James A.;
Kendziorski, Christina;
Stewart, Ron

Publication type:

Article

Reproducible bioinformatics project: a community for reproducible bioinformatics analysis pipelines.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 10, p. 211, doi. 10.1186/s12859-018-2296-x

By:

Kulkarni, Neha;
Alessandrì, Luca;
Panero, Riccardo;
Arigoni, Maddalena;
Olivero, Martina;
Ferrero, Giulio;
Cordero, Francesca;
Beccuti, Marco;
Calogero, Raffaele A.

Publication type:

Article

Public data and open source tools for multi-assay genomic investigation of disease.

Published in:

Briefings in Bioinformatics, 2016, v. 17, n. 4, p. 603, doi. 10.1093/bib/bbv080

By:

Kannan, Lavanya;
Ramos, Marcel;
Re, Angela;
El-Hachem, Nehme;
Safikhani, Zhaleh;
Gendoo, Deena M. A.;
Davis, Sean;
Gomez-Cabrero, David;
Castelo, Robert;
Hansen, Kasper D.;
Carey, Vincent J.;
Morgan, Martin;
Culhane, Aedín C.;
Haibe-Kains, Benjamin;
Waldron, Levi

Publication type:

Article

Reproducible probe-level analysis of the Affymetrix Exon 1.0 ST array with R/Bioconductor.

Published in:

Briefings in Bioinformatics, 2014, v. 15, n. 4, p. 519, doi. 10.1093/bib/bbt011

By:

Rodrigo-Domingo, Maria;
Waagepetersen, Rasmus;
Bødker, Julie Støve;
Falgreen, Steffen;
Kjeldsen, Malene Krag;
Johnsen, Hans Erik;
Dybkær, Karen;
Bøgsted, Martin

Publication type:

Article

affyPara--a Bioconductor Package for Parallelized Preprocessing Algorithms of Affymetrix Microarray Data.

Published in:

Bioinformatics & Biology Insights, 2009, n. 3, p. 83, doi. 10.4137/BBI.S3060

By:

Schmidberger, Markus;
Vicedo, Esmeralda;
Mansmann, Ulrich

Publication type:

Article

eUTOPIA: solUTion for Omics data PreprocessIng and Analysis.

Published in:

Source Code for Biology & Medicine, 2019, v. 14, n. 1, p. N.PAG, doi. 10.1186/s13029-019-0071-7

By:

Marwah, Veer Singh;
Scala, Giovanni;
Kinaret, Pia Anneli Sofia;
Serra, Angela;
Alenius, Harri;
Fortino, Vittorio;
Greco, Dario

Publication type:

Article

SVAw - a web-based application tool for automated surrogate variable analysis of gene expression studies.

Published in:

Source Code for Biology & Medicine, 2013, v. 8, n. 1, p. 1, doi. 10.1186/1751-0473-8-8

By:

Pirooznia, Mehdi;
Seifuddin, Fayaz;
Goes, Fernando S.;
Leek, Jeffrey T.;
Zandi, Peter P.

Publication type:

Article

GSAR: Bioconductor package for Gene Set analysis in R.

Published in:

BMC Bioinformatics, 2017, v. 18, p. 1, doi. 10.1186/s12859-017-1482-6

By:

Rahmatallah, Yasir;
Zybailov, Boris;
Emmert-Streib, Frank;
Glazko, Galina

Publication type:

Article

runibic: a Bioconductor package for parallel row-based biclustering of gene expression data.

Published in:

Bioinformatics, 2018, v. 34, n. 24, p. 4302, doi. 10.1093/bioinformatics/bty512

By:

Orzechowski, Patryk;
Pańszczyk, Artur;
Huang, Xiuzhen;
Moore, Jason H

Publication type:

Article

GenomicScores: seamless access to genomewide position-specific scores from R and Bioconductor.

Published in:

Bioinformatics, 2018, v. 34, n. 18, p. 3208, doi. 10.1093/bioinformatics/bty311

By:

Puigdevall, Pau;
Castelo, Robert

Publication type:

Article

DEsingle for detecting three types of differential expression in single-cell RNA-seq data.

Published in:

Bioinformatics, 2018, v. 34, n. 18, p. 3223, doi. 10.1093/bioinformatics/bty332

By:

Miao, Zhun;
Deng, Ke;
Wang, Xiaowo;
Zhang, Xuegong

Publication type:

Article

CTDquerier: a bioconductor R package for Comparative Toxicogenomics DatabaseTM data extraction, visualization and enrichment of environmental and toxicological studies.

Published in:

Bioinformatics, 2018, v. 34, n. 18, p. 3235, doi. 10.1093/bioinformatics/bty326

By:

Hernandez-Ferrer, Carles;
Gonzalez, Juan R

Publication type:

Article

diffloop: a computational framework for identifying and analyzing differential DNA loops from sequencing data.

Published in:

Bioinformatics, 2018, v. 34, n. 4, p. 672, doi. 10.1093/bioinformatics/btx623

By:

Lareau, Caleb A;
Aryee, Martin J

Publication type:

Article

Identification and visualization of differential isoform expression in RNA-seq time series.

Published in:

Bioinformatics, 2018, v. 34, n. 3, p. 524, doi. 10.1093/bioinformatics/btx578

By:

Nueda, María José;
Martorell-Marugan, Jordi;
Martí, Cristina;
Tarazona, Sonia;
Conesa, Ana

Publication type:

Article

clustComp, a bioconductor package for the comparison of clustering results.

Published in:

Bioinformatics, 2017, v. 33, n. 24, p. 4001, doi. 10.1093/bioinformatics/btx532

By:

Torrente, Aurora;
Brazma, Alvis

Publication type:

Article

ClusterSignificance: a bioconductor package facilitating statistical analysis of class cluster separations in dimensionality reduced data.

Published in:

Bioinformatics, 2017, v. 33, n. 19, p. 3126, doi. 10.1093/bioinformatics/btx393

By:

Serviss, Jason T.;
Gådin, Jesper R.;
Eriksson, Per;
Folkersen, Lasse;
Grandér, Dan

Publication type:

Article

RankProd 2.0: a refactored bioconductor package for detecting differentially expressed features in molecular profiling datasets.

Published in:

Bioinformatics, 2017, v. 33, n. 17, p. 2774, doi. 10.1093/bioinformatics/btx292

By:

Del Carratore, Francesco;
Breitling, Rainer;
Jankevics, Andris;
Eisinga, Rob;
Heskes, Tom;
Fangxin Hong

Publication type:

Article

twoddpcr: an R/Bioconductor package and Shiny app for Droplet Digital PCR analysis.

Published in:

Bioinformatics, 2017, v. 33, n. 17, p. 2743, doi. 10.1093/bioinformatics/btx308

By:

Chiu, Anthony;
Ayub, Mahmood;
Dive, Caroline;
Brady, Ged;
Miller, Crispin J.

Publication type:

Article

SeqArray--a storage-efficient high-performance data format for WGS variant calls.

Published in:

Bioinformatics, 2017, v. 33, n. 15, p. 2251, doi. 10.1093/bioinformatics/btx145

By:

Xiuwen Zheng;
Gogarten, Stephanie M.;
Lawrence, Michael;
Stilp, Adrienne;
Conomos, Matthew P.;
Weir, Bruce S.;
Laurie, Cathy;
Levine, David

Publication type:

Article

DeepBlueR: large-scale epigenomic analysis in R.

Published in:

Bioinformatics, 2017, v. 33, n. 13, p. 2063, doi. 10.1093/bioinformatics/btx099

By:

Albrecht, Felipe;
List, Markus;
Bock, Christoph;
Lengauer, Thomas

Publication type:

Article

annoPeak: a web application to annotate and visualize peaks from ChIP-seq/ChIP-exo-seq.

Published in:

Bioinformatics, 2017, v. 33, n. 10, p. 1570, doi. 10.1093/bioinformatics/btx016

By:

Xing Tang;
Srivastava, Arunima;
Huayang Liu;
Machiraju, Raghu;
Kun Huang;
Leone, Gustavo

Publication type:

Article

Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R.

Published in:

Bioinformatics, 2017, v. 33, n. 8, p. 1179, doi. 10.1093/bioinformatics/btw777

By:

McCarthy, Davis J.;
Campbell, Kieran R.;
Lun, Aaron T. L.;
Wills, Quin F.

Publication type:

Article

miRNAmeConverter: an R/bioconductor package for translating mature miRNA names to different miRBase versions.

Published in:

Bioinformatics, 2017, v. 33, n. 4, p. 592, doi. 10.1093/bioinformatics/btw660

By:

Haunsberger, Stefan J.;
Connolly, Niamh M. C.;
Prehn, Jochen H. M.

Publication type:

Article

Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi.

Published in:

Bioinformatics, 2017, v. 33, n. 4, p. 558, doi. 10.1093/bioinformatics/btw691

By:

Fortin, Jean-Philippe;
Triche Jr, Timothy J.;
Hansen, Kasper D.

Publication type:

Article

QUBIC: a bioconductor package for qualitative biclustering analysis of gene co-expression data.

Published in:

Bioinformatics, 2017, v. 33, n. 3, p. 450, doi. 10.1093/bioinformatics/btw635

By:

Yu Zhang;
Juan Xie;
Jinyu Yang;
Fennell, Anne;
Chi Zhang;
Qin Ma

Publication type:

Article

GenVisR: Genomic Visualizations in R.

Published in:

Bioinformatics, 2016, v. 32, n. 19, p. 3012, doi. 10.1093/bioinformatics/btw325

By:

Skidmore, Zachary L.;
Wagner, Alex H.;
Lesurf, Robert;
Campbell, Katie M.;
Kunisaki, Jason;
Griffith, Obi L.;
Griffith, Malachi

Publication type:

Article

compendiumdb: an R package for retrieval and storage of functional genomics data.

Published in:

2016

By:

Nandal, Umesh K.;
Moerland, Perry D.;
van Kampen, Antoine H. C.

Publication type:

Question & Answer

PAA: an R/bioconductor package for biomarker discovery with protein microarrays.

Published in:

Bioinformatics, 2016, v. 32, n. 10, p. 1577, doi. 10.1093/bioinformatics/btw037

By:

Turewicz, Michael;
Ahrens, Maike;
May, Caroline;
Marcus, Katrin;
Eisenacher, Martin

Publication type:

Article

DNAshapeR: an R/Bioconductor package for DNA shape prediction and feature encoding.

Published in:

Bioinformatics, 2016, v. 32, n. 8, p. 1211, doi. 10.1093/bioinformatics/btv735

By:

Tsu-Pei Chiu;
Comoglio, Federico;
Tianyin Zhou;
Lin Yang;
Paro, Renato;
Rohs, Remo

Publication type:

Article

traseR: an R package for performing trait-associated SNP enrichment analysis in genomic intervals.

Published in:

Bioinformatics, 2016, v. 32, n. 8, p. 1214, doi. 10.1093/bioinformatics/btv741

By:

Li Chen;
Qin, Zhaohui S.

Publication type:

Article

PaxtoolsR: pathway analysis in R using Pathway Commons.

Published in:

Bioinformatics, 2016, v. 32, n. 8, p. 1262, doi. 10.1093/bioinformatics/btv733

By:

Luna, Augustin;
Babur, Özgün;
Aksoy, Bülent Arman;
Demir, Emek;
Sander, Chris

Publication type:

Article

Genefu: an R/Bioconductor package for computation of gene expression-based signatures in breast cancer.

Published in:

Bioinformatics, 2016, v. 32, n. 7, p. 1097, doi. 10.1093/bioinformatics/btv693

By:

Gendoo, Deena M. A.;
Ratanasirigulchai, Natchar;
Schröder, Markus S.;
Paré, Laia;
Parker, Joel S.;
Prat, Aleix;
Haibe-Kains, Benjamin

Publication type:

Article

iPQF: a new peptide-to-protein summarization method using peptide spectra characteristics to improve protein quantification.

Published in:

Bioinformatics, 2016, v. 32, n. 7, p. 1040, doi. 10.1093/bioinformatics/btv675

By:

Fischer, Martina;
Renard, Bernhard Y.

Publication type:

Article

TiMEx: a waiting time model for mutually exclusive cancer alterations.

Published in:

Bioinformatics, 2016, v. 32, n. 7, p. 968, doi. 10.1093/bioinformatics/btv400

By:

Constantinescu, Simona;
Szczurek, Ewa;
Mohammadi, Pejman;
Rahnenführer, Jörg;
Beerenwinkel, Niko

Publication type:

Article

regioneR: an R/Bioconductor package for the association analysis of genomic regions based on permutation tests.

Published in:

Bioinformatics, 2016, v. 32, n. 2, p. 289, doi. 10.1093/bioinformatics/btv562

By:

Gel, Bernat;
Díez-Villanueva, Anna;
Serra, Eduard;
Buschbeck, Marcus;
Peinado, Miguel A.;
Malinverni, Roberto

Publication type:

Article