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

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

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

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

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

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

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

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

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

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

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

msa: an R package for multiple sequence alignment.

Published in:

Bioinformatics, 2015, v. 31, n. 24, p. 3997, doi. 10.1093/bioinformatics/btv494

By:

Bodenhofer, Ulrich;
Bonatesta, Enrico;
Horejš-Kainrath, Christoph;
Hochreiter, Sepp

Publication type:

Article

SomaticSignatures: inferring mutational signatures from single-nucleotide variants.

Published in:

Bioinformatics, 2015, v. 31, n. 22, p. 3673, doi. 10.1093/bioinformatics/btv408

By:

Gehring, Julian S.;
Fischer, Bernd;
Lawrence, Michael;
Huber, Wolfgang

Publication type:

Article

Sincell: an R/Bioconductor package for statistical assessment of cell-state hierarchies from single-cell RNA-seq.

Published in:

Bioinformatics, 2015, v. 31, n. 20, p. 3380, doi. 10.1093/bioinformatics/btv368

By:

Juliá, Miguel;
Telenti, Amalio;
Rausell, Antonio

Publication type:

Article

biRte: Bayesian inference of context-specific regulator activities and transcriptional networks.

Published in:

Bioinformatics, 2015, v. 31, n. 20, p. 3290, doi. 10.1093/bioinformatics/btv379

By:

Fröhlich, Holger

Publication type:

Article

COREGNET: reconstruction and integrated analysis of co-regulatory networks.

Published in:

Bioinformatics, 2015, v. 31, n. 18, p. 3066, doi. 10.1093/bioinformatics/btv305

By:

Nicolle, Rémy;
Radvanyi, François;
Elati, Mohamed

Publication type:

Article

Seq2pathway: an R/Bioconductor package for pathway analysis of next-generation sequencing data.

Published in:

Bioinformatics, 2015, v. 31, n. 18, p. 3043, doi. 10.1093/bioinformatics/btv289

By:

Bin Wang;
Cunningham, John M.;
Xinan (Holly) Yang

Publication type:

Article

Rcpi: R/Bioconductor package to generate various descriptors of proteins, compounds and their interactions.

Published in:

2015

By:

Cao, Dong-Sheng;
Xiao, Nan;
Xu, Qing-Song;
Chen, Alex F.

Publication type:

Product Review

Chimera: a Bioconductor package for secondary analysis of fusion products.

Published in:

Bioinformatics, 2014, v. 30, n. 24, p. 3556, doi. 10.1093/bioinformatics/btu662

By:

Beccuti, Marco;
Carrara, Matteo;
Cordero, Francesca;
Lazzarato, Fulvio;
Donatelli, Susanna;
Nadalin, Francesca;
Policriti, Alberto;
Calogero, Raffaele A.

Publication type:

Article

Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data.

Published in:

Bioinformatics, 2014, v. 30, n. 22, p. 3268, doi. 10.1093/bioinformatics/btu497

By:

Walter, Carolin;
Schuetzmann, Daniel;
Rosenbauer, Frank;
Dugas, Martin

Publication type:

Article

sapFinder: an R/Bioconductor package for detection of variant peptides in shotgun proteomics experiments.

Published in:

Bioinformatics, 2014, v. 30, n. 21, p. 3136, doi. 10.1093/bioinformatics/btu397

By:

Wen, Bo;
Xu, Shaohang;
Sheynkman, Gloria M.;
Feng, Qiang;
Lin, Liang;
Wang, Quanhui;
Xu, Xun;
Wang, Jun;
Liu, Siqi

Publication type:

Article

NetPathMiner: R/Bioconductor package for network path mining through gene expression.

Published in:

Bioinformatics, 2014, v. 30, n. 21, p. 3139, doi. 10.1093/bioinformatics/btu501

By:

Mohamed, Ahmed;
Hancock, Timothy;
Nguyen, Canh Hao;
Mamitsuka, Hiroshi

Publication type:

Article

Next maSigPro: updating maSigPro bioconductor package for RNA-seq time series.

Published in:

Bioinformatics, 2014, v. 30, n. 18, p. 2598, doi. 10.1093/bioinformatics/btu333

By:

Nueda, María José;
Tarazona, Sonia;
Conesa, Ana

Publication type:

Article

rTANDEM, an R/Bioconductor package for MS/MS protein identification.

Published in:

Bioinformatics, 2014, v. 30, n. 15, p. 2233, doi. 10.1093/bioinformatics/btu178

By:

Fournier, Frédéric;
Joly Beauparlant, Charles;
Paradis, René;
Droit, Arnaud

Publication type:

Article

Rgb: a scriptable genome browser for R.

Published in:

Bioinformatics, 2014, v. 30, n. 15, p. 2204, doi. 10.1093/bioinformatics/btu185

By:

Mareschal, Sylvain;
Dubois, Sydney;
Lecroq, Thierry;
Jardin, Fabrice

Publication type:

Article

CorMut: an R/Bioconductor package for computing correlated mutations based on selection pressure.

Published in:

Bioinformatics, 2014, v. 30, n. 14, p. 2073

By:

Li, Zhenpeng;
Huang, Yang;
Ouyang, Yabo;
Jiao, Yang;
Xing, Hui;
Liao, Lingjie;
Jiang, Shibo;
Shao, Yiming;
Ma, Liying

Publication type:

Article

flowFit: a Bioconductor package to estimate proliferation in cell-tracking dye studies.

Published in:

Bioinformatics, 2014, v. 30, n. 14, p. 2060, doi. 10.1093/bioinformatics/btu127

By:

Rambaldi, Davide;
Pece, Salvatore;
Di Fiore, Pier Paolo

Publication type:

Article

VariantAnnotation: a Bioconductor package for exploration and annotation of genetic variants.

Published in:

Bioinformatics, 2014, v. 30, n. 14, p. 2076, doi. 10.1093/bioinformatics/btu168

By:

Obenchain, Valerie;
Lawrence, Michael;
Carey, Vincent;
Gogarten, Stephanie;
Shannon, Paul;
Morgan, Martin

Publication type:

Article

Genome-wide quantitative analysis of DNA methylation from bisulfite sequencing data.

Published in:

Bioinformatics, 2014, v. 30, n. 13, p. 1933, doi. 10.1093/bioinformatics/btu142

By:

Akman, Kemal;
Haaf, Thomas;
Gravina, Silvia;
Vijg, Jan;
Tresch, Achim

Publication type:

Article

ADaCGH2: parallelized analysis of (big) CNA data.

Published in:

Bioinformatics, 2014, v. 30, n. 12, p. 1759, doi. 10.1093/bioinformatics/btu099

By:

Diaz-Uriarte, Ramon

Publication type:

Article

SeqGSEA: a Bioconductor package for gene set enrichment analysis of RNA-Seq data integrating differential expression and splicing.

Published in:

Bioinformatics, 2014, v. 30, n. 12, p. 1777, doi. 10.1093/bioinformatics/btu090

By:

Wang, Xi;
Cairns, Murray J.

Publication type:

Article

Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays.

Published in:

Bioinformatics, 2014, v. 30, n. 10, p. 1363, doi. 10.1093/bioinformatics/btu049

By:

Aryee, Martin J.;
Jaffe, Andrew E.;
Corrada-Bravo, Hector;
Ladd-Acosta, Christine;
Feinberg, Andrew P.;
Hansen, Kasper D.;
Irizarry, Rafael A.

Publication type:

Article

ChAMP: 450k Chip Analysis Methylation Pipeline.

Published in:

Bioinformatics, 2014, v. 30, n. 3, p. 428, doi. 10.1093/bioinformatics/btt684

By:

Morris, Tiffany J.;
Butcher, Lee M.;
Feber, Andrew;
Teschendorff, Andrew E.;
Chakravarthy, Ankur R.;
Wojdacz, Tomasz K.;
Beck, Stephan

Publication type:

Article

gCMAP: user-friendly connectivity mapping with R.

Published in:

Bioinformatics, 2014, v. 30, n. 1, p. 127, doi. 10.1093/bioinformatics/btt592

By:

Sandmann, Thomas;
Kummerfeld, Sarah K.;
Gentleman, Robert;
Bourgon, Richard

Publication type:

Article

ReportingTools: an automated result processing and presentation toolkit for high-throughput genomic analyses.

Published in:

Bioinformatics, 2013, v. 29, n. 24, p. 3220, doi. 10.1093/bioinformatics/btt551

By:

Huntley, Melanie A.;
Larson, Jessica L.;
Chaivorapol, Christina;
Becker, Gabriel;
Lawrence, Michael;
Hackney, Jason A.;
Kaminker, Joshua S.

Publication type:

Article

PING 2.0: an R/Bioconductor package for nucleosome positioning using next-generation sequencing data.

Published in:

Bioinformatics, 2013, v. 29, n. 16, p. 2049, doi. 10.1093/bioinformatics/btt348

By:

Woo, Sangsoon;
Zhang, Xuekui;
Sauteraud, Renan;
Robert, François;
Gottardo, Raphael

Publication type:

Article

Pathview: an R/Bioconductor package for pathway-based data integration and visualization.

Published in:

Bioinformatics, 2013, v. 29, n. 14, p. 1830, doi. 10.1093/bioinformatics/btt285

By:

Luo, Weijun;
Brouwer, Cory

Publication type:

Article