Tag analysis-tool [27 articles] Export

Recent papers classified by the tag analysis-tool.

	Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources [My Copy] Nature Protocols In Nat. Protocols, Vol. 4, No. 1. (18 December 2008), pp. 44-57. by Da W. Huang, Brad T. Sherman, Richard A. Lempicki posted to web-tool microarray david bioinformatics analysis-tool by rschulz on 2009-10-09 13:57:10 as along with 16 people and 2 groups darian jperkins tonamswish operon VGreiff jfr Stew bertelsen Sonix dswan guhjy wimufi brianb idonaldson mrochman daforerog Bioinformatics - CRUK Bioinformatics
	ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data [My Copy] Bioinformatics, Vol. 25, No. 19. (1 October 2009), pp. 2607-2608. by Martin Morgan, Simon Anders, Michael Lawrence, Patrick Aboyoun, Herve Pages, Robert Gentleman posted to shortread r next-gen-seq bioinformatics bioconductor analysis-tool by rschulz on 2009-10-05 08:36:54 as along with 14 people and 1 group manduca darian jforment fstrozzi djkt jmeppley dswan torfinnnome walshtp jamesmorris joaocarrico natstreet n00c druvus Bioinformatics Core Service
	Inferring Pathway Activity toward Precise Disease Classification [My Copy] PLoS Comput Biol, Vol. 4, No. 11. (7 November 2008), e1000217. by Eunjung Lee, Han-Yu Chuang, Jong-Won Kim, Trey Ideker, Doheon Lee posted to review pathway ontology analysis-tool by rschulz on 2009-08-19 13:22:58 as along with 13 people frohike isimpson yaredo ipark-kaist jfr aviad_work ajbattle zufar carlk renatomilani dragonrez tmmurali ptrobajo
	Bioinformatics applications for pathway analysis of microarray data [My Copy] Current Opinion in Biotechnology, Vol. 19, No. 1. (18 February 2008), pp. 50-54. by T. Werner posted to review pathway ontology microarray analysis-tool by rschulz on 2009-08-19 12:08:46 as along with 4 people saman_vp guhjy jfr AlexanderPico
	R/BHC: fast Bayesian hierarchical clustering for microarray data [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (6 August 2009), 242. by Richard Savage, Katherine Heller, Yang Xu, et al.Zoubin Ghahramani, William Truman, Murray Grant, Katherine Denby, David Wild posted to analysis-tool bayes clustering microarray r_bhc by rschulz on 2009-08-10 10:38:39 as along with 10 people and 1 group ptrobajo meanerelk nuin rdiaz guhjy lwaldron phoenixzxl barriot RamuAnandakrishnan erexhepa Bioinformatics
	BSMAP: whole genome bisulfite sequence MAPping program [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (2009), 232. by Yuanxin Xi, Wei Li posted to analysis-tool bs-seq bsmap sequence-alignment whole-genome by rschulz on 2009-07-28 08:26:13 as along with 2 people gdb iris42
	Swift: primary data analysis for the Illumina Solexa sequencing platform [My Copy] Bioinformatics, Vol. 25, No. 17. (1 September 2009), pp. 2194-2199. by Nava Whiteford, Tom Skelly, Christina Curtis, et al.Matt E. Ritchie, Andrea Lohr, Alexander W. Zaranek, Irina Abnizova, Clive Brown posted to swift solexa sanger next-gen-seq nanopore illumina analysis-tool by rschulz on 2009-07-15 12:13:18 as along with 23 people and 4 groups darian humburg n00c heliopais hzoltan dakelley sotacam lh49 djkt rtogawa cassj dswan torfinnnome natstreet druvus jasontsai jmeppley ghattem nuin polivares aprasad niallhaslam idoerg Bioinformatics BergmanLab SIMR bioinformatics Journal picks
	Comparative study on ChIP-seq data: normalization and binding pattern characterization [My Copy] Bioinformatics, Vol. 25, No. 18. (15 September 2009), pp. 2334-2340. by Cenny Taslim, Jiejun Wu, Pearlly Yan, et al.Greg Singer, Jeffrey Parvin, Tim Huang, Shili Lin, Kun Huang posted to analysis-tool chip-seq comparative normalization by rschulz on 2009-07-15 12:08:21 as along with 8 people and 2 groups Stew tonamswish stubrown inesdesantiago ewilban1 guhjy mkiyer humburg Bioinformatics - CRUK Chinnaiyan Lab
	Extracting transcription factor targets from ChIP-Seq data [My Copy] Nucl. Acids Res., Vol. 37, No. 17. (1 September 2009), e113. by Geetu Tuteja, Peter White, Jonathan Schug, Klaus H. Kaestner posted to analysis-tool chip-seq glitr by rschulz on 2009-07-15 12:06:57 as along with 14 people and 4 groups hzoltan Vincent_Rouilly mfgreen ewilban1 idonaldson guhjy mkiyer fenghezi clearbluespring thegoose robeirne inesdesantiago malcook polivares Chinnaiyan Lab SIMR bioinformatics BergmanLab Journal picks
	WebArrayDB: cross-platform microarray data analysis and public data repository [My Copy] Bioinformatics, Vol. 25, No. 18. (15 September 2009), pp. 2425-2429. by Xiao-Qin Xia, Michael McClelland, Steffen Porwollik, Wenzhi Song, Xianling Cong, Yipeng Wang posted to analysis-tool microarray webarraydb by rschulz on 2009-07-15 09:58:40 as along with 8 people ptrobajo lwaldron daforerog dswan natstreet guhjy brianb neils
	A pipeline for the quantitative analysis of CG dinucleotide methylation using mass spectrometry. [My Copy] Bioinformatics (Oxford, England) (26 June 2009) by Reid F. Thompson, Masako Suzuki, Kevin W. Lau, John M. Greally posted to analysis-tool bioinformatics dna-methylation maldi-tof r sequenom by rschulz on 2009-07-15 09:17:47 as along with 1 person nuin
	NTAP: for NimbleGen tiling array ChIP-chip data analysis [My Copy] Bioinformatics, Vol. 25, No. 14. (15 July 2009), pp. 1838-1840. by Kun He, Xueyong Li, Junli Zhou, Xing-Wang Deng, Hongyu Zhao, Jingchu Luo posted to analysis-tool bioinformatics chip-chip nimblegen ntap by rschulz on 2009-05-26 10:32:48 as along with 3 people and 1 group ashishanand dswan idonaldson Bioinformatics
	Design and analysis of ChIP-seq experiments for DNA-binding proteins. [My Copy] Nature biotechnology, Vol. 26, No. 12. (16 December 2008), pp. 1351-1359. by Peter V. Kharchenko, Michael Y. Tolstorukov, Peter J. Park posted to analysis-tool background benchmark bioinformatics chip-seq csp ctcf deep-seq experiment-planning msp mtc pipeline read-coverage wtd xset by rschulz to the group KCL & UCL Bioinformatics on 2009-05-15 11:34:45 as along with 19 people and 1 group hzoltan stubrown guhjy gdb tonamswish ewilban1 coela ekotelnikova jfr floatingpoint idonaldson inesdesantiago WanderingAengus vplagnol xwbcn fpattyn mutagenic kengg ghattem SIMR bioinformatics
	PASS: a program to align short sequences [My Copy] Bioinformatics, Vol. 25, No. 7. (1 April 2009), pp. 967-968. by Davide Campagna, Alessandro Albiero, Alessandra Bilardi, et al.Elisa Caniato, Claudio Forcato, Svetlin Manavski, Nicola Vitulo, Giorgio Valle posted to alignment analysis-tool bioinformatics pass solexa by rschulz on 2009-03-26 09:35:15 as along with 20 people and 1 group Julien_Fayolle cthachuk hzoltan seb1 bozdagd adijr heliopais darian maren n00c nuin skembel cassj Neeperando helminth_lab guhjy natstreet druvus renatomilani WanderingAengus iSEEM
	MOM: maximum oligonucleotide mapping [My Copy] Bioinformatics, Vol. 25, No. 7. (1 April 2009), pp. 969-970. by Hugh L. Eaves, Yuan Gao posted to alignment analysis-tool bioinformatics mom next-gen-seq solexa by rschulz on 2009-03-26 09:31:50 as along with 9 people Julien_Fayolle heliopais seb1 jfr n00c cassj mmartin guhjy druvus
	BioconductorBuntu - A Linux Distribution that Implements a Web-Based DNA Microarray Analysis Server. [My Copy] Bioinformatics (Oxford, England) (23 March 2009) by Paul Geeleher, Dermot Morris, John P P. Hinde, Aaron Golden posted to analysis-tool bioconductorbuntu bioinformatics microarray by rschulz on 2009-03-25 13:17:56 as along with 3 people druvus nuin sjcockell
	Power enhancement via multivariate outlier testing with gene expression arrays. [My Copy] Bioinformatics (Oxford, England) (16 November 2008) by Adam Asare, Zhong Gao, Vincent J J. Carey, Richard Wang, Vicki Seyfert-Margolis posted to analysis-tool bioconductor bioinformatics microarray quality-control by rschulz on 2009-01-12 10:50:57 as along with 3 people jfr lptolik guhjy
	Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment [My Copy] Bioinformatics (4 December 2008), btn630. by Benedict Paten, Javier Herrero, Kathryn Beal, Ewan Birney posted to analysis-tool bayes bioinformatics multiple-alignment pecan by rschulz on 2009-01-12 10:26:24 as along with 9 people BioNica guhjy dakelley semrich gjuggler djkt birney operon druvus
	arrayQualityMetrics--a bioconductor package for quality assessment of microarray data [My Copy] Bioinformatics, Vol. 25, No. 3. (1 February 2009), pp. 415-416. by Audrey Kauffmann, Robert Gentleman, Wolfgang Huber posted to analysis-tool arrayqualitymetrics bioconductor bioinformatics microarray quality-control by rschulz on 2009-01-12 10:11:46 as along with 16 people and 1 group jperkins VGreiff Zephyrus daforerog shikin lwaldron jfr ptrobajo rdiaz siebert bertelsen pkonings dswan renatomilani nuin guhjy Bioinformatics
	Multiperm: shuffling multiple sequence alignments while approximately preserving dinucleotide frequencies [My Copy] Bioinformatics (9 January 2009), btp006. by Parvez Anandam, Elfar Torarinsson, Walter L. Ruzzo posted to analysis-tool bioinformatics dinucleotide multiple-alignment permutation by rschulz on 2009-01-12 10:01:51 as along with 2 people idonaldson djkt
	Galaxy: A platform for interactive large-scale genome analysis [My Copy] Genome Research, Vol. 15, No. 10. (October 2005), pp. 1451-1455. by Belinda Giardine, Cathy Riemer, Ross C. Hardison, et al.Richard Burhans, Laura Elnitski, Prachi Shah, Yi Zhang, Daniel Blankenberg, Istvan Albert, James Taylor, Webb Miller, W. James Kent, Anton Nekrutenko posted to analysis-tool bioinformatics galaxy by rschulz on 2008-12-12 16:56:01 as along with 10 people farhat idoerg vijyendra antonkratz Thaverkamp ilyashl urgi daforerog guhjy aprasad
	Mapping short DNA sequencing reads and calling variants using mapping quality scores. [My Copy] Genome research, Vol. 18, No. 11. (19 November 2008), pp. 1851-1858. by Heng Li, Jue Ruan, Richard Durbin posted to alignment analysis-tool bayes bioinformatics deep-seq genotype maq read-quality stats-model by rschulz on 2008-12-06 11:06:30 as along with 39 people and 2 groups urgi seninp heliopais hzoltan cthachuk darshan adijr darian bozdagd jmanning2k stubrown APRegier ghattem jbhiatt mmartin michaelbarton polivares jonilaserson humburg n00c jessopher maren GeeSharpMinor vmsr vplagnol natstreet poschm jfr druvus dandaman xingxu jmcq inesdesantiago Neeperando nmohelli matthewsuderman bpb gdb farhat SIMR bioinformatics BergmanLab
	An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data [My Copy] Bioinformatics, Vol. 24, No. 20. (15 October 2008), pp. 2344-2349. by Han Xu, Chia-Lin Wei, Feng Lin, Wing-Kin Sung posted to analysis-tool bioinformatics chip-seq chipdiff deep-seq histone hmm stats-model by rschulz on 2008-12-06 10:55:11 as along with 8 people darian mkiyer tonamswish ewilban1 polivares caseybrown djkt epigenetics
	Model-based Analysis of ChIP-Seq (MACS) [My Copy] Genome Biology, Vol. 9, No. 9. (2008), R137. by Yong Zhang, Tao Liu, Clifford Meyer, et al.Jerome Eeckhoute, David Johnson, Bradley Bernstein, Chad Nussbaum, Richard Myers, Myles Brown, Wei Li, X. Shirley Liu posted to analysis-tool bioinformatics chip-seq deep-seq macs poisson stats-model by rschulz on 2008-12-06 10:51:20 as along with 24 people and 2 groups hzoltan Vincent_Rouilly darian stubrown mkiyer humburg cassj floatingpoint WanderingAengus bryankr jfr mcm polivares gdb ghattem yadadi djkt stajich mdperry fpattyn bcondon idonaldson caseybrown kengg SIMR bioinformatics Mycology
	F-Seq: a feature density estimator for high-throughput sequence tags [My Copy] Bioinformatics, Vol. 24, No. 21. (1 November 2008), pp. 2537-2538. by Alan P. Boyle, Justin Guinney, Gregory E. Crawford, Terrence S. Furey posted to analysis-tool bioinformatics chip-seq deep-seq f-seq java ucsc-browser by rschulz on 2008-12-06 10:48:41 as along with 18 people and 2 groups hzoltan n00c darian idonaldson michaelbarton inesdesantiago gdb ewilban1 tonamswish guhjy kmdaily cassj fhalbrit jfr polivares cthachuk zhouyu aprasad JLab BergmanLab
	An integrated software system for analyzing ChIP-chip and ChIP-seq data. [My Copy] Nature biotechnology, Vol. 26, No. 11. (02 November 2008), pp. 1293-1300. by Hongkai Ji, Hui Jiang, Wenxiu Ma, David S. Johnson, Richard M. Myers, Wing H. Wong posted to analysis-tool bioinformatics chip-chip chip-seq cisgenome deep-seq by rschulz on 2008-12-06 10:44:45 as along with 25 people and 3 groups bsamal hzoltan fpattyn stubrown isimpson huali tonamswish ewilban1 sebastien_vigneau jfr kmdaily cassj bryankr malcook mcm behindtherabbit psique renatomilani polivares guhjy inesdesantiago pengchy kengg bais idonaldson Neuroblastoma SIMR bioinformatics BenosLab
	FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology [My Copy] Bioinformatics In Bioinformatics, Vol. 24, No. 15. (1 August 2008), pp. 1729-1730. by Anthony P. Fejes, Gordon Robertson, Mikhail Bilenky, Richard Varhol, Matthew Bainbridge, Steven J. M. Jones posted to analysis-tool bioinformatics chip-seq deep-seq java ucsc-browser wiggle-track by rschulz on 2008-12-06 10:40:14 as along with 20 people and 2 groups torfinnnome hzoltan darian n00c polivares idonaldson tonamswish ewilban1 humburg Thaverkamp natstreet druvus stajich cassj WanderingAengus jfr sconlan reyez guhjy vega Bioinformatics Mycology

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bioinformatics	26
chip-seq	14
deep-seq	14
microarray	7
stats-model	6
alignment	4
bayes	4
background	3
benchmark	3
bioconductor	3
chip-chip	3
csp	3
ctcf	3
experiment-planning	3
java	3
msp	3
mtc	3
next-gen-seq	3
pipeline	3
read-coverage	3
solexa	3
ucsc-browser	3
wtd	3
xset	3
chipdiff	2
cisgenome	2
f-seq	2
genotype	2
histone	2
hmm	2
macs	2
maq	2
multiple-alignment	2
ontology	2
pathway	2
poisson	2
quality-control	2
r	2
read-quality	2
review	2
arrayqualitymetrics	1
bioconductorbuntu	1
bs-seq	1
bsmap	1
clustering	1
comparative	1
david	1
dinucleotide	1
dna-methylation	1
galaxy	1
glitr	1
illumina	1
maldi-tof	1
mom	1
nanopore	1
nimblegen	1
normalization	1
ntap	1
pass	1
pecan	1
permutation	1
r_bhc	1
sanger	1
sequence-alignment	1
sequenom	1
shortread	1
swift	1
web-tool	1
webarraydb	1
whole-genome	1
wiggle-track	1

Tag analysis-tool [27 articles] Export

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