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Results: 1 to 20 of 103

1.

h5vc: scalable nucleotide tallies with HDF5.

Pyl PT, Gehring J, Fischer B, Huber W.

Bioinformatics. 2014 May 15;30(10):1464-6. doi: 10.1093/bioinformatics/btu026. Epub 2014 Jan 21.

PMID:
24451629
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

HTSanalyzeR: an R/Bioconductor package for integrated network analysis of high-throughput screens.

Wang X, Terfve C, Rose JC, Markowetz F.

Bioinformatics. 2011 Mar 15;27(6):879-80. doi: 10.1093/bioinformatics/btr028. Epub 2011 Jan 22.

PMID:
21258062
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

WEP: a high-performance analysis pipeline for whole-exome data.

D'Antonio M, D'Onorio De Meo P, Paoletti D, Elmi B, Pallocca M, Sanna N, Picardi E, Pesole G, Castrignanò T.

BMC Bioinformatics. 2013;14 Suppl 7:S11. doi: 10.1186/1471-2105-14-S7-S11. Epub 2013 Apr 22.

PMID:
23815231
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

SeqWare Query Engine: storing and searching sequence data in the cloud.

O'Connor BD, Merriman B, Nelson SF.

BMC Bioinformatics. 2010 Dec 21;11 Suppl 12:S2. doi: 10.1186/1471-2105-11-S12-S2.

PMID:
21210981
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Rainbow: a tool for large-scale whole-genome sequencing data analysis using cloud computing.

Zhao S, Prenger K, Smith L, Messina T, Fan H, Jaeger E, Stephens S.

BMC Genomics. 2013 Jun 27;14:425. doi: 10.1186/1471-2164-14-425.

PMID:
23802613
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

CrossMap: a versatile tool for coordinate conversion between genome assemblies.

Zhao H, Sun Z, Wang J, Huang H, Kocher JP, Wang L.

Bioinformatics. 2014 Apr 1;30(7):1006-7. doi: 10.1093/bioinformatics/btt730. Epub 2013 Dec 18.

PMID:
24351709
[PubMed - indexed for MEDLINE]
7.

SInC: an accurate and fast error-model based simulator for SNPs, Indels and CNVs coupled with a read generator for short-read sequence data.

Pattnaik S, Gupta S, Rao AA, Panda B.

BMC Bioinformatics. 2014 Feb 5;15:40. doi: 10.1186/1471-2105-15-40.

PMID:
24495296
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

BamTools: a C++ API and toolkit for analyzing and managing BAM files.

Barnett DW, Garrison EK, Quinlan AR, Strömberg MP, Marth GT.

Bioinformatics. 2011 Jun 15;27(12):1691-2. doi: 10.1093/bioinformatics/btr174. Epub 2011 Apr 14.

PMID:
21493652
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

An integrative variant analysis suite for whole exome next-generation sequencing data.

Challis D, Yu J, Evani US, Jackson AR, Paithankar S, Coarfa C, Milosavljevic A, Gibbs RA, Yu F.

BMC Bioinformatics. 2012 Jan 12;13:8. doi: 10.1186/1471-2105-13-8.

PMID:
22239737
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Hadoop-BAM: directly manipulating next generation sequencing data in the cloud.

Niemenmaa M, Kallio A, Schumacher A, Klemelä P, Korpelainen E, Heljanko K.

Bioinformatics. 2012 Mar 15;28(6):876-7. doi: 10.1093/bioinformatics/bts054. Epub 2012 Feb 2.

PMID:
22302568
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

R453Plus1Toolbox: an R/Bioconductor package for analyzing Roche 454 Sequencing data.

Klein HU, Bartenhagen C, Kohlmann A, Grossmann V, Ruckert C, Haferlach T, Dugas M.

Bioinformatics. 2011 Apr 15;27(8):1162-3. doi: 10.1093/bioinformatics/btr102. Epub 2011 Feb 23.

PMID:
21349869
[PubMed - indexed for MEDLINE]
Free Article
12.

SmashCell: a software framework for the analysis of single-cell amplified genome sequences.

Harrington ED, Arumugam M, Raes J, Bork P, Relman DA.

Bioinformatics. 2010 Dec 1;26(23):2979-80. doi: 10.1093/bioinformatics/btq564. Epub 2010 Oct 21.

PMID:
20966005
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

DELLY: structural variant discovery by integrated paired-end and split-read analysis.

Rausch T, Zichner T, Schlattl A, Stütz AM, Benes V, Korbel JO.

Bioinformatics. 2012 Sep 15;28(18):i333-i339. doi: 10.1093/bioinformatics/bts378.

PMID:
22962449
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Wessim: a whole-exome sequencing simulator based on in silico exome capture.

Kim S, Jeong K, Bafna V.

Bioinformatics. 2013 Apr 15;29(8):1076-7. doi: 10.1093/bioinformatics/btt074. Epub 2013 Feb 14.

PMID:
23413434
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

synbreed: a framework for the analysis of genomic prediction data using R.

Wimmer V, Albrecht T, Auinger HJ, Schön CC.

Bioinformatics. 2012 Aug 1;28(15):2086-7. doi: 10.1093/bioinformatics/bts335. Epub 2012 Jun 10.

PMID:
22689388
[PubMed - indexed for MEDLINE]
Free Article
16.

MitoSeek: extracting mitochondria information and performing high-throughput mitochondria sequencing analysis.

Guo Y, Li J, Li CI, Shyr Y, Samuels DC.

Bioinformatics. 2013 May 1;29(9):1210-1. doi: 10.1093/bioinformatics/btt118. Epub 2013 Mar 6.

PMID:
23471301
[PubMed - indexed for MEDLINE]
Free Article
17.

Accurate estimation of short read mapping quality for next-generation genome sequencing.

Ruffalo M, Koyutürk M, Ray S, LaFramboise T.

Bioinformatics. 2012 Sep 15;28(18):i349-i355. doi: 10.1093/bioinformatics/bts408.

PMID:
22962451
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Indel-tolerant read mapping with trinucleotide frequencies using cache-oblivious kd-trees.

Mahmud MP, Wiedenhoeft J, Schliep A.

Bioinformatics. 2012 Sep 15;28(18):i325-i332. doi: 10.1093/bioinformatics/bts380.

PMID:
22962448
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Launching genomics into the cloud: deployment of Mercury, a next generation sequence analysis pipeline.

Reid JG, Carroll A, Veeraraghavan N, Dahdouli M, Sundquist A, English A, Bainbridge M, White S, Salerno W, Buhay C, Yu F, Muzny D, Daly R, Duyk G, Gibbs RA, Boerwinkle E.

BMC Bioinformatics. 2014 Jan 29;15:30. doi: 10.1186/1471-2105-15-30.

PMID:
24475911
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

PatternCNV: a versatile tool for detecting copy number changes from exome sequencing data.

Wang C, Evans JM, Bhagwate AV, Prodduturi N, Sarangi V, Middha M, Sicotte H, Vedell PT, Hart SN, Oliver GR, Kocher JP, Maurer MJ, Novak AJ, Slager SL, Cerhan JR, Asmann YW.

Bioinformatics. 2014 May 29. pii: btu363. [Epub ahead of print]

PMID:
24876377
[PubMed - as supplied by publisher]
Free Article

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