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Items: 1 to 20 of 207

1.

Pybedtools: a flexible Python library for manipulating genomic datasets and annotations.

Dale RK, Pedersen BS, Quinlan AR.

Bioinformatics. 2011 Dec 15;27(24):3423-4. doi: 10.1093/bioinformatics/btr539. Epub 2011 Sep 23.

2.

A Python package for parsing, validating, mapping and formatting sequence variants using HGVS nomenclature.

Hart RK, Rico R, Hare E, Garcia J, Westbrook J, Fusaro VA.

Bioinformatics. 2015 Jan 15;31(2):268-70. doi: 10.1093/bioinformatics/btu630. Epub 2014 Sep 30.

3.

BEDTools: a flexible suite of utilities for comparing genomic features.

Quinlan AR, Hall IM.

Bioinformatics. 2010 Mar 15;26(6):841-2. doi: 10.1093/bioinformatics/btq033. Epub 2010 Jan 28.

4.

HTSeq--a Python framework to work with high-throughput sequencing data.

Anders S, Pyl PT, Huber W.

Bioinformatics. 2015 Jan 15;31(2):166-9. doi: 10.1093/bioinformatics/btu638. Epub 2014 Sep 25.

5.

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.

Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM.

Bioinformatics. 2015 Oct 1;31(19):3210-2. doi: 10.1093/bioinformatics/btv351. Epub 2015 Jun 9.

PMID:
26059717
6.

BioServices: a common Python package to access biological Web Services programmatically.

Cokelaer T, Pultz D, Harder LM, Serra-Musach J, Saez-Rodriguez J.

Bioinformatics. 2013 Dec 15;29(24):3241-2. doi: 10.1093/bioinformatics/btt547. Epub 2013 Sep 23.

7.

OpenStructure: a flexible software framework for computational structural biology.

Biasini M, Mariani V, Haas J, Scheuber S, Schenk AD, Schwede T, Philippsen A.

Bioinformatics. 2010 Oct 15;26(20):2626-8. doi: 10.1093/bioinformatics/btq481. Epub 2010 Aug 23.

8.

Chado controller: advanced annotation management with a community annotation system.

Guignon V, Droc G, Alaux M, Baurens FC, Garsmeur O, Poiron C, Carver T, Rouard M, Bocs S.

Bioinformatics. 2012 Apr 1;28(7):1054-6. doi: 10.1093/bioinformatics/bts046. Epub 2012 Jan 28.

9.

Pyteomics--a Python framework for exploratory data analysis and rapid software prototyping in proteomics.

Goloborodko AA, Levitsky LI, Ivanov MV, Gorshkov MV.

J Am Soc Mass Spectrom. 2013 Feb;24(2):301-4. doi: 10.1007/s13361-012-0516-6. Epub 2013 Jan 5.

PMID:
23292976
10.

GenomeTools: a comprehensive software library for efficient processing of structured genome annotations.

Gremme G, Steinbiss S, Kurtz S.

IEEE/ACM Trans Comput Biol Bioinform. 2013 May-Jun;10(3):645-56. doi: 10.1109/TCBB.2013.68.

PMID:
24091398
11.

SNiPA: an interactive, genetic variant-centered annotation browser.

Arnold M, Raffler J, Pfeufer A, Suhre K, Kastenmüller G.

Bioinformatics. 2015 Apr 15;31(8):1334-6. doi: 10.1093/bioinformatics/btu779. Epub 2014 Nov 26.

12.

DendroPy: a Python library for phylogenetic computing.

Sukumaran J, Holder MT.

Bioinformatics. 2010 Jun 15;26(12):1569-71. doi: 10.1093/bioinformatics/btq228. Epub 2010 Apr 25.

PMID:
20421198
13.

CSB: a Python framework for structural bioinformatics.

Kalev I, Mechelke M, Kopec KO, Holder T, Carstens S, Habeck M.

Bioinformatics. 2012 Nov 15;28(22):2996-7. doi: 10.1093/bioinformatics/bts538. Epub 2012 Aug 31.

PMID:
22942023
14.

An intuitive Python interface for Bioconductor libraries demonstrates the utility of language translators.

Gautier L.

BMC Bioinformatics. 2010 Dec 21;11 Suppl 12:S11. doi: 10.1186/1471-2105-11-S12-S11.

15.

EggLib: processing, analysis and simulation tools for population genetics and genomics.

De Mita S, Siol M.

BMC Genet. 2012 Apr 11;13:27. doi: 10.1186/1471-2156-13-27.

16.

Utility library for structural bioinformatics.

Gront D, Kolinski A.

Bioinformatics. 2008 Feb 15;24(4):584-5. doi: 10.1093/bioinformatics/btm627. Epub 2008 Jan 28.

PMID:
18227118
17.

Genomation: a toolkit to summarize, annotate and visualize genomic intervals.

Akalin A, Franke V, Vlahoviček K, Mason CE, Schübeler D.

Bioinformatics. 2015 Apr 1;31(7):1127-9. doi: 10.1093/bioinformatics/btu775. Epub 2014 Nov 21.

PMID:
25417204
18.

pyOpenMS: a Python-based interface to the OpenMS mass-spectrometry algorithm library.

Röst HL, Schmitt U, Aebersold R, Malmström L.

Proteomics. 2014 Jan;14(1):74-7. doi: 10.1002/pmic.201300246.

PMID:
24420968
19.

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
20.

Biopython: freely available Python tools for computational molecular biology and bioinformatics.

Cock PJ, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kauff F, Wilczynski B, de Hoon MJ.

Bioinformatics. 2009 Jun 1;25(11):1422-3. doi: 10.1093/bioinformatics/btp163. Epub 2009 Mar 20.

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