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Source Code for Biology and Medicine, Volume 9
Volume 9, 2014
- David Campos, Quoc-Chinh Bui, Sérgio Matos
, José Luís Oliveira
:
TrigNER: automatically optimized biomedical event trigger recognition on scientific documents. 1 - Luís Paquete
, Pedro Matias, Maryam Abbasi
, Miguel Pinheiro:
MOSAL: software tools for multiobjective sequence alignment. 2 - Bernard J. Pope
, Tu Nguyen-Dumont
, Fleur Hammet, Daniel J. Park
:
ROVER variant caller: read-pair overlap considerate variant-calling software applied to PCR-based massively parallel sequencing datasets. 3 - Matthew I. Bellgard
, Christophe Béroud, Kay Parkinson, Tess Harris, Ségolène Aymé, Gareth Baynam, Tarun Weeramanthri, Hugh J. S. Dawkins, Adam Hunter:
Correction: Dispelling myths about rare disease registry system development. 4 - Khadija Musayeva, Tristan Henderson
, John B. O. Mitchell
, Lazaros Mavridis
:
PFClust: an optimised implementation of a parameter-free clustering algorithm. 5 - Kuruvilla Abraham
, Clara Diaz:
Identifying large sets of unrelated individuals and unrelated markers. 6 - Jesus Herrera-Galeano, Kenneth G. Frey, Regina Z. Cer, Alfred J. Mateczun, Kimberly A. Bishop-Lilly, Vishwesh P. Mokashi:
BLASTPLOT: a PERL module to plot next generation sequencing NCBI-BLAST results. 7 - Chuming Chen
, Sari S. Khaleel, Hongzhan Huang, Cathy H. Wu
:
Software for pre-processing Illumina next-generation sequencing short read sequences. 8 - Richard A. Erickson
, Wayne E. Thogmartin
, Jennifer A. Szymanski:
BatTool: an R package with GUI for assessing the effect of White-nose syndrome and other take events on Myotis spp. of bats. 9 - Moses P. Adoga
, Segun A. Fatumo
, Simon M. Agwale:
H3Africa: a tipping point for a revolution in bioinformatics, genomics and health research in Africa. 10 - Izaskun Mallona
, Anna Díez-Villanueva, Miguel A. Peinado
:
Methylation plotter: a web tool for dynamic visualization of DNA methylation data. 11 - Neda Zamani, Görel Sundström, Marc P. Höppner, Manfred G. Grabherr
:
Modular and configurable optimal sequence alignment software: Cola. 12 - German Tischler, Steven Leonard:
biobambam: tools for read pair collation based algorithms on BAM files. 13 - Matthew I. Bellgard
, Lee Render, Maciej Radochonski, Adam Hunter:
Second generation registry framework. 14 - Daniel J. Park
, Tu Nguyen-Dumont
, Sori Kang, Karin Verspoor
, Bernard J. Pope
:
Annokey: an annotation tool based on key term search of the NCBI Entrez Gene database. 15 - Guillaume Lamour
, Julius B. Kirkegaard
, Hongbin Li
, Tuomas P. J. Knowles
, Jörg Gsponer:
Easyworm: an open-source software tool to determine the mechanical properties of worm-like chains. 16 - Natapol Pornputtapong
, Kwanjeera Wanichthanarak, Avlant Nilsson
, Intawat Nookaew, Jens Nielsen
:
A dedicated database system for handling multi-level data in systems biology. 17 - Michel Petitjean
, Anne Vanet
:
VIRAPOPS2 supports the influenza virus reassortments. 18 - Aleksey A. Porollo
:
EC2KEGG: a command line tool for comparison of metabolic pathways. 19 - Harold R. Garner, Ashwin Puthige:
BioFlow: a web based workflow management software for design and execution of genomics pipelines. 20 - Christoph Wiedemann, Peter Bellstedt
, Matthias Görlach:
PREdator: a python based GUI for data analysis, evaluation and fitting. 21 - Daniel A. Wagenaar
:
Publication quality 2D graphs with less manual effort due to explicit use of dual coordinate systems. 22 - Yong Xu, Fuquan Zhang
, Guoqiang Wang, Hongbao Cao, Yin Yao Shugart, Zaohuo Cheng:
plot2groups: an R package to plot scatter points for two groups of values. 23 - David Keith Williams, Zoran Bursac
:
Three algorithms and SAS macros for estimating power and sample size for logistic models with one or more independent variables of interest in the presence of covariates. 24 - Mike Gavrielides, Simon J. Furney, Tim Yates, Crispin J. Miller, Richard Marais:
Onco-STS: a web-based Laboratory Information Management System for sample and analysis tracking in oncogenomic experiments. 25 - Robert V. Baron, Charles Kollar, Nandita Mukhopadhyay, Daniel E. Weeks:
Mega2: validated data-reformatting for linkage and association analyses. 26 - Thuy Nguyen, Kyungmin Song, Yury Tsoy, Jin Kim, Yong-Jun Kwon, Myungjoo Kang, Michael Edberg Hansen:
Robust dose-response curve estimation applied to high content screening data analysis. 27 - Héctor Echavarría-Heras, Cecilia Leal Ramírez, Enrique Villa-Diharce, Oscar Castillo:
Using the value of Lin's concordance correlation coefficient as a criterion for efficient estimation of areas of leaves of eelgrass from noisy digital images. 29 - Bohdan B. Khomtchouk, Derek J. Van Booven, Claes Wahlestedt:
HeatmapGenerator: high performance RNAseq and microarray visualization software suite to examine differential gene expression levels using an R and C++ hybrid computational pipeline. 30
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