Source code for biology and medicine

Keyphrases

Publications

volume 15, 2020

Julian S DeVille, Daisuke Kihara, Atilla Sit
2DKD: a toolkit for content-based local image search. Source code for biology and medicine 15 (2020)

volume 14, 2019

Guilhem Faure, Agnel Praveen Joseph, Pierrick Craveur, Tarun J Narwani, Narayanaswamy Srinivasan, Jean-Christophe Gelly, Joseph Rebehmed, Alexandre G De Brevern
iPBAvizu: a PyMOL plugin for an efficient 3D protein structure superimposition approach. Source code for biology and medicine 14 (2019)
Delfina Malandrino, Ilaria Manno, Alberto Negro, Andrea Petta, Luigi Serra, Concita Cantarella, Vittorio Scarano
Social support for collaboration and group awareness in life science research teams. Source code for biology and medicine 14 (2019)
Kridsadakorn Chaichoompu, Fentaw Abegaz, Sissades Tongsima, Philip James Shaw, Anavaj Sakuntabhai, Luísa Pereira, Kristel Van Steen
IPCAPS: an R package for iterative pruning to capture population structure. Source code for biology and medicine 14 (2019)
Achraf El Allali, Mariam Arshad
MZPAQ: a FASTQ data compression tool. Source code for biology and medicine 14 (2019)
Qing Yang, Xinming An, Wei Pan
Computing and graphing probability values of pearson distributions: a SAS/IML macro. Source code for biology and medicine 14 (2019)
Veer Singh Marwah, Giovanni Scala, Pia Anneli Sofia Kinaret, Angela Serra, Harri Alenius, Vittorio Fortino, Dario Greco
eUTOPIA: solUTion for Omics data PreprocessIng and Analysis. Source code for biology and medicine 14 (2019)

volume 13, 2018

Christina Nieuwoudt, Samantha J Jones, Angela Brooks-Wilson, Jinko Graham
Simulating pedigrees ascertained for multiple disease-affected relatives. Source code for biology and medicine 13 (2018)
Daniel A Machlab, Gabriel Velez, Alexander G Bassuk, Vinit B Mahajan
ProSave: an application for restoring quantitative data to manipulated subsets of protein lists. Source code for biology and medicine 13 (2018)
Tong Liu, Zheng Wang
SOV_refine: A further refined definition of segment overlap score and its significance for protein structure similarity. Source code for biology and medicine 13 (2018)

volume 12, 2017

Jörn Bethune, Lars Kraemer, Ingo Thomsen, Andreas Keller, David Ellinghaus, Andre Franke
LitDB - Keeping Track of Research Papers From Your Institute Made Simple. Source code for biology and medicine 12 (2017)
Jiho Kim, Yury Tsoy, Jan Persson, Regis Grailhe
FLIM-FRET analyzer: open source software for automation of lifetime-based FRET analysis. Source code for biology and medicine 12 (2017)
Syed Haider, Daryl Waggott, Emilie Lalonde, Clement Fung, Fei-Fei Liu, Paul C Boutros
Erratum to: A bedr way of genomic interval processing. Source code for biology and medicine 12 (2017)
Jana Lasser, Eleni Katifori
NET: a new framework for the vectorization and examination of network data. Source code for biology and medicine 12 (2017)
Yan Li, Jorge Andrade
DEApp: an interactive web interface for differential expression analysis of next generation sequence data. Source code for biology and medicine 12 (2017)
Brian D Bennett, Pierre R Bushel
goSTAG: gene ontology subtrees to tag and annotate genes within a set. Source code for biology and medicine 12 (2017)
Maria Rubega, Claudia Cecchetto, Stefano Vassanelli, Giovanni Sparacino
Algorithm and software to automatically identify latency and amplitude features of local field potentials recorded in electrophysiological investigation. Source code for biology and medicine 12 (2017)

volume 11, 2016

Vasanth R Singan, Jeremy C Simpson
Implementation of the Rank-Weighted Co-localization (RWC) algorithm in multiple image analysis platforms for quantitative analysis of microscopy images. Source code for biology and medicine 11 (2016)
Fuquan Zhang
A flexible tool to plot a genomic map for single nucleotide polymorphisms. Source code for biology and medicine 11 (2016)
Syed Haider, Daryl Waggott, Emilie Lalonde, Clement Fung, Fei-Fei Liu, Paul C Boutros
A bedr way of genomic interval processing. Source code for biology and medicine 11 (2016)
Toshiki Takeuchi, Atsuo Yamada, Takashi Aoki, Kunihiro Nishimura
cljam: a library for handling DNA sequence alignment/map (SAM) with parallel processing. Source code for biology and medicine 11 (2016)
Refat Sharmin, Abul B M M K Islam
Conserved antigenic sites between MERS-CoV and Bat-coronavirus are revealed through sequence analysis. Source code for biology and medicine 11 (2016)
Jitsuki Sawamura, Shigeru Morishita, Jun Ishigooka
Symmetrical treatment of "Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition", for major depressive disorders. Source code for biology and medicine 11 (2016)
Lindsay V Clark, Erik J Sacks
TagDigger: user-friendly extraction of read counts from GBS and RAD-seq data. Source code for biology and medicine 11 (2016)
Ana Gabriella de Oliveira Sardinha, Ceres Nunes de Resende Oyama, Armando de Mendonça Maroja, Ivan F Costa
Implementation and clinical application of a deformation method for fast simulation of biological tissue formed by fibers and fluid. Source code for biology and medicine 11 (2016)
John M Macdonald, Paul C Boutros
Log::ProgramInfo: A Perl module to collect and log data for bioinformatics pipelines. Source code for biology and medicine 11 (2016)
Markus Riester, Angad P Singh, A Rose Brannon, Kun Yu, Catarina D Campbell, Derek Y Chiang, Michael P Morrissey
PureCN: copy number calling and SNV classification using targeted short read sequencing. Source code for biology and medicine 11 (2016)
Deena M A Gendoo, Benjamin Haibe-Kains
MM2S: personalized diagnosis of medulloblastoma patients and model systems. Source code for biology and medicine 11 (2016)
Samson S Kiware, Tanya L Russell, Zacharia J Mtema, Alpha D Malishee, Prosper Chaki, Dickson Lwetoijera, Javan Chanda, Dingani Chinula, Silas Majambere, John E Gimnig, Thomas A Smith, Gerry F Killeen
A generic schema and data collection forms applicable to diverse entomological studies of mosquitoes. Source code for biology and medicine 11 (2016)
Brigitte Glanzmann, Hendri Herbst, Craig J Kinnear, Marlo Möller, Junaid Gamieldien, Soraya Bardien
A new tool for prioritization of sequence variants from whole exome sequencing data. Source code for biology and medicine 11 (2016)
Caleb F Davis, Deborah I Ritter, David A Wheeler, Hongmei Wang, Yan Ding, Shannon P Dugan, Matthew N Bainbridge, Donna M Muzny, Pulivarthi H Rao, Tsz-Kwong Man, Sharon E Plon, Richard A Gibbs, Ching C Lau
SV-STAT accurately detects structural variation via alignment to reference-based assemblies. Source code for biology and medicine 11 (2016)

volume 10, number 1, 2015

Timothy D O'Connor
AdmixKJump: identifying population structure in recently diverged groups. Source code for biology and medicine 10 (1) (2015)

volume 10, 2015

Maarten Lj Coonen, Daniel Hj Theunissen, Jos Cs Kleinjans, Danyel Gj Jennen
MagiCMicroRna: a web implementation of AgiMicroRna using shiny. Source code for biology and medicine 10 (2015)
Alexandros Kanterakis, Joël Kuiper, George Potamias, Morris A Swertz
PyPedia: using the wiki paradigm as crowd sourcing environment for bioinformatics protocols. Source code for biology and medicine 10 (2015)
Peter Frommolt, Björn Schumacher
Wormpath: searching for molecular interaction networks in Caenorhabditis elegans. Source code for biology and medicine 10 (2015)
Damien M O'Halloran
PrimerView: high-throughput primer design and visualization. Source code for biology and medicine 10 (2015)
Carol L Ecale Zhou
CombAlign: a code for generating a one-to-many sequence alignment from a set of pairwise structure-based sequence alignments. Source code for biology and medicine 10 (2015)
Md Anayet Hasan, Md Habibul Hasan Mazumder, Afrin Sultana Chowdhury, Amit Datta, Md Arif Khan
Molecular-docking study of malaria drug target enzyme transketolase in Plasmodium falciparum 3D7 portends the novel approach to its treatment. Source code for biology and medicine 10 (2015)
Elliot J Yates, Louise C Dixon
PageRank as a method to rank biomedical literature by importance. Source code for biology and medicine 10 (2015)
Alice Mantoan, Claudio Pizzolato, Massimo Sartori, Zimi Sawacha, Claudio Cobelli, Monica Reggiani
MOtoNMS: A MATLAB toolbox to process motion data for neuromusculoskeletal modeling and simulation. Source code for biology and medicine 10 (2015)
Gabriel Cuellar-Partida, Miguel E Renteria, Stuart MacGregor
LocusTrack: Integrated visualization of GWAS results and genomic annotation. Source code for biology and medicine 10 (2015)
Kimberly F McManus
popRange: a highly flexible spatially and temporally explicit Wright-Fisher simulator. Source code for biology and medicine 10 (2015)
Samad Jahandideh, Fatemeh Sharifi, Lukasz Jaroszewski, Adam Godzik
PROPER: Performance visualization for optimizing and comparing ranking classifiers in MATLAB. Source code for biology and medicine 10 (2015)
Madison Flannery, David M Budden, Alexandre Mendes
FlexDM: Simple, parallel and fault-tolerant data mining using WEKA. Source code for biology and medicine 10 (2015)
Matthew Carr, Cait E MacPhee
Membrainy: a 'smart', unified membrane analysis tool. Source code for biology and medicine 10 (2015)
Connor H Fortin, Katharina V Schulze, Gregory A Babbitt
TRX-LOGOS - a graphical tool to demonstrate DNA information content dependent upon backbone dynamics in addition to base sequence. Source code for biology and medicine 10 (2015)
Maciej Fronczuk, Adrian E Raftery, Ka Yee Yeung
CyNetworkBMA: a Cytoscape app for inferring gene regulatory networks. Source code for biology and medicine 10 (2015)

volume 9, number 1, 2014

Bernard J Pope, Tú 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. Source code for biology and medicine 9 (1) (2014)
Luís Paquete, Pedro Matias, Maryam Abbasi, Miguel Pinheiro
MOSAL: software tools for multiobjective sequence alignment. Source code for biology and medicine 9 (1) (2014)
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. Source code for biology and medicine 9 (1) (2014)