Source Code for Biology and Medicine

Title Publication Date Language Citations
Purposeful selection of variables in logistic regression2008/12/01English2,171
CONTIGuator: a bacterial genomes finishing tool for structural insights on draft genomes2011/06/21English212
Boolean network simulations for life scientists2008/11/14English157
biobambam: tools for read pair collation based algorithms on BAM files2014/06/20English141
Software for pre-processing Illumina next-generation sequencing short read sequences2014/05/03English140
Wndchrm – an open source utility for biological image analysis2008/07/08English130
Git can facilitate greater reproducibility and increased transparency in science2013/02/28English95
The non-negative matrix factorization toolbox for biological data mining2013/04/16English89
MOtoNMS: A MATLAB toolbox to process motion data for neuromusculoskeletal modeling and simulation2015/11/16English88
WordCloud: a Cytoscape plugin to create a visual semantic summary of networks2011/04/07English87
The GlycanBuilder: a fast, intuitive and flexible software tool for building and displaying glycan structures2007/08/07English87
BioPatRec: A modular research platform for the control of artificial limbs based on pattern recognition algorithms2013/04/18English85
Permutation – based statistical tests for multiple hypotheses2008/10/21English85
PureCN: copy number calling and SNV classification using targeted short read sequencing2016/12/01English79
Yabi: An online research environment for grid, high performance and cloud computing2012/02/15English72
A software pipeline for processing and identification of fungal ITS sequences2009/01/15English71
Easyworm: an open-source software tool to determine the mechanical properties of worm-like chains2014/07/10English67
PathNet: a tool for pathway analysis using topological information2012/09/24English51
Bio-samtools: Ruby bindings for SAMtools, a library for accessing BAM files containing high-throughput sequence alignments2012/05/28English51
CellSegm - a MATLAB toolbox for high-throughput 3D cell segmentation2013/08/09English49
Methylation plotter: a web tool for dynamic visualization of DNA methylation data2014/06/07English47
Combining de novo and reference-guided assembly with scaffold_builder2013/11/22English46
Motmot, an open-source toolkit for realtime video acquisition and analysis2009/07/22English43
HeatmapGenerator: high performance RNAseq and microarray visualization software suite to examine differential gene expression levels using an R and C++ hybrid computational pipeline2014/12/01English43
H3Africa: a tipping point for a revolution in bioinformatics, genomics and health research in Africa2014/05/08English43
DEApp: an interactive web interface for differential expression analysis of next generation sequence data2017/02/03English42
SAMMate: a GUI tool for processing short read alignments in SAM/BAM format2011/01/13English40
Dispelling myths about rare disease registry system development2013/10/16English36
Layout-aware text extraction from full-text PDF of scientific articles2012/05/28English34
eUTOPIA: solUTion for Omics data PreprocessIng and Analysis2019/01/29English34