ADAPT toolbox for Matlab - Analysis of Dynamic Adaptations in Parameter Trajectories
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Updated
Dec 1, 2014 - C
ADAPT toolbox for Matlab - Analysis of Dynamic Adaptations in Parameter Trajectories
MICA-aligner is a new short-read aligner that is optimized in view of MIC's limitation and the extra parallelism inside each MIC core.
GIMSAN: motif-finder with biologically realistic and reliable statistical significance analysis
Variant calling format (vcf) file genomics pipeline for HPC and cloud
Bio::PhyloXS - Core Bio::Phylo modules implemented in C
Calculates hydrogen-bond interaction tables for protein-small molecule complexes, based on protein PDB and protonated ligand MOL2 structure input. Raschka et al. (2018) J. Computer-Aided Molec. Design
A tool to extract mappable reads from various library preparation protocols.
Chiang, S., Shinohara, H., Huang, J. H., Tsai, H. K. & Okada, M. Inferring the transcriptional regulatory mechanism of signal-dependent gene expression via an integrative computational approach. FEBS Lett. (2020).
A short repo of some C implementation of Computational Biology programs
To tackle the exponentially increasing throughput of Next-Generation Sequencing (NGS), most of the existing short-read aligners can be configured to favor speed in trade of accuracy and sensitivity. SOAP3-dp, through leveraging the computational power of both CPU and GPU with optimized algorithms, delivers high speed and sensitivity simultaneously.
semi-automated regular-unit counting using photos
LibSBMLSim mathematical simulation program via BioSimulators-compliant command-line interface and Docker container
SOAPdenovo-Trans, a de novo transcriptome assembler designed specifically for RNA-Seq. We evaluated its performance on transcriptome datasets from rice and mouse.
Cross-platform GUI desktop application for making biological heatmaps
Sequential and Parallel Implementation of the Hodgkin-Huxley Neuron model.
Next generation sequencing reads de novo assembler.
10x Genomics Reads Simulator
An improved compression tool for DNA sequences
A numerical study on the phenomenon of sympatric speciation in both sexual and asexual species, within a static habitat with intra-species competition.
All UCSC Genome Browser source code that is under an open source license, mostly file format converters, command line tools and C libraries. A subset of the "kent" repo, updated every three weeks.
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