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MIRA - Sequence assembler and sequence mapping for whole genome shotgun and EST / RNASeq sequencing data. Can use Sanger, 454, Illumina and IonTorrent data. PacBio: CCS and error corrected data usable, uncorrected not yet.
... suite to examine differential gene expression levels using an R and C++ hybrid computational pipeline." Source Code for Biology and Medicine, 2014 9:30]
HeatmapGenerator source code is available at: https://github.com/Bohdan-Khomtchouk/HeatmapGenerator
Bohdan Khomtchouk wishes to acknowledge the support of the Department of Defense (DoD) through the National Defense Science & Engineering Graduate Fellowship (NDSEG) Program.
HeatmapGenerator is released under the GNU GPL.
4-Dimensional Cell Simulator (4DiCeS) is a framework on hybrid (stochastic and deterministic) modeling and simulation of (whole) cell environments in 4D. The framework may incorporate any reaction and diffusion algorithms applicable in a 4D grid layout.