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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
http://sourceforge.net/projects/exorca/
A Matlab package extending the scope of established COBRA metabolic modelling.
Proper citation: ORCA (RRID:SCR_012097) Copy
http://opencobra.sourceforge.net/openCOBRA/Welcome.html
Software Python package that provides support for basic COnstraint-Based Reconstruction and Analysis (COBRA) methods.
Proper citation: COBRApy (RRID:SCR_012096) Copy
http://knowtator.sourceforge.net/
A general-purpose text annotation tool that is integrated with the Prot����g���� knowledge representation system.
Proper citation: Knowtator (RRID:SCR_012099) Copy
http://sourceforge.net/projects/pb-jelly/
Software that automates the finishing process using long sequence reads in a reference-guided assembly process.
Proper citation: PBJelly (RRID:SCR_012091) Copy
https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/AHA
Contigs from a draft assembly generated by a different assembler can be joined using PacBio long reads.
Proper citation: AHA (RRID:SCR_012090) Copy
https://code.google.com/p/netcoffee/
A fast and accurate algorithm which allows to find a global alignment of multiple protein-protein interaction networks.
Proper citation: NetCoffee (RRID:SCR_012095) Copy
https://code.google.com/p/qsimscan/
A flexible open source protein similarity search software tool which provides a significant gain in speed compared to BLASTP at the price of controlled sensitivity loss.
Proper citation: PSimScan (RRID:SCR_012094) Copy
http://www.few.vu.nl/~mavdwiel/ShrinkBayes.html
Software for detecting differential features across the entire spectrum, including the lower counts.
Proper citation: ShrinkSeq (RRID:SCR_012022) Copy
http://www.stat.purdue.edu/~doerge/software/TSPM.R
Software using a statistical approach, based on a two-stage Poisson model, for modeling RNA sequencing data and testing for biologically important changes in gene expression.
Proper citation: TSPM.R (RRID:SCR_012021) Copy
A genome browser specialized in next-generation sequencing data.
Proper citation: GenomeJack (RRID:SCR_012026) Copy
http://www.nature.com/nmeth/journal/v5/n3/extref/nmeth.1184-S2.pdf
Software for decoding error-correcting barcodes.
Proper citation: Standalone hamming (RRID:SCR_012025) Copy
http://sourceforge.net/projects/dical-ibd/
Software tool for detecting identity-by-descent (IBD) tracts between pairs of genomic sequences.
Proper citation: diCal-IBD (RRID:SCR_012111) Copy
http://sourceforge.net/projects/ionwinze/
Software tool to pick out ion signals that discriminate two groups of samples (e.g. diseased/healthy, resistant/susceptible) by quasi-datapoint-wise comparison using univariate statistic procedures.
Proper citation: Ionwinze (RRID:SCR_012115) Copy
http://sourceforge.net/projects/genosight/
An adaptive imaging cytometry software environment.
Proper citation: GenoSIGHT (RRID:SCR_012119) Copy
https://github.com/stoeckli/MSImageViewer
Software for the conversion of data acquired with the FlashQuant (MALDI version of ABSciex 4000) into MS images.
Proper citation: MSImageViewer (RRID:SCR_012121) Copy
https://code.google.com/p/cell-motility/
An open source Java application that provides a clear and concise analysis workbench for large amounts of cell motion data.
Proper citation: Cell motility (RRID:SCR_012120) Copy
https://code.google.com/p/glycanbuilder/
An intuitive and flexible software tool for building and displaying glycan structures.
Proper citation: GlycanBuilder (RRID:SCR_012123) Copy
https://code.google.com/p/glycresoft/
A software package for automated recognition of glycans from LC/MS data.
Proper citation: GlycReSoft (RRID:SCR_012122) Copy
http://sourceforge.net/projects/isdtool/files/ISDTool-2.0/
Software that implements a computational model for predicting immunosuppressive domains (ISDs). The software could be used to identify typical ISDs in retroviruses including HERV, HTLV, HIV, STLV, SIV and MLV.
Proper citation: ISDTool (RRID:SCR_012125) Copy
http://sourceforge.net/projects/ngopt/
Software that produces high quality microbial genome assemblies on a laptop computer without any parameter tuning. A5-miseq does this by automating the process of adapter trimming, quality filtering, error correction, contig and scaffold generation, and detection of misassemblies. Unlike the original A5 pipeline, A5-miseq can use long reads from the Illumina MiSeq, use read pairing information during contig generation, and includes several improvements to read trimming.
Proper citation: A5-miseq (RRID:SCR_012148) Copy
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