Searching the RRID Resource Information Network
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http://sourceforge.net/projects/mirplant/
A user-friendly plant miRNA prediction tool.
Proper citation: miRPlant (RRID:SCR_012105) Copy
https://code.google.com/p/slidesort-bpr/
Software using a reference-free method for detecting clusters of breakpoints from the chromosomal rearrangements.
Proper citation: SlideSort-BPR (RRID:SCR_012079) Copy
http://www.bioinf.jku.at/software/fabia/fabia.html
A model-based technique for biclustering that is clustering rows and columns simultaneously.
Proper citation: FABIA (RRID:SCR_012002) Copy
Software that allows fast and user-friendly verification of Mascot result files, as well as data quantification using isotopic labeling methods (SILAC/ICAT) or label free approaches (spectral counting, MS signal comparison).
Proper citation: MFPaQ (RRID:SCR_012049) Copy
http://sourceforge.net/projects/multiplierz/
An open-source Python-based environment that provides a scriptable framework for efficient access to manufacturers'' proprietary data files via mzAPI.
Proper citation: multiplierz (RRID:SCR_012058) Copy
http://www.computationalbioenergy.org/meta-storms.html
Optimized GPU-based software to efficiently measure the quantitative phylogenetic similarity among massive amount of microbial community samples.
Proper citation: GPU-Meta-Storms (RRID:SCR_012029) 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
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/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
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
http://sourceforge.net/projects/plek/
An alignment-free software tool which uses a computational pipeline based on an improved k-mer scheme and a support vector machine (SVM) algorithm to distinguish lncRNAs from messenger RNAs (mRNAs), in the absence of genomic sequences or annotations. It is especially suitable for PacBio or 454 sequencing data and large-scale transcriptome data.
Proper citation: PLEK (RRID:SCR_012132) Copy
https://code.google.com/p/reditools/
A suite of python scripts to perform high-throughput investigation of RNA editing using next-generation sequencing data.
Proper citation: REDItools (RRID:SCR_012133) Copy
https://code.google.com/p/icelogo/
Software that builds on probability theory to visualize significant conserved sequence patterns in multiple peptide sequence alignments against background (reference) sequence sets that can be tailored to the studied system and the used protocol.
Proper citation: iceLogo (RRID:SCR_012137) Copy
https://code.google.com/p/automotifserver/
Software that predicts the wide selection of 88 different types of the single amino acid post-translational modifications (PTM) in protein sequences. The source code and precompiled binaries of brainstorming tool are available under Apache licensing.
Proper citation: AMS (RRID:SCR_012140) Copy
http://sourceforge.net/projects/phosphosite/
A bioinformatical software tool for analyzing (quantitative) phosphoproteome datasets. The program retrieves kinase-substrate predictions from NetworKIN and contains various statistical modules for futher analysis.
Proper citation: PhosphoSiteAnalyzer (RRID:SCR_012142) Copy
http://www.bioconductor.org/packages/2.12/bioc/html/DNAcopy.html
Software that segments DNA copy number data using circular binary segmentation to detect regions with abnormal copy number.
Proper citation: DNAcopy (RRID:SCR_012560) Copy
Software suite of automated docking tools. Designed to predict how small molecules, such as substrates or drug candidates, bind to receptor of known 3D structure. AutoDock consist of AutoDock 4 and AutoDock Vina. AutoDock 4 consists of autodock to perform docking of ligand to set of grids describing target protein, and autogrid to pre calculate these grids.
Proper citation: AutoDock (RRID:SCR_012746) Copy
http://sourceforge.net/p/krona/home/krona/
Software that allows hierarchical data to be explored with zoomable pie charts.
Proper citation: Krona (RRID:SCR_012785) Copy
http://bioinf.wehi.edu.au/featureCounts/
A read summarization program, which counts mapped reads for the genomic features such as genes and exons.
Proper citation: featureCounts (RRID:SCR_012919) Copy
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