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http://bioinformatics.mdanderson.org/main/PRADA:Overview
A pipeline to analyze paired end RNA-Seq data to generate gene expression values (RPKM) and gene-fusion candidates.
Proper citation: PRADA (RRID:SCR_011906) Copy
http://sourceforge.net/projects/mirplant/
A user-friendly plant miRNA prediction tool.
Proper citation: miRPlant (RRID:SCR_012105) Copy
https://code.google.com/p/chibe/
An editing and visualization software tool for pathway models represented by the BioPAX format, using SBGN Process Description Language, based on Chisio.
Proper citation: ChiBE (RRID:SCR_012110) 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://sketchel.sourceforge.net/
An interactive chemical molecule sketching tool, and molecular spreadsheet data entry application.
Proper citation: SketchEl (RRID:SCR_012082) Copy
http://sourceforge.net/projects/mcdl/
A small Java molecular viewer/editor for chemical structures, stored in Modular Chemical Descriptor Language linear notation.
Proper citation: MCDL (RRID:SCR_012084) Copy
https://code.google.com/p/searchgui/
Software providing a user-friendly, lightweight and open-source graphical user interface for configuring and running the freely available OMSSA and X!Tandem search engines simultaneously.
Proper citation: SearchGUI (RRID:SCR_012054) 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://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
Chemical 2D structure editor and viewer application/applet based on the Chemistry Development Kit (CDK).
Proper citation: JChemPaint (RRID:SCR_000095) Copy
http://www.bioconductor.org/packages/release/bioc/html/flowCL.html
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software for semantic labelling of flow cytometric cell populations.
Proper citation: flowCL (RRID:SCR_000046) Copy
https://code.google.com/p/cbrowse/
Software providing an AJAX-based web browser for visualizing and analyzing transcriptome assemblies and contigs.
Proper citation: Cbrowse (RRID:SCR_000044) Copy
http://www.bioconductor.org/packages/release/data/annotation/html/RmiR.Hs.miRNA.html
Software package for various databases of microRNA Targets.
Proper citation: RmiR.Hs.miRNA (RRID:SCR_000101) Copy
https://github.com/SciLifeLab/facs
Software for classification of Sequences using Bloom filters that can accurately and rapidly align sequences to a reference sequence.
Proper citation: FACS (RRID:SCR_000055) Copy
http://cran.r-project.org/web/packages/metaMA/
Software R package for meta-analysis for microarrays. It combines either p-values or modified effect sizes from different studies to find differentially expressed genes.
Proper citation: metaMA (RRID:SCR_000408) Copy
http://sourceforge.net/projects/skewer/
Software program for adapter trimming that is specially designed for processing Illumina paired-end sequences.
Proper citation: skewer (RRID:SCR_001151) Copy
http://www.liu.se/hu/mdl/main/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. An on-line database and publically accessible depository that is dedicated to the omics of small biomolecules.
Proper citation: NMR metabolomics database of Linkoping (RRID:SCR_002758) Copy
http://www.bioconductor.org/packages/release/bioc/html/RMassBank.html
Workflow software to process tandem MS files and build MassBank records. Functions include automated extraction of tandem MS spectra, formula assignment to tandem MS fragments, recalibration of tandem MS spectra with assigned fragments, spectrum cleanup, automated retrieval of compound information from Internet databases, and export to MassBank records.
Proper citation: RMassBank (RRID:SCR_002797) Copy
http://cran.r-project.org/web/packages/VennDiagram/
Software providing a set of functions to generate high-resolution Venn and Euler plots. Includes handling for several special cases, including two-case scaling, and extensive customization of plot shape and structure.
Proper citation: VennDiagram (RRID:SCR_002414) Copy
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