Tools   Select Another Resource Report Type

http://sourceforge.net/projects/virtools/

Software for a low frequency Virus Variant detection pipeline for Illumina data.

Proper citation: VirVarSeq (RRID:SCR_012116) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/pegasus-fus/

Software that annotates biologically functional gene fusion candidates.

Proper citation: Pegasus-fus (RRID:SCR_012118) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/nailsystemsbiology/

A set of software tools to simplify the range of computational activities involved in regulatory network inference. It is technology-independent and includes an interface layer to allow easy integration of components into other applications. It is implemented in MATLAB and is available for all researchers to use.

Proper citation: NAIL (RRID:SCR_012134) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/imsat/

A python program that uses the polymorphism data obtained from mapping individual Illumina sequence reads onto a reference genome to identify polymorphic STRs.

Proper citation: iMSAT (RRID:SCR_012135) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/nesmapper/

A computational software tool to predict leucine-rich nuclear export signals (NESs) by using profiles that had been further optimized by training and combining the amino acid properties of the NES-flanking regions. It is a multiplatform command-line Perl application with activity-based NES profiles.

Proper citation: NESmapper (RRID:SCR_012138) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/dhacdist/

Software for clustering time-evolving networks.

Proper citation: DHAC (RRID:SCR_012139) Copy   

•   Source: SciCrunch Registry

http://xmsanalyzer.sourceforge.net

A software package of utilities for data extraction, quality control assessment, detection of overlapping and unique metabolites in multiple datasets, and batch annotation of metabolites. xMSanalyzer comprises of utilities that can be classified into five main modules: 1) merging apLCMS or XCMS sample processing results from multiple sets of parameter settings, 2) evaluation of sample quality, feature consistency, and batch-effect, 3) feature matching, and 4) characterization of m/z using KEGG REST; 5) Batch-effect correction using ComBat.

Proper citation: xMSanalyzer (RRID:SCR_012144) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/excavatortool/

A software package for the detection of copy number variants (CNVs) from whole-exome sequencing data.

Proper citation: EXCAVATOR-tool (RRID:SCR_012766) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/trowel-ec/

An error correction module for Illumina sequencing reads, which is based on the k-mer spectrum approach.

Proper citation: Trowel (RRID:SCR_012890) Copy   

•   Source: SciCrunch Registry

http://fmatoolbox.sourceforge.net

Matlab toolbox used to help analyze electrophysiological and behavioral data recorded from freely moving animals.

Proper citation: FMAToolbox (RRID:SCR_015533) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/metavar/

Software package that enables detection of sequence variation between metagenomic samples.

Proper citation: MaryGold (RRID:SCR_000528) Copy   

•   Source: SciCrunch Registry

Ratings or validation data are available for this resource

http://broadinstitute.github.io/picard/

Java toolset for working with next generation sequencing data in the BAM format.

Proper citation: Picard (RRID:SCR_006525) Copy   

•   Source: SciCrunch Registry

http://neurospy.org

neurospy is a free software for functional imaging of fast neuronal activity. neurospy is a modular cross-platform application framework written in Java for the NetBeans Platform. At this time it runs on Windows XP-based LeCroy oscilloscopes and drives acousto-optic scanners via USB using the Analog Devices 9959 Direct Digital Synthesis chip. This combination makes one of the most powerful systems for scanning microscopy available today at any price. neurospy is very easy to port to other kinds of acquisition and scanning hardware.

Proper citation: neurospy (RRID:SCR_007016) Copy   

•   Source: SciCrunch Registry

http://cudasw.sourceforge.net/

CUDASW++ is a bioinformatics software for Smith-Waterman protein database searches that takes advantage of the massively parallel CUDA architecture of NVIDIA Tesla GPUs to perform sequence searches 10x-50x faster than NCBI BLAST. In this algorithm, we deeply explore the SIMT (Single Instruction, Multiple Thread) and virtualized SIMD (Single Instruction, Multiple Data) abstractions to achieve fast speed. This algorithm has been fully tested on Tesla C1060, Tesla C2050, GeForce GTX 280 and GTX 295 graphics cards, and has been incorporated to NVIDIA Tesla Bio Workbench. * Operating System: Linux * Programming language: CUDA and C * Other requirements: CUDA SDK and Toolkits 2.0 or higher

Proper citation: CUDASW++ (RRID:SCR_008862) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/cnvhitseq/

A set of Java-based command-line tools for detecting Copy Number Variants (CNVs) using next-generation sequencing data.

Proper citation: cnvHiTSeq (RRID:SCR_013160) Copy   

•   Source: SciCrunch Registry

http://bowtie-bio.sourceforge.net/recount/

RNA-seq gene count datasets built using the raw data from 18 different studies. The raw sequencing data (.fastq files) were processed with Myrna to obtain tables of counts for each gene. For ease of statistical analysis, they combined each count table with sample phenotype data to form an R object of class ExpressionSet. The count tables, ExpressionSets, and phenotype tables are ready to use and freely available. By taking care of several preprocessing steps and combining many datasets into one easily-accessible website, we make finding and analyzing RNA-seq data considerably more straightforward.

Proper citation: ReCount - A multi-experiment resource of analysis-ready RNA-seq gene count datasets (RRID:SCR_001774) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/avalontoolkit/

Software toolkit containing tools to render and canonicalize SMILES and manipulate MOL file and related formats, as well as structure fingerprinting.

Proper citation: Avalon Cheminformatics Toolkit (RRID:SCR_014273) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/bva-io/

Software package for interfacing the Brain Vision Analyser data files (load/save) for ongoing development of Matlab routines . This package is also compatible with the EEGLAB software, and may be uncompressed in the plugin folder of this software.

Proper citation: BVA import/export EEGLAB plugin (RRID:SCR_016333) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/metabnorm/

Software tool as mixed model normalization method for metabolomics data.Uses normalization approach based on mixed model, with simultaneous estimation of correlation matrix.

Proper citation: metabnorm (RRID:SCR_001266) Copy   

•   Source: SciCrunch Registry

http://xournal.sourceforge.net/

Free software application for notetaking, sketching, keeping a journal using a stylus that runs on Linux (recent distributions) and other GTK+/Gnome platforms. It is similar to Microsoft Windows Journal or to other alternatives such as Jarnal, Gournal, and NoteLab. Note: is open source and allows some annotation, but its PDF reading ability is very limited. It also uses its own format to store annotations.

Proper citation: Xournal (RRID:SCR_003233) Copy   

•   Source: SciCrunch Registry