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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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ReCount - A multi-experiment resource of analysis-ready RNA-seq gene count datasets Resource Report Resource Website 10+ mentions |
ReCount - A multi-experiment resource of analysis-ready RNA-seq gene count datasets (RRID:SCR_001774) | ReCount | data or information resource, data set | 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. | rna-seq, gene count, gene, phenotype, r |
is listed by: OMICtools is related to: Myrna has parent organization: SourceForge has parent organization: Johns Hopkins Bloomberg School of Public Health; Maryland; USA |
NIGMS T32GM074906 | PMID:22087737 | Free, Available for download, Freely available | OMICS_01953 | SCR_001774 | 2026-09-03 05:05:41 | 35 | ||||||
|
Picard Resource Report Resource Website 10000+ mentions Rating or validation data |
Picard (RRID:SCR_006525) | software resource, software toolkit, source code | Java toolset for working with next generation sequencing data in the BAM format. | next generation sequencing, java, bam |
is listed by: OMICtools is listed by: Debian is listed by: SoftCite has parent organization: SourceForge has parent organization: Broad Institute is required by: SL-quant |
Available for download, Free | OMICS_01066 | http://sourceforge.net/projects/picard/, https://github.com/broadinstitute/picard, https://sources.debian.org/src/picard-tools/ | SCR_006525 | 2026-09-03 05:06:17 | 15653 | ||||||||
|
neurospy Resource Report Resource Website |
neurospy (RRID:SCR_007016) | neurospy | software resource, source code | 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. | imaging, neuron, microscopy, functional imaging, java, neuronal activity |
has parent organization: SourceForge has parent organization: Howard Hughes Medical Institute has parent organization: Salk Institute for Biological Studies has parent organization: University of California at San Diego; California; USA |
Howard Hughes Medical Institute ; NIH |
PMID:17684546 | Open unspecified license | nlx_149367 | SCR_007016 | 2026-09-03 05:06:21 | 0 | ||||||
|
HTQC Resource Report Resource Website 10+ mentions |
HTQC (RRID:SCR_006448) | HTQC | software resource, software toolkit | A software toolkit including statistics tool for illumina high-throughput sequencing data, and filtration tools for sequence quality, length, tail quality, etc.. | c++, illumina, command-line |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
PMID:23363224 DOI:10.1186/1471-2105-14-33 |
GNU General Public License, v3 | OMICS_01052 | https://sources.debian.org/src/htqc/ | SCR_006448 | HTQC - Quality control and filtration for illumina sequencing data | 2026-09-03 05:04:30 | 43 | |||||
|
Avalon Cheminformatics Toolkit Resource Report Resource Website |
Avalon Cheminformatics Toolkit (RRID:SCR_014273) | software resource, software toolkit | Software toolkit containing tools to render and canonicalize SMILES and manipulate MOL file and related formats, as well as structure fingerprinting. | software toolkit, chemistry, canonicalize smiles, render smiles, manipulate mol file, structure fingerprinting | is listed by: SourceForge | Free, Available for download | SCR_014273 | 2026-09-03 05:04:49 | 0 | ||||||||||
|
BVA import/export EEGLAB plugin Resource Report Resource Website 1+ mentions |
BVA import/export EEGLAB plugin (RRID:SCR_016333) | bva-io | software application, software resource, software toolkit | 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. | interfacing, brain, vision, analyser, data, file, load, save, Matlab, routine, compatible, EEGLAB |
is related to: SourceForge is related to: EEGLAB is related to: MATLAB |
Free, Available for download, Freely available | SCR_016333 | Brain Vision Analyser | 2026-09-03 05:04:35 | 4 | ||||||||
|
CUDASW++ Resource Report Resource Website 1+ mentions |
CUDASW++ (RRID:SCR_008862) | CUDASW++ | software resource, source code | 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 | smith-waterman, bioinformatics, protein, protein database, sequence, simt, simd, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: SourceForge has parent organization: Nanyang Technological University; Singapore; Singapore |
PMID:19416548 PMID:20370891 |
Open-source | nlx_149212, biotools:cudasw | https://bio.tools/cudasw | SCR_008862 | CUDASW++ (Smith Waterman) | 2026-09-03 05:06:11 | 5 | |||||
|
PhenoFam Resource Report Resource Website |
PhenoFam (RRID:SCR_000640) | PhenoFam | software application, software resource | A web-based application that performs gene set enrichment analysis (GSEA) by employing structural and functional information on families of protein domains as annotation terms. | java, javascript, gene, gene set enrichment analysis, structure, function, protein domain, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:20478033 | Free, Available for download, Freely available | OMICS_02230, biotools:phenofam | https://bio.tools/phenofam | SCR_000640 | 2026-09-03 05:03:45 | 0 | ||||||
|
Magnolya Resource Report Resource Website 1+ mentions |
Magnolya (RRID:SCR_000164) | data analytics software, software application, software resource | A software which enables copy number variation (CNV) detections without using a reference genome. Magnolya directly compares the two next-generation sequences datasets. | algorithm, copy number, next-generation, reference genome, dataset comparison |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23047563 | Free, Available for download, Freely available | OMICS_00347 | SCR_000164 | 2026-09-03 05:03:53 | 2 | ||||||||
|
UTR Resource Report Resource Website |
UTR (RRID:SCR_000045) | software application, software resource, standalone software | Software application that uses change point model for detecting 3-prime UTR changes by RNA-Seq. | java, 3 prime utr, rna sequence, change point model, detecting 3-prime UTR changes, RNA-Seq |
uses: R Project for Statistical Computing has parent organization: SourceForge |
PMID:24728858 | Free, Available for download, Freely available | OMICS_04052 | SCR_000045 | 2026-09-03 05:03:57 | 0 | ||||||||
|
mzMatch Resource Report Resource Website 1+ mentions |
mzMatch (RRID:SCR_000543) | software resource, software toolkit | A software to provide small tools for common processing tasks for LC/MS data. It is an extension to the metabolomics analysis pipeline mzMatch.R. The software is modular, open source, platform independent and written in Java. | metabolomics, analysis, java, tool, peak extraction, filtering, normalization, derivative detection, identification, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:23162054 | Free, Available for download, Freely available, | biotools:mzmatch, OMICS_02642 | https://bio.tools/mzmatch | SCR_000543 | 2026-09-03 05:03:44 | 5 | |||||||
|
metabnorm Resource Report Resource Website |
metabnorm (RRID:SCR_001266) | software application, software resource, standalone software | Software tool as mixed model normalization method for metabolomics data.Uses normalization approach based on mixed model, with simultaneous estimation of correlation matrix. | Metabolomics datasets, corelation, normalization, identifying metabolites, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
Cancer Research UK Cambridge Institute ; Cancer Research UK ; Erik and Edith Fernström foundation |
PMID:24711654 | Free, Available for download, Freely available | OMICS_03548, biotools:metabnorm | https://bio.tools/metabnorm | SCR_001266 | 2026-09-03 05:04:33 | 0 | ||||||
|
Xournal Resource Report Resource Website |
Xournal (RRID:SCR_003233) | Xournal | software application, software resource | 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. | annotation, markup |
is listed by: FORCE11 has parent organization: SourceForge |
Free, Available for download, Freely available | nlx_157272 | SCR_003233 | 2026-09-03 05:04:20 | 0 | ||||||||
|
TARQUIN Resource Report Resource Website 50+ mentions |
TARQUIN (RRID:SCR_002598) | TARQUIN | software application, software resource | An analysis tool for automatically determining the quantities of molecules present in NMR spectroscopic data. The intended purpose of TARQUIN is to aid the characterisation of pathologies, in particular brain tumours, both non-invasively with in-vivo 1H MRS and ex-vivo with 1H HR-MAS. TARQUIN has the following features: * Free to use and modify under the GPL licence. * Based on a flexible time-domain fitting routine designed to give accurate rapid and automated quantitation for routine analysis. * Cross platform, works on Windows, Linux and OSX. * Comes packaged with a quantum mechanically based metabolite simulator to allow basis set construction optimised for the investigation of particular pathologies sequence parameters. * Includes both GUI and command line interface for one-off and batch analyses. | magnetic resonance, mrs, mas, molecule, nmr spectroscopy |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: SourceForge |
PMID:20878762 | Free, Available for download, Freely available | nlx_156002 | http://www.nitrc.org/projects/tarquin | SCR_002598 | TARQUIN MRS analysis package | 2026-09-03 05:03:34 | 64 | |||||
|
cnvHiTSeq Resource Report Resource Website 1+ mentions |
cnvHiTSeq (RRID:SCR_013160) | cnvHiTSeq | commercial organization, software resource | A set of Java-based command-line tools for detecting Copy Number Variants (CNVs) using next-generation sequencing data. | matlab |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23259578 | Commercial license | OMICS_00342 | SCR_013160 | cnvHiTSeq - A set of tools for detecting CNVs using sequencing data | 2026-09-03 05:08:00 | 4 |
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