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http://www.bioconductor.org/packages/release/bioc/html/eisa.html

A biclustering method; it finds correlated blocks (transcription modules) in gene expression (or other tabular) data.

Proper citation: eisa (RRID:SCR_012883) Copy   

•   Source: SciCrunch Registry

http://www.geneprof.org/GeneProf/

A database of curated, integrated and reusable high-throughput genomics experiments and a web-based, graphical software suite that allows users to analyse data produced using high-throughput sequencing platforms (RNA-seq and ChIP-seq; Next-Generation Sequencing or NGS). Algorithm developers and computer programmers can develop their own modules and extend the functionality of GeneProf. Existing software can be easily wrapped and integrated in the GeneProf framework and data from GeneProf may be used externally.

Proper citation: GeneProf (RRID:SCR_012927) 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://bioconductor.org/packages/release/bioc/html/CSAR.html

Statistical tools for the analysis of ChIP-seq data.

Proper citation: CSAR (RRID:SCR_012930) Copy   

•   Source: SciCrunch Registry

https://github.com/jstjohn/SeqPrep

A program to merge paired end Illumina reads that are overlapping into a single longer read.

Proper citation: SeqPrep (RRID:SCR_013004) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.12/bioc/html/phyloseq.html

Software for handling and analysis of high-throughput microbiome census data.

Proper citation: phyloseq (RRID:SCR_013080) Copy   

•   Source: SciCrunch Registry

https://sites.google.com/site/quantisnp/

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.Software to detect rare or de novo copy number alterations in normal DNA samples. Please note that QuantiSNP is no longer under active development.

Proper citation: QuantiSNP (RRID:SCR_013091) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/amos/

A collection of tools and class interfaces for the assembly of DNA reads.

Proper citation: AMOS (RRID:SCR_013067) Copy   

•   Source: SciCrunch Registry

http://aluru-sun.ece.iastate.edu/doku.php?id=reptile

A software developed in C++ for correcting sequencing errors in short reads from next-gen sequencing platforms.

Proper citation: Reptile (RRID:SCR_013075) Copy   

•   Source: SciCrunch Registry

http://www.guidetopharmacology.org

Portal and searchable database of pharmacological information. Information is presented at two levels, the initial view or landing pages for each target family provide expert-curated overviews of the key properties and the available selective ligands and tool compounds. For selected targets, more detailed introductory chapters for each family are available along with curated information on the pharmacological, physiological, structural, genetic and pathophysiogical properties of each target.

Proper citation: IUPHAR/BPS Guide to Pharmacology (RRID:SCR_013077) Copy   

•   Source: SciCrunch Registry

http://www.sci.utah.edu/software/fluorender.html

Interactive rendering tool for confocal microscopy data visualization. Combines rendering of multi-channel volume data and polygon mesh data, where properties of each dataset can be adjusted independently and quickly. Designed for neurobiologists, allowing them to better visualize confocal data from fluorescently-stained brains, but it is also useful for other biological samples. Features include feature tracking, 3D measurement tools, multiple render modes for multi-channel confocal data, and volume paint selection and segmentation.

Proper citation: FluoRender (RRID:SCR_014303) Copy   

•   Source: SciCrunch Registry

https://cmiclab.cs.ucl.ac.uk/CMIC/NiftyFit-Release

Software package for multi-parametric model-fitting of 4D Magnetic Resonance Imaging data. Software library to facilitate voxel wise fitting on a number of datatypes including T1 and T2 relaxometry, Arterial Spin Labeled MRI, Diffusion Weighted Imaging and Dynamic Contrast Enhanced MRI. T

Proper citation: NiftyFit (RRID:SCR_014301) Copy   

•   Source: SciCrunch Registry

http://bioinfo.lifl.fr/RNA/sortmerna/

Sequence analysis software for filtering, mapping and OTU-picking NGS reads. SortMeRNA takes as input a file of reads (fasta or fastq format) and one or multiple rRNA database file(s), and sorts apart rRNA and rejected reads into two files specified by the user., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SortMeRNA (RRID:SCR_014402) Copy   

•   Source: SciCrunch Registry

http://www.matrixscience.com/server.html

A software package and server used to identify and characterize proteins from primary sequence databases using mass spectrometry data. Mascot integrates peptide mass fingerprinting, sequence querying, and MS/MS ion searching in order to search for proteins in databases like SwissProt, NCBInr, EMBL EST divisions, contaminants, and cRAP. If a license is purchased, users may: search data sets that exceed the 1200 spectrum limit of the free version; set up automated, high throughput work; add and edit proteins and quantification methods; and search a preferred collection of sequence databases. The software package works with instruments from AB Sciex, Agilent, Bruker, Jeol, Shimadzu, Thermo Scientific, and Waters.

Proper citation: Mascot (RRID:SCR_014322) Copy   

•   Source: SciCrunch Registry

http://www.openworm.org/

3D web browser that allows users to simulate and dissect virtual C. elegans. Users can explore the anatomy of a virtual, 3D worm by zooming in and out, rotating the model, and viewing the worm's different layers. NeuroML format and connector are used to enhance the simulation, and supporting programs and code are available for coders.

Proper citation: OpenWorm (RRID:SCR_014650) Copy   

•   Source: SciCrunch Registry

http://darwin.uvigo.es/software/prottest_server.html

Web-based software used for the selection of best-fit models of protein evolution., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: ProtTest (RRID:SCR_014628) Copy   

•   Source: SciCrunch Registry

http://fatcat.burnham.org/

Web server for flexible protein structure comparison. Structure alignment is formulated as the aligned fragment pairs chaining process allowing at most t twists, and the flexible structure alignment is transformed into a rigid structure alignment when t is forced to be 0., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: FATCAT (RRID:SCR_014631) Copy   

•   Source: SciCrunch Registry

http://compbio.mit.edu/cummeRbund/index.html

Software R package used for simplifying and analyzing Cufflink RNA-Seq output. This program takes various output files from a cuffdiff run and creates a SQLite database of the results that will describe the appropriate relationships between the genes, transcripts, transcription start sites and CDS regions.

Proper citation: CummeRbund (RRID:SCR_014568) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/ggplot2/index.html

Open source software package for statistical programming language R to create plots based on grammar of graphics. Used for data visualization to break up graphs into semantic components such as scales and layers.

Proper citation: ggplot2 (RRID:SCR_014601) Copy   

•   Source: SciCrunch Registry

http://metastats.cbcb.umd.edu/detection.html

A statistical software package for comparing metagenomic datasets and clinical data sets comprised of two treatment populations, with each treatment population being made up of multiple samples. It relies on a non-parametric t-test.

Proper citation: Metastats (RRID:SCR_014610) Copy   

•   Source: SciCrunch Registry