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

Software package to read bead-level data (raw TIFFs and text files) output by BeadScan as well as bead-summary data from BeadStudio. Methods for quality assessment and low-level analysis are provided.

Proper citation: beadarray (RRID:SCR_001314) Copy   

•   Source: SciCrunch Registry

https://posit.co/

Open source and enterprise ready professional software for R statistical computing environment. Integrated development environment for R. Includes console, syntax highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management. Available in open source and commercial editions and runs on desktop Windows, Mac, and Linux or in browser connected to RStudio Server or RStudio Server Pro (Debian/Ubuntu, RedHat/CentOS, and SUSE Linux).

Proper citation: RStudio (RRID:SCR_000432) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.ccdc.cam.ac.uk/Solutions/GoldSuite/Pages/GOLD.aspx

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software for virtual screening and identifying the binding mode of active molecules. It is comprehensively validated, widely used, and allows for high database enrichments. The software utilizes a novel methodology which avoids computationally expensive sequential docking of ligands into multiple protein structures.

Proper citation: GOLD (RRID:SCR_000188) Copy   

•   Source: SciCrunch Registry

http://proteinprophet.sourceforge.net/

Software that automatically validates protein identifications made on the basis of peptides assigned to MS/MS spectra by database search programs such as SEQUEST.

Proper citation: ProteinProphet (RRID:SCR_000286) Copy   

•   Source: SciCrunch Registry

http://graphpad.com/

A commercial graphing software company that offers scientific software for statistical analyses, curve fitting and data analysis. It offers four programs: Prism, InStat, StatMate and QuickCalcs.

Proper citation: GraphPad (RRID:SCR_000306) Copy   

•   Source: SciCrunch Registry

http://ims.cochrane.org/revman/about-revman-5

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023.A software package that does meta-analysis and provides results in tabular format and graphically., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: RevMan (RRID:SCR_003581) Copy   

•   Source: SciCrunch Registry

http://wiki.solariseclipse.net/PrimerDesigner

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2025. Software program to aid in designing of primers and creation of primer sheets. The program allows users to select a background and enter mutaions. An initial primer is then suggested. User can manipulate the selected primer to add or remove nucleotides from either 5? or 3? ends. A set of parameters reflecting the goodness of the primer is updated on the fly, as the user makes changes. Once happy with the primer, the information is saved in a primer sheet, which can then be uploaded to the BGME lab primer database on the Wiki.

Proper citation: Primer Designer (RRID:SCR_003189) Copy   

•   Source: SciCrunch Registry

http://www.bioextract.org/GuestLogin

An open, web-based system designed to aid researchers in the analysis of genomic data by providing a platform for the creation of bioinformatic workflows. Scientific workflows are created within the system by recording tasks performed by the user. These tasks may include querying multiple, distributed data sources, saving query results as searchable data extracts, and executing local and web-accessible analytic tools. The series of recorded tasks can then be saved as a reproducible, sharable workflow available for subsequent execution with the original or modified inputs and parameter settings. Integrated data resources include interfaces to the National Center for Biotechnology Information (NCBI) nucleotide and protein databases, the European Molecular Biology Laboratory (EMBL-Bank) non-redundant nucleotide database, the Universal Protein Resource (UniProt), and the UniProt Reference Clusters (UniRef) database. The system offers access to numerous preinstalled, curated analytic tools and also provides researchers with the option of selecting computational tools from a large list of web services including the European Molecular Biology Open Software Suite (EMBOSS), BioMoby, and the Kyoto Encyclopedia of Genes and Genomes (KEGG). The system further allows users to integrate local command line tools residing on their own computers through a client-side Java applet.

Proper citation: BioExtract (RRID:SCR_005397) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/hydra-sv/

Software that detects structural variation (SV) breakpoints by clustering discordant paired-end alignments whose signatures corroborate the same putative breakpoint. Hydra can detect breakpoints caused by all classes of structural variation. Moreover, it was designed to detect variation in both unique and duplicated genomic regions; therefore, it will examine paired-end reads having multiple discordant alignments. Hydra does not attempt to classify SV breakpoints based on the mapping distances and orientations of each breakpoint cluster, it merely detects and reports breakpoints. This is an intentional decision, as it was observed that in loci affected by complex rearrangements, the type of variant suggested by the breakpoint signature is not always correct. Hydra does report the orientations, distances, number of supporting read-pairs, etc., for each breakpoint. It is suggested that downstream methods be used to classify variants based on the genomic features that they overlap and the co-occurrence of other breakpoints. For example, they developed BEDTools for exactly this purpose and the breakpoints reported by Hydra are in the BEDPE format used by BEDTools. Future releases of Hydra will include scripts that assist in the classification process.

Proper citation: Hydra (RRID:SCR_005260) Copy   

•   Source: SciCrunch Registry

http://pass.cribi.unipd.it/cgi-bin/pass.pl

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 19, 2020.A program to align short sequences that has been developed with an innovative strategy to perform fast gapped and ungapped alignment onto a reference sequence. It supports several data formats and allows the user to modulate very finely the sensitivity of the alignments. The program is designed to handle huge amounts of short reads generated by ILLUMINA, SOLiD and Roche-454 technology. The optimization of the internal data structure and a filter based on precomputed short-word alignments allow the program to skip false positives in the extension phase, thus reducing the execution time without loss of sensitivity. The final alignment is performed by dynamic programming., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: PASS (RRID:SCR_005490) Copy   

•   Source: SciCrunch Registry

http://maq.sourceforge.net/

A set of programs that map and assemble fixed-length Solexa/SOLiD reads in a fast and accurate way.

Proper citation: Maq (RRID:SCR_005485) Copy   

•   Source: SciCrunch Registry

http://drive5.com/usearch/manual/uchime_algo.html

An algorithm for detecting chimeric sequences.

Proper citation: UCHIME (RRID:SCR_008057) Copy   

•   Source: SciCrunch Registry

http://www.scioncorp.com/pages/product_prices.htm#Software

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. Commercial software vendor.

Proper citation: Scion Image (RRID:SCR_008673) Copy   

•   Source: SciCrunch Registry

http://autodock.scripps.edu/

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   

•   Source: SciCrunch Registry

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

Software package that includes functions to retrieve the sequences around the peak, obtain enriched Gene Ontology terms, find the nearest gene, exon, miRNA or custom features such as most conserved elements.

Proper citation: ChIPpeakAnno (RRID:SCR_012828) Copy   

•   Source: SciCrunch Registry

http://repeatmasker.org/

Software tool that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). Currently over 56% of human genomic sequence is identified and masked by the program. Sequence comparisons in RepeatMasker are performed by one of several popular search engines including nhmmer, cross_match, ABBlast/WUBlast, RMBlast and Decypher. RepeatMasker makes use of curated libraries of repeats and currently supports Dfam ( profile HMM library ) and RepBase ( consensus sequence library ).

Proper citation: RepeatMasker (RRID:SCR_012954) Copy   

•   Source: SciCrunch Registry

http://www.ici.upmc.fr/cluego/

A Cytoscape plug-in that visualizes the non-redundant biological terms for large clusters of genes in a functionally grouped network. It can be used in combination with GOlorize. The identifiers can be uploaded from a text file or interactively from a network of Cytoscape. The type of identifiers supported can be easily extended by the user. ClueGO performs single cluster analysis and comparison of clusters. From the ontology sources used, the terms are selected by different filter criteria. The related terms which share similar associated genes can be combined to reduce redundancy. The ClueGO network is created with kappa statistics and reflects the relationships between the terms based on the similarity of their associated genes. On the network, the node colour can be switched between functional groups and clusters distribution. ClueGO charts are underlying the specificity and the common aspects of the biological role. The significance of the terms and groups is automatically calculated. ClueGO is easy updatable with the newest files from Gene Ontology and KEGG. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: ClueGO (RRID:SCR_005748) Copy   

•   Source: SciCrunch Registry

http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss

A software pipeline for analyzing ABySS-assembled contigs from shotgun transcriptome data.

Proper citation: Trans-ABySS (RRID:SCR_013322) Copy   

•   Source: SciCrunch Registry

http://www.eisenlab.org/eisen/?page_id=42

Software to graphically browse results of clustering and other analyses from Cluster.

Proper citation: TreeView (RRID:SCR_013503) Copy   

•   Source: SciCrunch Registry