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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://www.broadinstitute.org/igv/

A high-performance visualization tool for interactive exploration of large, integrated genomic datasets.

Proper citation: Integrative Genomics Viewer (RRID:SCR_011793) 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://www.moleculardevices.com/Products/Software/GenePix-Pro.html

Industry standard microarray image analysis software because of its unique combination of imaging and analysis tools, visualizations, automation capabilities, performance and intuitive workflows.

Proper citation: GenePix Pro (RRID:SCR_010969) Copy   

•   Source: SciCrunch Registry

http://www.illumina.com/software/genomestudio_software.ilmn

Visualize and analyze data generated by all of Illumina''s platforms.

Proper citation: GenomeStudio (RRID:SCR_010973) Copy   

•   Source: SciCrunch Registry

http://www.bu.edu/jlab/wp-assets/ComBat/Abstract.html

Adjusting batch effects in microarray expression data using Empirical Bayes methods.

Proper citation: ComBat (RRID:SCR_010974) Copy   

•   Source: SciCrunch Registry

http://base.thep.lu.se/

A comprehensive management application for information, data, and analysis of microarray experiments, available as free open source software.

Proper citation: BASE (RRID:SCR_010937) Copy   

•   Source: SciCrunch Registry

http://linus.nci.nih.gov/BRB-ArrayTools.html

An integrated software package for the visualization and statistical analysis of DNA microarray gene expression data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: BRB-ArrayTools (RRID:SCR_010938) 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.jalview.org/

A free program for multiple sequence alignment editing, visualisation and analysis that is available in two forms: a lightweight Java applet for use in web applications, and a powerful desktop application that employs web services for sequence alignment, secondary structure prediction and the retrieval of alignments, sequences, annotation and structures from public databases and any DAS 1.53 compliant sequence or annotation server. Use it to view and edit sequence alignments, analyse them with phylogenetic trees and principal components analysis (PCA) plots and explore molecular structures and annotation. Jalview has built in DNA, RNA and protein sequence and structure visualisation and analysis capabilities. It uses Jmol to view 3D structures, and VARNA to display RNA secondary structure.

Proper citation: Jalview (RRID:SCR_006459) Copy   

•   Source: SciCrunch Registry

https://github.com/arq5x/bedtools2

A powerful toolset for genome arithmetic allowing one to address common genomics tasks such as finding feature overlaps and computing coverage. Bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF. While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), quite sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line.

Proper citation: BEDTools (RRID:SCR_006646) 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.bioconductor.org/packages/2.11/bioc/html/ShortRead.html

Software package for input, quality assessment and exploration of high-throughput sequence data. Used for input, quality assurance, and basic manipulation of `short read'' DNA sequences such as those produced by Solexa, 454, and related technologies, including exible import of common short read data formats.

Proper citation: ShortRead (RRID:SCR_006813) 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

http://www.definiens.com/research/tissue-studio/developer-xd

A development environment designed to create automated image analysis solutions for segmentation and classification tasks. It delivers quantitative and consistent data for any type of image (e.g., IHC, ISH, IF images in different formats). Developer XD also contains a large library of image analysis algorithms, which users can add to, for whole slide images and tissue microarrays (TMAs). It can be integrated with an existing Tissue Studio installation.

Proper citation: Definiens Developer XD (RRID:SCR_014283) Copy   

•   Source: SciCrunch Registry

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