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http://www.genabel.org/packages/GenABEL

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. R software library for genome-wide association analysis for quantitative, binary and time-till-event traits.

Proper citation: GenABEL (RRID:SCR_001842) Copy   

•   Source: SciCrunch Registry

http://surfer.nmr.mgh.harvard.edu/

Open source software suite for processing and analyzing human brain MRI images. Used for reconstruction of brain cortical surface from structural MRI data, and overlay of functional MRI data onto reconstructed surface. Contains automatic structural imaging stream for processing cross sectional and longitudinal data. Provides anatomical analysis tools, including: representation of cortical surface between white and gray matter, representation of the pial surface, segmentation of white matter from rest of brain, skull stripping, B1 bias field correction, nonlinear registration of cortical surface of individual with stereotaxic atlas, labeling of regions of cortical surface, statistical analysis of group morphometry differences, and labeling of subcortical brain structures.Operating System: Linux, macOS.

Proper citation: FreeSurfer (RRID:SCR_001847) Copy   

•   Source: SciCrunch Registry

http://jcb-dataviewer.rupress.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. A web-based, multi-dimensional image data-viewing application for original microscopy image datasets associated with articles published in The Journal of Cell Biology, a peer-reviewed journal published by The Rockefeller University Press. The JCB DataViewer can host multidimensional fluorescence microscopy images, 3D tomogram data, very large (gigapixel) images, and high content imaging screens. Images are presented in an interactive viewer, and the scores from high content screens are presented in interactive graphs with data points linked to the relevant images. The JCB DataViewer uses the Bio-Formats library to read over 120 different imaging file formats and convert them to the OME-TIFF image data standard. Image data are archived by the Journal and may be freely accessed by readers using the JCB DataViewer. Download of author-provided image data and associated metadata in OME-TIFF format is also possible with author permission, allowing for independent analysis of image data irrespective of acquisition or viewing software. Although the JCB DataViewer is designed to host and facilitate sharing and analysis of original microscopy image data, authors may also upload other types of original image data as supplements to their manuscripts, including histology and electron micrographs and digital scans of gels or blots.

Proper citation: JCB DataViewer (RRID:SCR_002633) Copy   

•   Source: SciCrunch Registry

http://www.fmrib.ox.ac.uk/fsl/

Software library of image analysis and statistical tools for fMRI, MRI and DTI brain imaging data. Include registration, atlases, diffusion MRI tools for parameter reconstruction and probabilistic taractography, and viewer. Several brain atlases, integrated into FSLView and Featquery, allow viewing of structural and cytoarchitectonic standard space labels and probability maps for cortical and subcortical structures and white matter tracts. Includes Harvard-Oxford cortical and subcortical structural atlases, Julich histological atlas, JHU DTI-based white-matter atlases, Oxford thalamic connectivity atlas, Talairach atlas, MNI structural atlas, and Cerebellum atlas.

Proper citation: FSL (RRID:SCR_002823) Copy   

•   Source: SciCrunch Registry

http://www.bioinformatics.nl/cgi-bin/primer3plus/primer3plus.cgi

A web interface to the Primer3 primer design program as an enhanced alternative for the CGI- scripts that come with Primer3.

Proper citation: Primer3Plus (RRID:SCR_003081) Copy   

•   Source: SciCrunch Registry

http://bibiserv.techfak.uni-bielefeld.de/dialign/

Tool for multiple sequence alignment using various sources of external information that is particularly useful to detect local homologies in sequences with low overall similarity. While standard alignment methods rely on comparing single residues and imposing gap penalties, DIALIGN constructs pairwise and multiple alignments by comparing entire segments of the sequences. No gap penalty is used. This approach can be used for both global and local alignment, but it is particularly successful in situations where sequences share only local homologies. Several versions of DIALIGN are available online at GOBICS, http://dialign.gobics.de/

Proper citation: DIALIGN (RRID:SCR_003041) Copy   

•   Source: SciCrunch Registry

https://www.schrodinger.com/glide

Software package which approximates a complete search of the conformational, orientational, and positional space of the ligand in a given receptor. Used in drug development for predicting protein ligand binding modes and ranking ligands via high throughput virtual screening.

Proper citation: Glide (RRID:SCR_000187) 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://www.wavemetrics.com/products/igorpro/igorpro.htm

Software used for visualizing and graphing data, image processing, and programming. It is designed for use by scientists and engineers and supports large data sets, evenly spaced data, and various data import formats. The software includes a suite of image processing operations for image filtering, manipulation, and quantification and is completely programmable.

Proper citation: IGOR Pro (RRID:SCR_000325) 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

http://www.mediacy.com/imageproplus

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 18,2023. Software package to capture, process, measure, analyze and share images and data.

Proper citation: Image Pro Plus (RRID:SCR_007369) 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

https://genorm.cmgg.be/

Software to determine most stable reference (housekeeping) genes from set of tested candidate reference genes in given sample panel. From this, gene expression normalization factor can be calculated for each sample based geometric mean of user-defined number of reference genes.

Proper citation: geNORM (RRID:SCR_006763) 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://shiny.chemgrid.org/boxplotr/

Web tool written in R for generation of box plots with R packages shiny, beanplot4, vioplot, beeswarm and RColorBrewer, and hosted on shiny server to allow for interactive data analysis. Data are held temporarily and discarded as soon as session terminates.Represents both summary statistics and distribution of primary data. Enables visualization of minimum, lower quartile, median, upper quartile and maximum of any data set.Data matrix can be uploaded as file or pasted into application. May be downloaded to run locally or as virtual machine for VMware and VirtualBox.

Proper citation: BoxPlotR (RRID:SCR_015629) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/oligo.html

Software package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files).

Proper citation: oligo (RRID:SCR_015729) Copy   

•   Source: SciCrunch Registry

http://www.softgenetics.com/GeneMarker.php

Genotype analysis software which enhances the speed, accuracy, and ease of analysis. The software is an alternative to Applied BioSystems Genotyper®, GeneScan®, and other genotype analysis software.

Proper citation: GeneMarker (RRID:SCR_015661) Copy   

•   Source: SciCrunch Registry