Tools   Select Another Resource Report Type

http://homer.ucsd.edu/

Software tools for Motif Discovery and next-gen sequencing analysis. Used for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets. Collection of command line programs for unix style operating systems written in Perl and C++.

Proper citation: HOMER (RRID:SCR_010881) Copy   

•   Source: SciCrunch Registry

http://nipy.org

Community site to make brain imaging research easier that aims to build software that is clearly written, clearly explained, a good fit for the underlying ideas, and a natural home for collaboration.

Proper citation: Neuroimaging in Python (RRID:SCR_013141) Copy   

•   Source: SciCrunch Registry

Ratings or validation data are available for this resource

http://ccb.jhu.edu/software/tophat/index.shtml

Software tool for fast and high throughput alignment of shotgun cDNA sequencing reads generated by transcriptomics technologies. Fast splice junction mapper for RNA-Seq reads. Aligns RNA-Seq reads to mammalian-sized genomes using ultra high-throughput short read aligner Bowtie, and then analyzes mapping results to identify splice junctions between exons.TopHat2 is accurate alignment of transcriptomes in presence of insertions, deletions and gene fusions.

Proper citation: TopHat (RRID:SCR_013035) Copy   

•   Source: SciCrunch Registry

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

Software R package of functions and classes for the analysis of oligonucleotide arrays manufactured by Affymetrix. Used to process probe level data and for exploratory oligonucleotide array analysis.

Proper citation: affy (RRID:SCR_012835) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/edgeR/

Bioconductor software package for Empirical analysis of Digital Gene Expression data in R. Used for differential expression analysis of RNA-seq and digital gene expression data with biological replication.

Proper citation: edgeR (RRID:SCR_012802) Copy   

•   Source: SciCrunch Registry

http://PlasmoDB.org

Functional genomic database for malaria parasites. Database for Plasmodium spp. Provides resource for data analysis and visualization in gene-by-gene or genome-wide scale. PlasmoDB 5.5 contains annotated genomes, evidence of transcription, proteomics evidence, protein function evidence, population biology and evolution data. Data can be queried by selecting from query grid or drop down menus. Results can be combined with each other on query history page. Search results can be downloaded with associated functional data and registered users can store their query history for future retrieval or analysis.Key community database for malaria researchers, intersecting many types of laboratory and computational data, aggregated by gene.

Proper citation: PlasmoDB (RRID:SCR_013331) Copy   

•   Source: SciCrunch Registry

http://animaltracker.elte.hu/

A universal tracking application specifically designed to support animal behavioral analysis. AnimalTracker consists of three main modules which can be used independently: Tracker is responsible for image processing and providing the coordinates of the identified object; Zone Designer provides tools to create custom-made investigation areas in order to design a maze-setup; and Tracking Analyzer module serves to define and obtain the parameters needed for the evaluation.

Proper citation: AnimalTracker (RRID:SCR_014397) Copy   

•   Source: SciCrunch Registry

Ratings or validation data are available for this resource

http://www.olympus-lifescience.com/en/software/cellsens/

Software suite for image acquisition and analysis. The software can be paired with high-quality cameras to maximize output quality and export it for sharing and research applications.

Proper citation: Olympus cellSens Software (RRID:SCR_014551) Copy   

•   Source: SciCrunch Registry

http://www.ccdc.cam.ac.uk/free_services/relibase_free

Web-based system for searching and analysing protein-ligand structures in the Protein Data Bank (PDB). The database provides an easily accessible web-browser interface and clear 3D structure visualisation that allows for 3D protein-ligand interaction searches, automatic superimposition and detailed analysis of related binding sites to identify protein flexibility, ligand overlap, and conserved water positions.

Proper citation: Relibase (RRID:SCR_014888) Copy   

•   Source: SciCrunch Registry

http://www2.chemie.uni-erlangen.de/software/cactvs/

Computational chemistry related-software used for the computation management, analysis and visualisation of chemical information of any defined type. This software uses a worldwide network of databases with property descriptions, computational modules, data analysis tools, visualization servers, data type handlers and I/O modules to increase the software�s capacity extensibility.

Proper citation: CACTVS System (RRID:SCR_014919) Copy   

•   Source: SciCrunch Registry

http://www.analog-electronics.eu/slicap/slicap.html

A software toolbox containing a symbolic linear circuit analysis program. It is a MATLAB application that helps set up and solve design equations of electronic circuits.

Proper citation: SLiCAP (RRID:SCR_014742) 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

http://niag.ir/

Project to house templates used to build other projects. It is also known as the NeuroImaging and Analysis Group, which employs various physiological, functional and structural neuroimaging methodologies in both research and clinical domains.

Proper citation: Template Project (RRID:SCR_015516) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/voxbo

Software package for brain image manipulation and analysis, focusing on fMRI and lesion analysis. VoxBo can be used independently or in conjunction with other packages. It provides GLM-based statistical tools, an architecture for interoperability with other tools (they encourage users to incorporate SPM and FSL into their processing pipelines), an automation system, a system for parallel distributed computing, numerous stand-alone tools, decent wiki-based documentation, and lots more.

Proper citation: VoxBo (RRID:SCR_002166) 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://sourceforge.net/projects/bio-rainbow/

Software developed to provide an ultra-fast and memory-efficient solution to clustering and assembling short reads produced by RAD-seq.

Proper citation: Rainbow (RRID:SCR_002724) Copy   

•   Source: SciCrunch Registry

https://github.com/sqjin/CellChat

Software R toolkit for inference, visualization and analysis of cell-cell communication from single cell data.Quantitatively infers and analyzes intercellular communication networks from single-cell RNA-sequencing data. Predicts major signaling inputs and outputs for cells and how those cells and signals coordinate for functions using network analysis and pattern recognition approaches. Classifies signaling pathways and delineates conserved and context specific pathways across different datasets.

Proper citation: CellChat (RRID:SCR_021946) Copy   

•   Source: SciCrunch Registry

http://www.kcl.ac.uk/ioppn/depts/neuroimaging/research/imaginganalysis/Software/PIPR.aspx

Software toolbox designed to provide machine learning methods for pre-processed imaging data allowing for two (or more) class classification in the context of drug development. The Toolbox includes implementations of Gaussian Process Classification, Support Vector Machines, Ordinal Regression and Sparse Multinomial Logistic Regression for fMRI, Structural and ASL imaging data.

Proper citation: Pharmacological Imaging and Pattern Recognition toolbox (RRID:SCR_003874) Copy   

•   Source: SciCrunch Registry

http://www.clcbio.com/products/clc-main-workbench/

A suite of software for DNA, RNA and protein sequence data analysis. The software allows for the analysis and visualization of Sanger sequencing data as well as gene expression analysis, molecular cloning, primer design, phylogenetic analyses, and sequence data management.

Proper citation: CLC Main Workbench (RRID:SCR_000354) Copy   

•   Source: SciCrunch Registry

http://www.biochem.mpg.de/en/rd/baumeister/research/ContentCEM/Software_development

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software platform for low dose electron tomography (ET) for all processing steps: acquisition, alignment, reconstruction, and analysis. Requires: Matlab R2008a and Image Processing Toolbox (V6.1)

Proper citation: Acquisition and Analysis for Electron Tomography (RRID:SCR_000192) Copy   

•   Source: SciCrunch Registry