Tools   Select Another Resource Report Type

https://github.com/legrandp/xdsme

Software package of python scripts made to simplify the processing of crystal diffraction images.

Proper citation: XDSME (RRID:SCR_016943) Copy   

•   Source: SciCrunch Registry

https://www.mbfbioscience.com/neurolucida360

Software for automatic neuron 3D reconstruction and analysis. Used by neuroscientists to reconstruct intricate neuronal structures that range in scale from complex, multicellular networks of neurons to sub-cellular dendritic spines and putative synapses.

Proper citation: Neurolucida 360 (RRID:SCR_016788) Copy   

•   Source: SciCrunch Registry

https://www.networkanalyst.ca/

Web tool for gene expression profiling, meta-analysis and systems understanding. Used for statistical, visual and network-based meta-analysis of gene expression data.

Proper citation: NetworkAnalyst (RRID:SCR_016909) Copy   

•   Source: SciCrunch Registry

http://prosightlite.northwestern.edu/

Software application for matching a single candidate protein sequence and its modifications against a set of mass spectrometric observations. Used to analyze top-down mass spectrometry data.

Proper citation: ProSight Lite (RRID:SCR_016908) Copy   

•   Source: SciCrunch Registry

https://github.com/PGB-LIV/VAPPER

Software tool for analysis of variant antigens in African trypanosomes. Used for quantitative analysis of antigenic diversity in systems data of genomes, transcriptomes, and proteomes, called Variant Antigen Profiling to understand how antigenic diversity relates to clinical outcome, how antigen genes may be used as epidemiological markers of virulence, and in measuring gene expression during experimental infections.

Proper citation: VAPPER (RRID:SCR_016993) Copy   

•   Source: SciCrunch Registry

http://marrvel.org/

Web tool to search multiple public variant databases simultaneously and provide a unified interface to facilitate the search process. Used for integration of human and model organism genetic resources to facilitate functional annotation of the human genome. Used for analysis of human genes and variants by cross-disciplinary integration of records available in public databases to facilitate clinical diagnosis and basic research.

Proper citation: MARRVEL (RRID:SCR_016871) Copy   

•   Source: SciCrunch Registry

http://cab.spbu.ru/software/rnaspades/

Software tool for assembling transcripts from RNA-Seq data. Explores surprising computational parallels between assembly of transcriptomes and single cell genomes. Suitable for all kind of organisms. Part of SPAdes package since version 3.9.

Proper citation: rnaSPAdes (RRID:SCR_016992) Copy   

•   Source: SciCrunch Registry

https://github.com/Crop-Phenomics-Group/CropSight

Software tool which is a PHP and SQL based server platform. Provides automated data collation, storage, and information management through distributed IoT sensors and phenotyping workstations. It provides a two-component solution to monitor biological experiments through networked sensing devices, with interfaces specifically designed for distributed plant phenotyping and centralized data management.

Proper citation: CropSight (RRID:SCR_016870) Copy   

•   Source: SciCrunch Registry

https://github.com/PathwayAnalysisPlatform/PathwayMatcher

Software tool for multi omics pathway mapping and proteoform network generation. Open source software writen in Java to search for pathways related to a list of proteins in Reactome.

Proper citation: PathwayMatcher (RRID:SCR_016759) Copy   

•   Source: SciCrunch Registry

https://github.com/reinkk/Growth-Profiling-Toolbox

Software package as a growth curve automatic processing pipeline in Matlab.

Proper citation: Growth Profiling Toolbox (RRID:SCR_016878) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/jtreeview/

Software as a cross platform gene expression visualization tool. Extensible viewer for microarray data in the PCL or CDT format. Interactive display of clustered gene expression data. Java application for visualizing large data matrices. It can load a dataset, cluster it, browse it, customize its appearance and export it into a figure.

Proper citation: Java Treeview (RRID:SCR_016916) Copy   

•   Source: SciCrunch Registry

https://pachterlab.github.io/sleuth/about

Software tool for analysis of RNA-Seq experiments for which transcript abundances have been quantified with kallisto. Used for the differential analysis of gene expression data that utilizes bootstrapping in conjunction with response error linear modeling to decouple biological variance from inferential variance.

Proper citation: sleuth (RRID:SCR_016883) Copy   

•   Source: SciCrunch Registry

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

Software R package for multivariate analysis and feature selection of omics data. Used for visualization, regression, classification, and feature selection of omics data where the number of variables exceeds the number of samples and with multicollinearity among variables.

Proper citation: ropls (RRID:SCR_016888) Copy   

•   Source: SciCrunch Registry

http://www.bx.psu.edu/~giardine/vision/

International project to analyze mouse and human hematopoiesis, and provide a tractable system with clear clinical significance and importance to NIDDK. Collection of information from the flood of epigenomic data on hematopoietic cells as catalogs of validated regulatory modules, quantitative models for gene regulation, and a guide for translation of research insights from mouse to human.

Proper citation: ValIdated Systematic IntegratiON of epigenomic data (RRID:SCR_016921) Copy   

•   Source: SciCrunch Registry

http://www.thomaskoenig.ch/index.php/software/ragu

Software tool for the analysis of EEG and MEG event-related scalp field data using global randomization statistics.

Proper citation: Ragu (RRID:SCR_016851) Copy   

•   Source: SciCrunch Registry

https://sites.google.com/view/diegoalvarezestevez/projects/polyman

Software tool as an European Data Format EDF/EDF+ viewer and manual sleep scoring program. Used in EEG and Sleep investigations, but can be used for almost any (also non-medical) sequential time series and event lists.

Proper citation: Polyman (RRID:SCR_016850) Copy   

•   Source: SciCrunch Registry

https://github.com/yarden/MISO/blob/fastmiso/docs/source/sashimi.rst

Software tool for quantitative visualization of aligned RNA-Seq reads that enables quantitative comparison of exon usage across samples or experimental conditions.

Proper citation: Sashimiplot (RRID:SCR_016861) Copy   

•   Source: SciCrunch Registry

https://github.com/CPernet/spmup/

Software Project Management (SPM) tools which contain a collection of functions that can be used at different stage of a standard massive univariate fMRI data analysis. Used to improve mass univariate analysis.

Proper citation: SPM U+ (RRID:SCR_016743) Copy   

•   Source: SciCrunch Registry

https://networkx.github.io/

Software Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.

Proper citation: NetworkX (RRID:SCR_016864) Copy   

•   Source: SciCrunch Registry

https://github.com/TGAC/RAMPART

Software for workflow management system for de novo genome assembly of DNA sequence data.Designed to exploit high performance computing environments, such as clusters and shared memory systems.

Proper citation: Rampart (RRID:SCR_016742) Copy   

•   Source: SciCrunch Registry