Tools   Select Another Resource Report Type

https://github.com/ISUgenomics/SequelQC

Software tool that calculates key statistics and generates publication quality plots for raw PacBio Sequel data. Open source software for analyzing PacBio Sequel raw sequence data.

Proper citation: SequelQC (RRID:SCR_017279) Copy   

•   Source: SciCrunch Registry

https://www.qtiplot.com/

Software tool for data analysis and scientific visualization by IONDEV SRL.

Proper citation: QtiPlot (RRID:SCR_017311) Copy   

•   Source: SciCrunch Registry

http://www.bioisis.net

Software JAVA based application for basic analysis of Small Angle X-ray Scattering datasets.

Proper citation: SCÅTTER (RRID:SCR_017271) Copy   

•   Source: SciCrunch Registry

https://www.immport.org/home

Data sharing repository of clinical trials, associated mechanistic studies, and other basic and applied immunology research programs. Platform to store, analyze, and exchange datasets for immune mediated diseases. Data supplied by NIAID/DAIT funded investigators and genomic, proteomic, and other data relevant to research of these programs extracted from public databases. Provides data analysis tools and immunology focused ontology to advance research in basic and clinical immunology.

Proper citation: The Immunology Database and Analysis Portal (ImmPort) (RRID:SCR_012804) Copy   

•   Source: SciCrunch Registry

http://www.hedtags.org/

Strategy guide for HED Annotation. Framework for systematically describing laboratory and real world events.HED tags are comma separated path strings. Organized in forest of groups with roots Event, Item, Sensory presentation, Attribute, Action, Participant, Experiment context, and Paradigm. Used for preparing brain imaging data for automated analysis and meta analysis. Applied to brain imaging EEG, MEG, fNIRS, multimodal mobile brain or body imaging, ECG, EMG, GSR, or behavioral data. Part of Brain Imaging Data Structure standard for brain imaging.

Proper citation: HED Tags (RRID:SCR_014074) Copy   

•   Source: SciCrunch Registry

https://skyline.gs.washington.edu/labkey/project/home/software/Skyline/begin.view

Software tool as Windows client application for targeted proteomics method creation and quantitative data analysis. Open source document editor for creating and analyzing targeted proteomics experiments. Used for large scale quantitative mass spectrometry studies in life sciences.

Proper citation: Skyline (RRID:SCR_014080) Copy   

•   Source: SciCrunch Registry

http://www.originlab.com/index.aspx?go=PRODUCTS/Origin

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 4, 2025.Software application for data analysis and graphing. Origin contains a variety of different graph types, including statistical plots, 2D and 3D vector graphs, and counter graphs. More advance version is OriginPro which offers advanced analysis tools and Apps for Peak Fitting, Surface Fitting, Statistics and Signal Processing.

Proper citation: Origin (RRID:SCR_014212) Copy   

•   Source: SciCrunch Registry

http://factominer.free.fr/index.html

Software R package for multivariate analysis which takes into account different types of data structure. Data can be organized in groups of variable, groups of individuals, or into hierarchy of variables.

Proper citation: FactoMineR (RRID:SCR_014602) Copy   

•   Source: SciCrunch Registry

http://www.heka.com/downloads/downloads_main.html#down_tida

A software which is used to acquire physiological data from the HEKA Patch Clamp Amplifiers and HEKA interfaces.

Proper citation: TIDA (RRID:SCR_014582) Copy   

•   Source: SciCrunch Registry

http://web.bioinformatics.ic.ac.uk/eqtlexplorer/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1,2023. eQTL Explorer was developed as a computational resource to visualize and explore data from combined genome-wide expression and linkage studies is essential for the development of testable hypotheses. This visualization tool stores expression profiles, linkage data and information from external sources in a relational database and enables simultaneous visualization and intuitive interpretation of the combined data via a Java graphical interface. eQTL Explorer also provides a new and powerful tool to interrogate these very large and complex datasets. eQTLexplorer allows users to mine and understand data from a repository of genetical genomics experiments. It will graphically display eQTL information based on a certain number of selection criteria, including: tissue type, p-value, cis/trans, probeset Affymetrix id and PQTL type. Sponsors: This work was funded by the MRC Clinical Sciences Centre and the Wellcome Trust programme for Cardiovascular Functional Genomics.

Proper citation: eQTL Visualization Tool (RRID:SCR_013413) Copy   

•   Source: SciCrunch Registry

http://www.sas.com

Software platform to explore, analyze and visualize data. SAS 9.4 is part of SAS Platform. Standardized data governance and management from statistical software company SAS.

Proper citation: Statistical Analysis System (RRID:SCR_008567) Copy   

•   Source: SciCrunch Registry

http://www.statsoft.com/Products/STATISTICA/Product-Index

Analytics platform with various sub platforms, each with specific performance capabilities for tasks such as data analysis, data management, data visualization, and data mining procedures.

Proper citation: STATISTICA (RRID:SCR_014213) Copy   

•   Source: SciCrunch Registry

https://cibersort.stanford.edu/

Software tool to provide an estimation of the abundances of member cell types in a mixed cell population, using gene expression data. Used for characterizing cell composition of complex tissues from their gene expression profiles, large scale analysis of RNA mixtures for cellular biomarkers and therapeutic targets.

Proper citation: CIBERSORT (RRID:SCR_016955) Copy   

•   Source: SciCrunch Registry

https://github.com/AllenInstitute/scrattch.hicat

Software R package as hierarchical, iterative clustering for analysis of transcriptomics data.Used for single cell RNA-seq analysis for transcriptomic type characterization from Allen Institute.

Proper citation: Scrattch.Hicat (RRID:SCR_018099) Copy   

•   Source: SciCrunch Registry

https://github.com/quest-bih/oddpub

Text mining algorithm to screen biomedical publications to find data sharing statements. Algorithm that parses set of publications and detects which publications disseminated Open Data or Open Code together with publication. Tailored towards biomedical literature.

Proper citation: ODDPub (RRID:SCR_018385) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/bva-io/

Software package for interfacing the Brain Vision Analyser data files (load/save) for ongoing development of Matlab routines . This package is also compatible with the EEGLAB software, and may be uncompressed in the plugin folder of this software.

Proper citation: BVA import/export EEGLAB plugin (RRID:SCR_016333) Copy   

•   Source: SciCrunch Registry

http://www.broad.mit.edu/mpr/lung

Data set of a molecular taxonomy of lung carcinoma, the leading cause of cancer death in the United States and worldwide. Using oligonucleotide microarrays, researchers analyzed mRNA expression levels corresponding to 12,600 transcript sequences in 186 lung tumor samples, including 139 adenocarcinomas resected from the lung. Hierarchical and probabilistic clustering of expression data defined distinct sub-classes of lung adenocarcinoma. Among these were tumors with high relative expression of neuroendocrine genes and of type II pneumocyte genes, respectively. Retrospective analysis revealed a less favorable outcome for the adenocarcinomas with neuroendocrine gene expression. The diagnostic potential of expression profiling is emphasized by its ability to discriminate primary lung adenocarcinomas from metastases of extra-pulmonary origin. These results suggest that integration of expression profile data with clinical parameters could aid in diagnosis of lung cancer patients.

Proper citation: Classification of Human Lung Carcinomas by mRNA Expression Profiling Reveals Distinct Adenocarcinoma Sub-classes (RRID:SCR_003010) Copy   

•   Source: SciCrunch Registry

http://eyebrowse.cit.nih.gov/

EyeBrowse displays expressed sequence tag (EST) cDNA clones from eye tissues (derived from NEIBank and other sources) aligned with current versions of the human, rhesus, mouse, rat, dog, cow, chicken, or zebrafish genomes, including reference sequences for known genes. This gives a simplified view of gene expression activity from different parts of the eye across the genome. The data can be interrogated in several ways. Specific gene names can be entered into the search window. Alternatively, regions of the genome can be displayed. For example, entering two STS markers separated by a semicolon (e.g. RH18061;RH80175) allows the display of the entire chromosomal region associated with the mapping of a specific disease locus. ESTs for each tissue can then be displayed to help in the selection of candidate genes. In addition, sequences can be entered into a BLAT search and rapidly aligned on the genome, again showing eye derived ESTs for the same region. EyeBrowse includes a custom track display SAGE data for human eye tissues derived from the EyeSAGE project. The track shows the normalized sum of SAGE tag counts from all published eye-related SAGE datasets centered on the position of each identifiable Unigene cluster. This indicates relative activity of each gene locus in eye. Clicking on the vertical count bar for a particular location will bring up a display listing gene details and linking to specific SAGE counts for each eye SAGE library and comparisons with normalized sums for neural and non-neural tissues. To view or alter settings for the EyeSAGE track on EyeBrowse, click on the vertical gray bar at the left of the display. Other custom tracks display known eye disease genes and mapped intervals for candidate loci for retinal disease, cataract, myopia and cornea disease. These link back to further information at NEIBank. For mouse, there is custom track data for ChIP-on-Chip of RNA-Polymerase-II during photoreceptor maturation.

Proper citation: EyeBrowse (RRID:SCR_008000) Copy   

•   Source: SciCrunch Registry

https://cancer.dartmouth.edu/researchers/bioinformatics-resource.html

THIS RESOURCE IS NO LONGER IN SERVICE.Documented on July 29,2022. Core to support the implementation of bioinformatics resources for cancer research at Dartmouth. Provides consultation and collaboration for research projects of NCCC members, regular workshops, seminars, services including applied bioinformatics and data mining, computer programming and software engineering, database development and programming and high performance computing and systems administration.

Proper citation: Dartmouth-Hitchcock Bioinformatics Shared Resource (RRID:SCR_009758) Copy   

•   Source: SciCrunch Registry

http://howard.eagle-i.net/i/00000134-a517-1426-bf4c-ca4080000000

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 27,2023. Core for bioinformatics consultation and software access. Laboratory of Molecular Computations and Bioinformatics (LMCB) is a resource facility dedicated to the support of computational biomedical research at Howard University. Provides molecular modeling, molecular dynamics, bioinformatics, and computational quantum chemistry capabilities and support to a variety of research projects at Howard University.

Proper citation: Howard University Center for Computational Biology and Bioinformatics Core Facility (RRID:SCR_009864) Copy   

•   Source: SciCrunch Registry