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https://resistomedb.com

Web tool to explore and visualize Antibiotic Resistance Genes found on Tara Oceans samples. Can be explored by individual ARG or grouped by antibiotic class.

Proper citation: ResistomeDB (RRID:SCR_018305) Copy   

•   Source: SciCrunch Registry

http://meme-suite.org/tools/dreme

Software tool to discover short, ungapped motifs (recurring, fixed-length patterns) that are relatively enriched in sequences compared with shuffled sequences or control sequences (sample output from sequences).

Proper citation: DREME (RRID:SCR_016860) Copy   

•   Source: SciCrunch Registry

http://platform.cerebellum.neuroinf.jp/

THIS RESOURCE IS NO LONGER IN SERVICE, documented January 13, 2022. Digital research archive for cerebellar research including mini-reviews of contemporary cerebellar research, list of papers and mathematical models for cerebellar operation.

Proper citation: Cerebellar Platform (RRID:SCR_001700) 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://github.com/jefferis/elmr

Software tool as support for working with light and electron microscopy fly brain data. Part of suite of R packages based on NeuroAnatomy Toolbox. Provides tools to move between adult brain EM and light level data, emphasising interaction between CATMAID web application and R Neuroanatomy Toolbox package.

Proper citation: elmr (RRID:SCR_017249) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/metagear/index.html

Software R package for research synthesis taxonomy from applying systematic review approach to assemble and screen literature, to extract data from studies, and to summarize and analyze these data with statistics of meta analysis.

Proper citation: metagear (RRID:SCR_017085) 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://ascl.net/

Registry for source codes of interest to astronomers and astrophysicists, including solar system astronomers, and lists codes that have been used in research that has appeared in, or been submitted to, peer-reviewed publications. ASCL is indexed by SAO/NASA Astrophysics Data System (ADS) and Web of Science and is citable by using unique ascl ID assigned to each code. The ascl ID can be used to link to the code entry by prefacing the number with ascl.net .

Proper citation: Astrophysics Source Code Library (RRID:SCR_017604) Copy   

•   Source: SciCrunch Registry

https://gitlab.com/biomerieux-data-science/clustlasso

Software R package to build predictive signatures of microbial phenotypes. Software package implementing cluster lasso approach.

Proper citation: clustLasso (RRID:SCR_018820) 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

https://github.com/alleninstitute/cocoframer

Software R package contains various functions for using the data from the Allen Mouse Brain Atlas that is registered to the Common Coordinate Framework. The functionality includes retrieving 3D, CCF aligned, gridded ISH data from the Allen Brain Atlas API, rendering 2D plots of slices of ISH data, retrieving the Mouse Brain Atlas structural ontology, and generating 3D plots of brain structures like those presented in the Allen Brain Explorer.

Proper citation: Cocoframer (RRID:SCR_023817) 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

http://harvard.eagle-i.net/i/0000012e-5e87-861a-55da-381e80000000

Core for data driven projects related to basic, clinical and translational research, with a particular emphasis on diabetes. Aims to ensure that researchers take advantage of the most modern and robust methods available in the field of Bioinformatics and Biostatistics.

Proper citation: Harvard Bioinformatics Core at Joslin Diabetes Center (RRID:SCR_009827) Copy   

•   Source: SciCrunch Registry

http://www.ukbiobank.ac.uk/

Biobank provides data collected at Assessment Center and via online questionnaires on participants aged 40-69 years recruited throughout United Kingdom and provides summary information to improve prevention, diagnosis and treatment of serious and life threatening illnesses.

Proper citation: UK Biobank (RRID:SCR_012815) Copy   

•   Source: SciCrunch Registry

http://www.sbpdiscovery.org/technology/sr/Pages/LaJolla_Crystallography.aspx

Facility equipped with X-ray crystallography equipment, such as the Rigaku FR-E SuperBright Ultra high-intensity rotating anode generator. The instrument is inteded for self-usage by trained users. It utilizes both ports with two independent diffraction stations that can run simultaneously. Each station is equipped with an X-stream cryogenic system for standard low temperature (~100 K) data collection. The system is used to collect high resolution diffraction data from native and inhibitor-bound crystals or to test and optimize diffraction quality (cryo-protectant conditions, etc.) and screen for further data collection at synchrotron sources.

Proper citation: Sanford Burnham Prebys Medical Discovery Institute X-ray Crystallography Facility (RRID:SCR_014860) Copy   

•   Source: SciCrunch Registry