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Repository for EEG data. The International Epilepsy Electrophysiology Portal is a collaborative initiative funded by the National Institutes of Neurological Disease and Stroke. This initiative seeks to advance research towards the understanding of epilepsy by providing a platform for sharing data, tools and expertise between researchers. The portal includes a large database of scientific data and tools to analyze these datasets.
Proper citation: ieeg.org (RRID:SCR_010000) Copy
http://hkbic.cuhk.edu.hk/software/abmapper
A portable, easy-to-use package for spliced alignment, junction site detection, and reads mapping. The core module was written in C++ and wrapped in PERL scripts.
Proper citation: ABMapper (RRID:SCR_010242) Copy
http://www.bioconductor.org/packages/release/bioc/html/RchyOptimyx.html
Software that constructs a hierarchy of cells using flow cytometry for maximization of an external variable (e.g., a clinical outcome or a cytokine response).
Proper citation: RchyOptimyx (RRID:SCR_001889) Copy
http://www.bioconductor.org/packages/2.13/bioc/html/cqn.html
A normalization tool for RNA-Seq data, implementing the conditional quantile normalization method.
Proper citation: CQN (RRID:SCR_001786) Copy
Portal for researchers to locate information relevant to interpretation and follow-up of human genetic epidemiological discoveries, including: a range of population and case and family genetic epidemiological studies, relevant gene and sequence databases, genetic variation databases, trait measurement, resource labs, journals, software, general information, disease genes and genetic diversity.
Proper citation: Online Encyclopedia for Genetic Epidemiology studies (RRID:SCR_001825) Copy
https://cran.r-project.org/src/contrib/Archive/PoissonSeq/
Software package that implements a method for normalization, testing, and false discovery rate estimation for RNA-sequencing data.
Proper citation: PoissonSeq (RRID:SCR_001784) Copy
Suite of motif-based sequence analysis tools to discover motifs using MEME, DREME (DNA only) or GLAM2 on groups of related DNA or protein sequences; search sequence databases with motifs using MAST, FIMO, MCAST or GLAM2SCAN; compare a motif to all motifs in a database of motifs; associate motifs with Gene Ontology terms via their putative target genes, and analyze motif enrichment using SpaMo or CentriMo. Source code, binaries and a web server are freely available for noncommercial use.
Proper citation: MEME Suite - Motif-based sequence analysis tools (RRID:SCR_001783) Copy
https://www.bioconductor.org/packages//2.10/bioc/html/spade.html
An analysis and visualization software tool for high dimensional flow cytometry data that organizes cells into hierarchies of related phenotypes.
Proper citation: SPADE (RRID:SCR_001810) Copy
http://www.kindai.ac.jp/english/
Private non-sectarian and coeducational university based in Higashiosaka, Osaka, Japan.
Proper citation: Kindai University; Osaka; Japan (RRID:SCR_001814) Copy
http://sammeth.net/confluence/display/ASTA/2+-+Download
Tool that extracts and displays alternative splicing (AS) events from a given genomic annotation of exon-intron gene coordinates. By comparing all given transcripts, it detects the variations in their splicing structure and identifies all AS events (like exon skipping, alternate donor, etc) by assigning to each of them an AS code. It provides a visual summary of the AS landscape in the analyzed dataset, the possibility to browse the results on the UCSC website or to download them in GTF or ASTA format. You can use AStalavista for any genome by providing your own annotation set, the identifier of your gene(s) of interest, or analyze the AS landscape of reference annotation datasets like Gencode, RefSeq, Ensembl, FlyBase, etc.
Proper citation: AStalavista (RRID:SCR_001815) Copy
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. A collaborative initiative of Parkinson's organizations dedicated to increasing education and awareness about clinical research. PDtrials provides up-to-date information on Parkinson's disease trials currently enrolling participants in the U.S. and Canada, as well as information about Parkinson's studies for people living with PD, their families and caregivers. Researchers can list their own trials on the PDtrials website. Patients can browse trial listings by type, location, symptom, or keyword.
Proper citation: PDtrials- Parkinsons Disease Clinical Trials (RRID:SCR_002027) Copy
Software package for a DNA assembly program designed for de novo assembly of 25-40mer input fragments and deep sequence coverage.
Proper citation: SHARCGS (RRID:SCR_002026) Copy
Retrieve known single-nucleotide polymorphisms (SNPs) by position or by association with a gene; save, filter, analyze, display or export SNP sets; explore known genes using names or chromosome positions.
Proper citation: SNPper (RRID:SCR_001963) Copy
We are the center of excellence for research and education on the prevention, understanding, and treatment of PTSD. Our Center has seven divisions across the country. Although we provide no direct clinical care, our purpose is to improve the well-being and understanding of American Veterans. We conduct cutting edge research and apply resultant findings to: Advance the Science and Promote Understanding of Traumatic Stress. The National Center has emerged as the world's leading research and educational center of excellence on PTSD. Its vision is to be the foremost leader in information on PTSD and trauma; information generated internally through its extensive research program, and information synthesized from published scientific research and collective clinical experience that is efficiently disseminated to the field. The Center is organized to facilitate rapid translation of science into practice, assuring that the latest research findings inform clinical care; and translation of practice into science, assuring that questions raised by clinical challenges are addressed using rigorous experimental protocols. By drawing on the specific expertise vested at each separate division (e.g., behavioral, neuroscientific, etc.), the National Center provides a unique infrastructure within which to implement multidisciplinary initiatives regarding the etiology, pathophysiology, diagnosis and treatment of PTSD.
Proper citation: National Center for PTSD (RRID:SCR_001967) Copy
A not-for-profit, volunteer based charity whose purpose is to find a cure for Parkinson's disease through research, advocacy, education and support services. Parkinson Society Canadas leads initiatives that include: raising funds for research through national events; funding research, movement disorder clinics, and outreach programs across Canada; staffing a national Information and Referral Centre; developing educational and information materials; providing up to date detailed information about Parkinson's disease; and providing support for regional partners to better meet the needs of people living with Parkinson's services. Researchers can apply for various funding awards and fellowships by following the funding process outlined by Parkinson Society Canada.
Proper citation: Parkinson Society Canada (RRID:SCR_002014) Copy
https://i4sa.com/wp-content/uploads/2021/01/1025ManualRevJ.pdf
Magnetic resonance compatible monitoring and gating system, including software, that enables monitoring rectal temperature, electrocardiogram and respiration rate during magnetic resonance imaging scan time. The PC displays multiple waveforms, measured values, trends and gating pulses. The data Acquisition modules are controlled by menu driven software from the PC. Data acquisition modules are available to measure the following parameters: ECG, respiration (three ways), temperature (two ways), pressure including invasive blood pressure (two ways), oxygen saturation and end-tidal CO2.
Proper citation: SA Instruments: Model 1025 MR-compatible Small Animal Monitoring and Gating System (RRID:SCR_002090) Copy
http://www.nih.go.kr/NIH/eng/main.jsp
Institute dedicated to medical research to improve biomedical innovation and public health in South Korea.
Proper citation: Korea National Institute of Health (RRID:SCR_001959) Copy
http://brainarray.mbni.med.umich.edu/Brainarray/Database/SearchSNP/snpfunc.aspx
Database for exploring the function implication of single nucleotide polymorphism (SNP) alleles. It is designed to be a clearing house for all public domain SNP functional annotation data, as well as in-house functional annotations derived from different data sources. It currently contains SNP functional annotations in six major categories including genomic elements, transcription regulation, protein function, pathway, disease and population genetics. Besides extensive SNP functional annotations, it includes a search engine that accepts different types of genetic markers as input and identifies all genetically related SNPs based on the HapMap Phase II data as well as the relationship of different markers to known genes. As a result, the system allows users to identify the potential biological impact of genetic markers and complex relationships among genetic markers and genes, and it greatly facilitates knowledge discovery in genome-wide SNP scanning experiments.
Proper citation: SNP Function Portal (RRID:SCR_001954) Copy
http://www.bioconductor.org/packages/release/bioc/html/flowType.html
Software for phenotyping Flow Cytometry assays using multidimentional expansion of single dimentional partitions.
Proper citation: flowType (RRID:SCR_001957) Copy
https://biosharing.org/collection/MIBBI
A common portal for minimum information (MI) checklists to act as a one-stop shop for those exploring the range of extant projects, foster collaborative development and ultimately promote gradual integration. Goals include * To increase the visibility of projects developing guidance for the reporting of biological and biomedical science. * To encourage appropriate collaborative development between projects to avoid duplication of effort or competition. * To promote the adoption of consensus guidance on reporting by journals and funders.
Proper citation: Minimum Information for Biological and Biomedical Investigations (RRID:SCR_002042) Copy
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