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http://deweylab.biostat.wisc.edu/rsem/
Software package for quantifying gene and isoform abundances from single end or paired end RNA Seq data. Accurate transcript quantification from RNA Seq data with or without reference genome. Used for accurate quantification of gene and isoform expression from RNA-Seq data.
Proper citation: RSEM (RRID:SCR_000262) Copy
http://www.unavco.org/data/web-services/documentation/unavco-ws-api/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Web services to access UNAVCO data collection. Adding /gps, /met, /pore, /tilt, and /strain gives the sensor JSON description.
Proper citation: UNAVCO Geodetic Web Services (RRID:SCR_000181) Copy
http://harvard.eagle-i.net/i/0000012e-58c7-d44f-55da-381e80000000
Core to provide gene expression data analysis service. Activities range from the provision of services to fully collaborative grant funded investigations.
Proper citation: Harvard Partners HealthCare Center for Personalized Genetic Medicine Bioinformatics Core Facility (RRID:SCR_000882) Copy
http://www.bioconductor.org/packages/2.12/bioc/html/jmosaics.html
R software that detects enriched regions of ChIP-seq data sets jointly.
Proper citation: Jmosaics (RRID:SCR_001094) Copy
Harvard University''s central service for sharing and preserving work. In addition to the scholarly journal articles targeted by Harvard''s several open access resolutions, DASH maybe used to self-archive manuscripts and materials. DASH supports a variety of file formats, and users are encouraged to deposit related materials with manuscripts (including data, images, audio and video files, etc.) When users deposit their work in DASH, it becomes visible to colleagues around the world by virtue of metadata harvesting, Google Scholar, and other indexing services. Higher visibility leads to higher rates of citation and impact. When users post early versions of their work, before publication, they establish intellectual priority sooner. Users act in their own best interests by taking part in the University''s mission to share and preserve the knowledge produced there. Because Harvard now has a prior, non-exclusive license to faculty journal articles in schools with open access policies, those faculty members are required to act accordingly when publishing journal articles, either by attaching an addendum to their publication agreement or obtaining a waiver. They then must deposit the publication in DASH.
Proper citation: Digital Access to Scholarship at Harvard (RRID:SCR_004122) Copy
Open platform for analyzing and sharing neuroimaging data from human brain imaging research studies. Brain Imaging Data Structure ( BIDS) compliant database. Formerly known as OpenfMRI. Data archives to hold magnetic resonance imaging data. Platform for sharing MRI, MEG, EEG, iEEG, and ECoG data.
Proper citation: OpenNeuro (RRID:SCR_005031) Copy
https://www.ncbi.nlm.nih.gov/geo/
Functional genomics data repository supporting MIAME-compliant data submissions. Includes microarray-based experiments measuring the abundance of mRNA, genomic DNA, and protein molecules, as well as non-array-based technologies such as serial analysis of gene expression (SAGE) and mass spectrometry proteomic technology. Array- and sequence-based data are accepted. Collection of curated gene expression DataSets, as well as original Series and Platform records. The database can be searched using keywords, organism, DataSet type and authors. DataSet records contain additional resources including cluster tools and differential expression queries.
Proper citation: Gene Expression Omnibus (GEO) (RRID:SCR_005012) Copy
Seattle based independent, nonprofit medical research organization dedicated to accelerating the understanding of how human brain works. Provides free data and tools to researchers and educators and variety of unique online public resources for exploring the nervous system. Integrates gene expression data and neuroanatomy, along with data search and viewing tools, these resources are openly accessible via the Allen Brain Atlas data portal. Provides Allen Mouse Brain, Allen Spinal Cord Atlas, Allen Developing Mouse Brain Atlas, Allen Human Brain Atlas,Allen Mouse Brain Connectivity Atlas, Allen Cell Type Database, The Ivy Glioblastoma Atlas Project (Ivy GAP), The BrainSpan Atlas of the Developing Human Brain.
Proper citation: Allen Institute for Brain Science (RRID:SCR_006491) Copy
Issue
Software package for analysis of brain imaging data sequences. Sequences can be a series of images from different cohorts, or time-series from same subject. Current release is designed for analysis of fMRI, PET, SPECT, EEG and MEG.
Proper citation: SPM (RRID:SCR_007037) Copy
http://harvester.fzk.de/harvester/
Harvester is a Web-based tool that bulk-collects bioinformatic data on human proteins from various databases and prediction servers. It is a meta search engine for gene and protein information. It searches 16 major databases and prediction servers and combines the results on pregenerated HTML pages. In this way Harvester can provide comprehensive gene-protein information from different servers in a convenient and fast manner. As full text meta search engine, similar to Google trade mark, Harvester allows screening of the whole genome proteome for current protein functions and predictions in a few seconds. With Harvester it is now possible to compare and check the quality of different database entries and prediction algorithms on a single page. Sponsors: This work has been supported by the BMBF with grants 01GR0101 and 01KW0013.
Proper citation: Bioinformatic Harvester IV (beta) at Karlsruhe Institute of Technology (RRID:SCR_008017) Copy
Site for collection and distribution of clinical data related to genetic analysis of drug abuse phenotypes. Anonymous data on family structure, age, sex, clinical status, and diagnosis, DNA samples and cell line cultures, and data derived from genotyping and other genetic analyses of these clinical data and biomaterials, are distributed to qualified researchers studying genetics of mental disorders and other complex diseases at recognized biomedical research facilities. Phenotypic and Genetic data will be made available to general public on release dates through distribution mechanisms specified on website.
Proper citation: National Institute on Drug Abuse Center for Genetic Studies (RRID:SCR_013061) Copy
https://www.niaid.nih.gov/diseases-conditions/coronaviruses
Information about coronaviruses, including COVID-19. NIAID provides research funding and resources for scientific community to facilitate development of vaccines, therapeutics, and diagnostics for infectious diseases, including those caused by coronaviruses.
Proper citation: NIAID Overview of Coronaviruses (RRID:SCR_018290) Copy
https://github.com/nservant/HiC-Pro
Software tool as optimized and flexible pipeline for Hi-C data processing. Used to process Hi-C data, from raw fastq files, paired end Illumina data, to normalized contact maps.
Proper citation: HiC-Pro (RRID:SCR_017643) Copy
https://github.com/sansomlab/tenx
Pipeline for the analysis of 10x single cell RNA sequencing data. Collection of python3 pipelines and Rscripts to analyze data generated with the 10x Genomics platform. The pipelines are based on 10x's Cell Ranger pipeline for mapping and quantitation and the R Seurat package for downstream analysis.
Proper citation: tenx (RRID:SCR_016957) Copy
https://github.com/NOCIONS/letswave6/wiki/Download-and-setup
Open source electroencephalogram (EEG) signal processing toolbox to process and visualise EEG/MEG data and other neurophysiological signals.
Proper citation: Letswave (RRID:SCR_016414) Copy
https://www.fil.ion.ucl.ac.uk/spm/ext/#TSDiffAna
Software tool developed for Statistical Parametric Mapping (SPM) that computes slicewise scan by scan difference and standard deviations. Used to examine quality of image timeseries.
Proper citation: TSDiffAna (RRID:SCR_016656) Copy
http://www.nitrc.org/projects/nutil/
Software toolbox to simplify and streamline mechanism of pre and post processing 2D brain image data. Neuroscience image processing and analysis utilities. Stand alone application that runs on all operating systems.
Proper citation: Nutil - Neuroimaging utilities (RRID:SCR_017183) Copy
https://kidsfirstdrc.org/portal/portal-features/
Portal for analysis and interpretation of pediatric genomic and clinical data to advance personalized medicine for detection, therapy, and management of childhood cancer and structural birth defects. For patients, researchers, and clinicians to create centralized database of well curated clinical and genetic sequence data from patients with childhood cancer or structural birth defects.
Proper citation: Kids First Data Resource Portal (RRID:SCR_016493) Copy
Committee provides expert consultation on data elements and systems design for modeling and decision making for COVID-19 pandemic. Assembled at request of White House Office of Science and Technology Policy and Office of Assistant Secretary for Preparedness and Response in response to COVID-19 outbreak. Provides expert consultations on several topics, such as surface stability and incubation, social distancing, and crisis standards of care.
Proper citation: NASEM Standing Committee on Emerging Infectious Diseases and 21st Century Health Threats (RRID:SCR_018289) Copy
Cloud based platform for simplified, standardized and reproducible microbiome data analysis. Allows users to process microbiome datasets through pipelines of existing software tools.
Proper citation: Nephele (RRID:SCR_016595) Copy
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