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https://wholetale.org/

Platform for reproducible research. Code base for publishing data. For merging science and cyberinfrastructure pathways. Data Infrastructure Building Block (DIBBS) initiative to build scalable, open source, web-based, multi-user platform for reproducible research enabling creation, publication, and execution of tales – executable research objects that capture data, code, and complete software environment used to produce research findings. To enable researchers to define and create computational environment to manage complete conduct of computational experiments and expose them for analysis and reproducibility.

Proper citation: Whole Tale (RRID:SCR_017537) Copy   

•   Source: SciCrunch Registry

https://clarivate.com

Data analytics company that operates a collection of services: Web of Science (EndNote, InCites, Journal Citation Reports, Publons, Kopernio), Cortellis, Derwent, Derwent World Patents Index, CompuMark, MarkMonitor, Techstreet, Publons, EndNote, Kopernio, and ScholarOne. Deliver critical data, information, workflow solutions and deep domain expertise to innovators everywhere.

Proper citation: Clarivate Analytics (RRID:SCR_017657) Copy   

•   Source: SciCrunch Registry

http://nhprtr.org/

Nonhuman Primate reference transcriptome resource consisting of deep sequencing complete transcriptomes (RNA-seq) from multiple NHP species.

Proper citation: Nonhuman Primate Reference Transcriptome Resource (RRID:SCR_017534) Copy   

•   Source: SciCrunch Registry

https://github.com/Waller-Lab/DiffuserCam

Software tool as processing code. Alternating direction method of multipliers (ADMM) algorithm for recovering 3D volumes from 2D raw data captured with DiffuserCam.

Proper citation: DiffuserCam (RRID:SCR_017466) Copy   

•   Source: SciCrunch Registry

https://www.drugabuse.gov

Portal provides list of genetic resources such as Brain Atlases and genomes for various species provided by National Institute of Drug Abuse.

Proper citation: Compilation of Genetics Resource Databases (RRID:SCR_017501) Copy   

•   Source: SciCrunch Registry

https://www.jax.org/research-and-faculty/resources/optogenetics-resource

Mouse lines expressing proteins that activate, inhibit or detect neuronal activity are available from The Jackson Laboratory Repository. Many of these strains have been generated by HHMI Janelia Farm GENIE Project or by Allen Institute for Brain Science.

Proper citation: Optogenetics Resource at JAX (RRID:SCR_017508) Copy   

•   Source: SciCrunch Registry

https://github.com/cran/CopyNumber450kCancer

Software R package baseline correction for accurate copy number calling from 450k methylation array. Baseline correction for copy number data from cancer samples. Implements maximum density peak estimation (MDPE) method together with interactive reviewing to efficiently correct baseline in cancer samples.

Proper citation: CopyNumber450kCancer (RRID:SCR_017965) Copy   

•   Source: SciCrunch Registry

http://www.proteometools.org/index.php?id=home

Project for building molecular and digital tools from human proteome to facilitate biomedical research, drug discovery, personalized medicine and life science research.

Proper citation: ProteomeTools (RRID:SCR_018535) Copy   

•   Source: SciCrunch Registry

https://github.com/bjohnnyd/fs-tool

Software tool to calculate fraction of shared bound peptides between HLA proteins. Command-line tool to calculate fraction of shared bound peptides between HLA alleles from NetMHCpan binding predictions. Compares fraction shared between HLA allele and individual taking into account HLA and KIR genotypes.

Proper citation: fs-tool (RRID:SCR_018250) Copy   

•   Source: SciCrunch Registry

https://databrowser.researchallofus.org/

National research resource to provide interactive views of publicly available All of Us Research Program participant data including electronic health record data, biospecimens, surveys, and other measures taken at time of participant enrollment. Data platform will be open to researchers all over world and show data for groups of de-identified participants. Data is updated periodically.

Proper citation: Data Browser (RRID:SCR_017561) Copy   

•   Source: SciCrunch Registry

https://github.com/ncbi/SRPRISM/

Software tool as single read paired read indel substitution minimizer.

Proper citation: Single Read Paired Read Indel Substitution Minimizer (RRID:SCR_018023) Copy   

•   Source: SciCrunch Registry

https://github.com/nipy/heudiconv

Software tool as flexible DICOM converter for organizing brain imaging data into structured directory layouts.

Proper citation: HeuDiConv: a heuristic-centric DICOM converter (RRID:SCR_017427) Copy   

•   Source: SciCrunch Registry

https://github.com/lufuhao/ATACseqMappingPipeline

Software tool as pipeline to map ATAC-seq data to large genome, for example, for wheat. It splits large genome files into parts and do mapping and then finally merge them.

Proper citation: ATACseqMappingPipeline (RRID:SCR_017558) Copy   

•   Source: SciCrunch Registry

http://younglab.wi.mit.edu/super_enhancer_code.html

To create stitched enhancers, and to separate super enhancers from typical enhancers using sequencing data given file of previously identified constituent enhancers .

Proper citation: ROSE (RRID:SCR_017390) Copy   

•   Source: SciCrunch Registry

https://www.lungepigenome.org/

Project to provide data on genome and epigenome of human lung to facilitate research efforts of investigators studying diseases of lung including COVID-19.Collaboration among multiple groups at University of California including Center for Epigenomics, Gaulton lab and Sun lab at UCSD Department of Pediatrics. This work is conducted as part of LungMAP consortitum.

Proper citation: Lung Genome Browser (RRID:SCR_019255) Copy   

•   Source: SciCrunch Registry

https://broadinstitute.github.io/warp/docs/Pipelines/Single_Cell_ATAC_Seq_Pipeline/README

Pipeline developed in collaboration with Bing Ren lab and supports processing of BICCN single-cell/nucleus ATAC-seq datasets. Pipeline uses python module SnapTools to align and process paired reads in form of FASTQ files. Produces hdf5-structured Snap file that includes cell-by-bin count matrix. Final outputs also include GA4GH compliant aligned BAM and QC metrics.

Proper citation: scATAC Pipeline (RRID:SCR_018919) Copy   

•   Source: SciCrunch Registry

http://rgd.mcw.edu/rgdCuration/?module=portal&func=show&name=nuro

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. Portal that provides researchers with easy access to data on rat genes, QTLs, strain models, biological processes and pathways related to neurological diseases. This resource also includes dynamic data analysis tools.

Proper citation: Rat Genome Database: Neurological Disease Portal (RRID:SCR_008685) Copy   

•   Source: SciCrunch Registry

http://www.blogmydata.org/

Software tool for data sharing, incorporating blogs and spatial registration of data. Mainly used in geological data sets. A Virtual Research Environment (VRE) aims to combine the capabilities of two existing technologies that have already seen wide adoption among scientists: - The Godiva2 data visualization system provides a means for scientists to browse interactively in a ''Google Maps-like'' fashion through large environmental datasets, including numerical model outputs and high-resolution satellite imagery, using only a web browser. - The LabBlog is a web-based blogging tool specifically designed for the practising scientist to record, disseminate and evaluate their research. The Blog can also be used as a collaboration tool that allows secure discussion between colleagues. Although initially designed for the use of laboratory chemists, the LabBlog is being adapted in this project to meet the needs of environmental scientists. The BlogMyData VRE will allow scientists to explore data visually using Godiva2, then make comments about features in the data on a blog. Colleagues will discover these blog entries and offer further information, providing answers to research questions through comments. Through RSS and GeoRSS feeds, colleagues, investigators and other interested parties can be notified of research activity, and scientists can discover hitherto-unknown colleagues working with similar data in similar geographic regions. Sponsors: BlogMyData is a collaboration between the Reading e-Science Centre and the University of Southampton and is one of the JISC VRERI projects.

Proper citation: BlogMyData (RRID:SCR_008697) Copy   

•   Source: SciCrunch Registry

http://neuro-information.org/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. The International Observatory on Neuro-Information is the central source of knowledge, research and data on all skills and issues for Neuroscience applied in Information Sciences. It is an initiative of the Documentation Sciences Foundation, from Spain, which aims to gather information, express opinions, prepare documents, make comparative research, support and promote policy-making, evaluate trends, and take other appropriate action relating to the Neuroscience and its application to the Information Sciences (Libraries, Archives, Documentation centers), and how the traditional knowledge of Information Sciences can bring expertise in data visualization and retrieval techniques, records management, quality assurance and usability in Neuroscience. The Observatory may work together, or in agreement with other national or international organizations pursuing similar or compatible aims.

Proper citation: International Observatory on Neuro-Information (RRID:SCR_008690) Copy   

•   Source: SciCrunch Registry

https://www.brainproducts.com/

Commercial organization for hardware and software for neurophysiological research. Provides EEG and ERP amplifier systems, EEG recording caps, Data recording and analysis software, TMS Stimulator for combined EEG/TMS coregistrations and more.

Proper citation: Brain Products (RRID:SCR_009443) Copy   

•   Source: SciCrunch Registry