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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://www.glygen.org

Data integration and dissemination project for carbohydrate and glycoconjugate related data. Computational and informatics resources for glycoscience. Portal provides user-friendly interface that facilitates exploration of glycoscience data from diverse international bioinformatics resources, including National Center for Biotechnology Information (NCBI), UniProt, Protein Data Bank (PDB), UniCarbKB, and GlyTouCan glycan structure repository. Retrieves information from data sources and integrates and harmonizes this data. Includes knowledge about molecular, biophysical and functional properties of glycans, genes, proteins and lipids organized in pathways and ontologies, plus data related to mutation and expression.

Proper citation: GlyGen (RRID:SCR_023438) Copy   

•   Source: SciCrunch Registry
  

https://cran.r-project.org/package=wavethresh

Software R package to perform 1, 2 and 3D real and complex-valued wavelet transforms, nondecimated transforms, wavelet packet transforms, nondecimated wavelet packet transforms, multiple wavelet transforms, complex-valued wavelet transforms, wavelet shrinkage for various kinds of data, locally stationary wavelet time series, nonstationary multiscale transfer function modeling, density estimation.

Proper citation: wavethresh (RRID:SCR_024311) Copy   

•   Source: SciCrunch Registry
  

http://pmap.burnham.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23, 2022. A database of proteolytic pathways. Its goal is to contribute to the scientific community and the understanding of proteolysis by providing better tools and data to researchers and medical researchers.

Proper citation: PMAP (RRID:SCR_000740) Copy   

•   Source: SciCrunch Registry
  

https://wiki.nci.nih.gov/display/cageneindex/Cancer+Gene+Index+End+User+Documentation

THIS RESOURCE IS NO LONGER IN SERVICE, documented on November 17, 2016. A database of genes that have been experimentally associated with human cancer diseases and/or pharmacological compounds, the evidence of these associations, and relevant annotations on the data.

Proper citation: Cancer Gene Index (RRID:SCR_001117) Copy   

•   Source: SciCrunch Registry
  

https://epd.expasy.org/epd/

EPDnew databases are the result of merging Eukaryotic Promoter Database, EPD, promoters within house analysis of promoter specific high throughput data for selected organisms only. EPDnew is a set of species specific databases of experimentally validated promoters.

Proper citation: EPDnew (RRID:SCR_002485) Copy   

•   Source: SciCrunch Registry
  

https://pdc.cancer.gov/pdc/

Portal to make cancer related proteomic datasets easily accessible to public. Facilitates multiomic integration in support of precision medicine through interoperability with other resources. Developed to advance our understanding of how proteins help to shape risk, diagnosis, development, progression, and treatment of cancer. One of several repositories within NCI Cancer Research Data Commons which enables researchers to link proteomic data with other data sets (e.g., genomic and imaging data) and to submit, collect, analyze, store, and share data throughout cancer data ecosystem. PDC provides access to highly curated and standardized biospecimen, clinical, and proteomic data, intuitive interface to filter, query, search, visualize and download data and metadata. Provides common data harmonization pipeline to uniformly analyze all PDC data and provides advanced visualization of quantitative information. Cloud based (Amazon Web Services) infrastructure facilitates interoperability with AWS based data analysis tools and platforms natively. Application programming interface (API) provides cloud-agnostic data access and allows third parties to extend functionality beyond PDC. Structured workspace that serves as private user data store and also data submission portal. Distributes controlled access data, such as patient-specific protein fasta sequence databases, with dbGaP authorization and eRA Commons authentication.

Proper citation: Proteomic Data Commons (RRID:SCR_018273) Copy   

•   Source: SciCrunch Registry
  

https://www.ncbi.nlm.nih.gov/genbank/sars-cov-2-seqs/

Collection of SARS-CoV-2 sequences currently available in GenBank genetic sequence database and Sequence Read Archive. Updated as additional sequences are released.

Proper citation: SARS-CoV-2-Sequences (RRID:SCR_018319) Copy   

•   Source: SciCrunch Registry
  

https://amp.pharm.mssm.edu/covid19/

Software tool as interface to submit, serve, and analyze COVID19 related gene and drug sets. Collection of gene and drug sets related to COVID-19 research contributed by community.

Proper citation: COVID-19 Crowd Generated Gene and Drug Set Library (RRID:SCR_018252) Copy   

•   Source: SciCrunch Registry
  

https://github.com/sysu-yanglab/TDimpute

Software tool to transfer learning based deep neural network to impute missing gene expression data from DNA methylation data.

Proper citation: TDimpute (RRID:SCR_018306) Copy   

•   Source: SciCrunch Registry
  

http://glycam.org/

Web provides tools for modeling 3D structures of molecules and complexes containing carbohydrates including oligosaccharide conformation modeling and glycoprotein 3D structure modeling. Used to simplify prediction of three dimensional structures of carbohydrates and macromolecular structures involving carbohydrates.

Proper citation: GLYCAM-Web (RRID:SCR_018260) Copy   

•   Source: SciCrunch Registry
  

http://lrpath.ncibi.org/

Web tool to perform gene set enrichment testing. Used to test for predefined biologically relevant gene sets that contain more significant genes from experimental dataset than expected by chance. Logistic regression approach for identifying enriched biological groups in gene expression data.

Proper citation: LRPath (RRID:SCR_018572) Copy   

•   Source: SciCrunch Registry
  

http://www.nitrc.org/projects/reproman/

Software tool to simplify creation and management of computing environments in Neuroimaging.

Proper citation: ReproMan (RRID:SCR_018468) Copy   

•   Source: SciCrunch Registry
  

http://www.evolvedmicrobe.com/CurveFitter/

Software tool for growth curve fitting and visualization. Program allows to fit growth curve using simple GUI or advanced scripting environment. Used to fit growth curves generated for data collected in microtiter plates or elsewhere.

Proper citation: CurveFitter (RRID:SCR_018461) Copy   

•   Source: SciCrunch Registry
  

https://github.com/embl-cba/fiji-plugin-bigDataProcessor/blob/master/README.md

Software tool for visual inspection and processing of big image data. Enables loading of Tiff and Hdf5 based image data. BDC supports cropping and saving of big image data including binning and bit depth conversion. Used for analysis of TB sized image data like light sheet microscopy or electron microscopy.

Proper citation: Big Data Processor (RRID:SCR_018484) Copy   

•   Source: SciCrunch Registry