Tools   Select Another Resource Report Type

https://delaney.shinyapps.io/FairSubset/

Web tool to choose representative subsets of data for use with replicates or groups of different sample sizes. Used to retain distribution information at single datum level and may be considered for standardized use in fair publishing practices.

Proper citation: FairSubset (RRID:SCR_019102) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages/release/bioc/html/GSVA.html

Open source software R package for assaying variation of gene set enrichment over sample population.Used for microarray and RNA-seq data analysis. Gene set enrichment method that estimates variation of pathway activity over sample population in unsupervised manner.

Proper citation: GSVA (RRID:SCR_021058) Copy   

•   Source: SciCrunch Registry

https://github.com/labsyspharm/cylinter

Open source software tool as interactive image segmentation filter for multiplex microscopy that aids in identification and removal of cell segmentation instances corrupted by optical and image processing artifacts.

Proper citation: CyLinter (RRID:SCR_021157) Copy   

•   Source: SciCrunch Registry

https://www.archrproject.com/

Software R package for processing and analyzing single-cell ATAC-seq data. Used for integrative single cell chromatin accessibility analysis.Provides intuitive, user focused interface for complex single cell analysis, including doublet removal, single cell clustering and cell type identification, unified peak set generation, cellular trajectory identification, DNA element-to-gene linkage, transcription factor footprinting, mRNA expression level prediction from chromatin accessibility and multi-omic integration with single-cell RNA sequencing.

Proper citation: ArchR (RRID:SCR_020982) Copy   

•   Source: SciCrunch Registry

https://david.ncifcrf.gov/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. Bioinformatics resource system including web server and web service for functional annotation and enrichment analyses of gene lists. Consists of comprehensive knowledgebase and set of functional analysis tools. Includes gene centered database integrating heterogeneous gene annotation resources to facilitate high throughput gene functional analysis.

Proper citation: DAVID (RRID:SCR_001881) Copy   

•   Source: SciCrunch Registry

http://www.phosphosite.org

A freely accessible on-line systems biology resource devoted to all aspects of protein modification, as well as other post-translational modifications. It provides valuable and unique tools for both cell biologists and mass spectroscopists. PhosphoSite is a human- and mouse-centric database. It includes features such as: viewing the locations of modified residues on molecular models; browsing and searching MS2 records by disease, tissue, and cell line; submitting lists of peptides to identify previously reported genes; searching by sub-cellular localization, treatment, tissues, cell types, cell lines and diseases, and protein types and protein domains; searching for experimentally-verified kinase substrates and viewing preferred substrate motifs; and viewing MS2 spectra for peptides and sites not previously published.

Proper citation: PhosphoSitePlus: Protein Modification Site (RRID:SCR_001837) Copy   

•   Source: SciCrunch Registry

http://www.pathwaycommons.org/

Data management software that runs the Pathway Commons web service. It makes it easy to aggregate custom pathway data sets available in standard exchange formats from multiple databases, present pathway data to biologists via a customizable web interface, and export pathway data via a web service to third-party software, such as Cytoscape, for visualization and analysis. cPath is software only, and does not include new pathway information. Main features: * Import pipeline capable of aggregating pathway and interaction data sets from multiple sources, including: MINT, IntAct, HPRD, DIP, BioCyc, KEGG, PUMA2 and Reactome. * Import/Export support for the Proteomics Standards Initiative Molecular Interaction (PSI-MI) and the Biological Pathways Exchange (BioPAX) XML formats. * Data visualization and analysis via Cytoscape. * Simple HTTP URL based XML web service. * Complete software is freely available for local install. Easy to install and administer. * Partly funded by the U.S. National Cancer Institute, via the Cancer Biomedical Informatics Grid (caBIG) and aims to meet silver-level requirements for software interoperability and data exchange.

Proper citation: cPath (RRID:SCR_001749) Copy   

•   Source: SciCrunch Registry

http://www.webarraydb.org/webarray/index.html

An open source integrated microarray database and analysis suite that features convenient uploading of data for storage in a MIAME (Minimal Information about a Microarray Experiment) compliant fashion. It allows data to be mined with a large variety of R-based tools, including data analysis across multiple platforms. Different methods for probe alignment, normalization and statistical analysis are included to account for systematic bias. Student's t-test, moderated t-tests, non-parametric tests and analysis of variance or covariance (ANOVA/ANCOVA) are among the choices of algorithms for differential analysis of data. Users also have the flexibility to define new factors and create new analysis models to fit complex experimental designs. All data can be queried or browsed through a web browser. The computations can be performed in parallel on symmetric multiprocessing (SMP) systems or Linux clusters.

Proper citation: WebArrayDB (RRID:SCR_005577) Copy   

•   Source: SciCrunch Registry

http://edwardslab.bmcb.georgetown.edu/ws/peptideMapper/

The PeptideMapper Web-Service provides alignments of peptide sequence alignments to proteins, mRNA, EST, and HTC sequences from Genbank, RefSeq, UniProt, IPI, VEGA, EMBL, and HInvDb. This mapping infrastructure is supported, in part, by the compressed peptide sequence database infrastructure (Edwards, 2007) which enables a fast, suffix-tree based mapping of peptide sequences to gene identifiers and a gene-focused detailed mapping of peptide sequences to source sequence evidence. The PeptideMapper Web-Service can be used interactively or as a web-service using either HTTP or SOAP requests. Results of HTTP requests can be returned in a variety of formats, including XML, JSON, CSV, TSV, or XLS, and in some cases, GFF or BED; results of SOAP requests are returned as SOAP responses. The PeptideMapper Web-Service maps at most 20 peptides with length between 5 and 30 amino-acids in each request. The number of alignments returned, per peptide, gene, and sequence type, is set to 10 by default. The default can be changed on the interactive alignments search form or by using the max web-service parameter.

Proper citation: PeptideMapper (RRID:SCR_005763) Copy   

•   Source: SciCrunch Registry

http://www.chemnavigator.com/cnc/services/SCSORS_Overview.asp

ChemNavigator has extended its agreement with NCI to include the development of a new Semi-Custom Synthesis On-line Request System (SCSORS), funded mostly by NCI with additional financial support from the NIH Chemical Genomics Center (NCGC). The new SCSORS project will provide the NIH access to the world''s supply of synthetic chemistry available for drug discovery. Once fully formed, SCSORS will provide a strategy for all NIH scientists to circulate requests for specific chemical samples among thousands, if not tens of thousands, of synthetic chemists at suppliers registered in the system. Sample quantities will range from milligram up to kilogram scale requests. Suppliers will be provided tools that allow them to review these requests and make proposals to NIH scientists for the synthesis of substances. It is expected that using the SCSORS strategy will allow the NIH to acquire chemical samples at less than 10% of the internal cost of synthesis while offering access to world wide chemical expertise and diversity. Once fully implemented, SCSORS will become an archive of commercially accessible custom chemistry products for pharmaceutical research. It is expected that this database of commercially accessible substances will grow to over 250 million substances in the coming two years.

Proper citation: SCSORS - Semi-Custom Synthesis On-line Request System (RRID:SCR_005636) Copy   

•   Source: SciCrunch Registry

http://cgap.nci.nih.gov/Genes/GOBrowser

With the CGAP GO browser, you can browse through the GO vocabularies, and find human and mouse genes assigned to each term. GO data updated every few months. Platform: Online tool

Proper citation: CGAP GO Browser (RRID:SCR_005676) Copy   

•   Source: SciCrunch Registry

http://oligogenome.stanford.edu/

The Stanford Human OligoGenome Project hosts a database of capture oligonucleotides for conducting high-throughput targeted resequencing of the human genome. This set of capture oligonucleotides covers over 92% of the human genome for build 37 / hg19 and over 99% of the coding regions defined by the Consensus Coding Sequence (CCDS). The capture reaction uses a highly multiplexed approach for selectively circularizing and capturing multiple genomic regions using the in-solution method developed in Natsoulis et al, PLoS One 2011. Combined pools of capture oligonucleotides selectively circularize the genomic DNA target, followed by specific PCR amplification of regions of interest using a universal primer pair common to all of the capture oligonucleotides. Unlike multiplexed PCR methods, selective genomic circularization is capable of efficiently amplifying hundreds of genomic regions simultaneously in multiplex without requiring extensive PCR optimization or producing unwanted side reaction products. Benefits of the selective genomic circularization method are the relative robustness of the technique and low costs of synthesizing standard capture oligonucleotide for selecting genomic targets.

Proper citation: OligoGenome (RRID:SCR_006025) Copy   

•   Source: SciCrunch Registry

https://www.phenxtoolkit.org/

Set of measures intended for use in large-scale genomic studies. Facilitate replication and validation across studies. Includes links to standards and resources in effort to facilitate data harmonization to legacy data. Measurement protocols that address wide range of research domains. Information about each protocol to ensure consistent data collection.Collections of protocols that add depth to Toolkit in specific areas.Tools to help investigators implement measurement protocols.

Proper citation: Phenotypes and eXposures Toolkit (RRID:SCR_006532) Copy   

•   Source: SciCrunch Registry

http://wiki.chasmsoftware.org/index.php/Main_Page

CHASM is a method that predicts the functional significance of somatic missense mutations observed in the genomes of cancer cells, allowing mutations to be prioritized in subsequent functional studies, based on the probability that they give the cells a selective survival advantage. SNV-Box is a database of pre-computed features of all possible amino acid substitutions at every position of the annotated human exome. Users can rapidly retrieve features for a given protein amino acid substitution for use in machine learning.

Proper citation: CHASM/SNV-Box (RRID:SCR_006445) Copy   

•   Source: SciCrunch Registry

http://www.webgestalt.org/

Web based gene set analysis toolkit designed for functional genomic, proteomic, and large-scale genetic studies from which large number of gene lists (e.g. differentially expressed gene sets, co-expressed gene sets etc) are continuously generated. WebGestalt incorporates information from different public resources and provides a way for biologists to make sense out of gene lists. This version of WebGestalt supports eight organisms, including human, mouse, rat, worm, fly, yeast, dog, and zebrafish.

Proper citation: WebGestalt: WEB-based GEne SeT AnaLysis Toolkit (RRID:SCR_006786) Copy   

•   Source: SciCrunch Registry

http://cancercontrol.cancer.gov/tcrb/tturc/

A transdisciplinary approach to the full spectrum of basic and applied research on tobacco use to reduce the disease burden of tobacco use, including: * Etiology of tobacco use and addiction * Impact of advertising and marketing * Prevention of tobacco use * Treatment of tobacco use and addiction * Identification of biomarkers of tobacco exposure * Identification of genes related to addiction and susceptibility to harm from tobacco Goals * Increase the number of investigators from relevant disciplines who focus on the study of tobacco use as part of transdisciplinary teams. * Generate basic research evidence to improve understanding of the etiology and natural history of tobacco use. * Produce evidence-based tobacco use interventions that can translate to the community and specific understudied or underserved populations. * Increase the number of evidence-based interventions that are novel, including the development, testing and dissemination of innovative behavioral treatments and prevention strategies based upon findings from basic research. * Train transdisciplinary investigators capable of conducting cutting-edge tobacco use research. * Increase the number of peer-reviewed publications in the areas of tobacco use, nicotine addiction, and treatment.

Proper citation: Transdisciplinary Tobacco Use Research Centers (RRID:SCR_006858) Copy   

•   Source: SciCrunch Registry

http://biospecimens.cancer.gov/

The NCI Office of Biorepositories and Biospecimen Research (OBBR) was established in 2005 in recognition of the critical role that biospecimens play in cancer research. The OBBR is responsible for developing a common biorepository infrastructure that promotes resource sharing and team science, in order to facilitate multi-institutional, high throughput genomic and proteomic studies. OBBR is focused on the following objectives: * Establish biobanking as a new area of research, in order to determine the impact of various collection and processing protocols on the usefulness of biospecimens in genomic and proteomic studies * Disseminate first-generation Best Practices in order to harmonize policies and procedures of NCI-supported biorepositories * Develop future generations of biorepository best practices, based on the data generated in the biobanking research programs above * Promote professional oversight of biospecimen standards development by standards organizations * Develop new technologies for biorepository operations * Develop a biorepository accreditation program * Coordinate with the international biobanking community to harmonize policies and procedures to facilitate multi-national research

Proper citation: NCI Office of Biospecimens (RRID:SCR_007076) Copy   

•   Source: SciCrunch Registry

http://senselab.med.yale.edu/modeldb/

Curated database of published models so that they can be openly accessed, downloaded, and tested to support computational neuroscience. Provides accessible location for storing and efficiently retrieving computational neuroscience models.Coupled with NeuronDB. Models can be coded in any language for any environment. Model code can be viewed before downloading and browsers can be set to auto-launch the models. The model source code has to be available from publicly accessible online repository or WWW site. Original source code is used to generate simulation results from which authors derived their published insights and conclusions.

Proper citation: ModelDB (RRID:SCR_007271) Copy   

•   Source: SciCrunch Registry

https://discover.nci.nih.gov/rsconnect/cellminercdb/

Web application integrating cancer cell line pharmacogenomics. Enables exploration and analysis of cancer cell line pharmacogenomic data across different sources. Focuses on cancer patient-derived human cell line molecular and pharmacological data. CellMinerCDB (v1.2) includes several improvements.

Proper citation: CellMinerCDB (RRID:SCR_025649) Copy   

•   Source: SciCrunch Registry

https://github.com/dviraran/xCell

Software R package for generating cell type scores and R scripts for development of xCell. Web tool that performs cell type enrichment analysis from gene expression data for immune and stroma cell types. Used for Cell types enrichment analysis.

Proper citation: xCell (RRID:SCR_026446) Copy   

•   Source: SciCrunch Registry