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https://mygene.info/

Web service for querying or retrieving gene annotation data.

Proper citation: MyGene.info (RRID:SCR_018660) Copy   

•   Source: SciCrunch Registry

https://rosie.graylab.jhu.edu/docking2

Unified web framework for Rosetta applications. Web interface for selected Rosetta protocols. Web front end for Rosetta software suite. Provides common user interface for Rosetta protocols, stable application programming interface for developers to add additional protocols, flexible back-end to allow leveraging of computer cluster resources shared by Rosetta Commons member institutions, and centralized administration by Rosetta Commons to ensure continuous maintenance. Offers general and speedy paradigm for serverification of Rosetta applications. Lowers barriers to Rosetta use for broader biological community.

Proper citation: ROSIE (RRID:SCR_018764) Copy   

•   Source: SciCrunch Registry

https://delaney.shinyapps.io/CAIRN/

Web tool to graph all copy number alterations present in segment file. Custom data is permitted. Allows to display copy number alterations which overlap user specified region, to quantify number of amplified CNAs and deleted CNAs. Visualization tool to explore copy number alterations discovered in published cancer datasets. Intended to help oncology community observe of relative rates of amplification, deletion, and mutation of interesting genes and regions.

Proper citation: CAIRN (RRID:SCR_019101) Copy   

•   Source: SciCrunch Registry

https://www.robotreviewer.net/about

Open source web based system that uses machine learning and NLP to semi automate biomedical evidence synthesis, to aid practice of Evidence Based Medicine. Processes full text journal articles describing randomized controlled trials. Designed to automatically extract key data items from reports of clinical trials.

Proper citation: RobotReviewer (RRID:SCR_021064) Copy   

•   Source: SciCrunch Registry

https://github.com/r3fang/SnapATAC

Software package for analyzing scATAC-seq datasets.Used to dissects cellular heterogeneity in unbiased manner and map trajectories of cellular states. Can process data from up to million cells. Incorporates existing tools into comprehensive package for analyzing single cell ATAC-seq dataset.

Proper citation: SnapATAC (RRID:SCR_020981) Copy   

•   Source: SciCrunch Registry

https://www.synapse.org/#!Synapse:syn22345748/wiki/605339

Reference dataset of multiplexed immunofluorescence microscopy images collected at HMS Laboratory of Systems Pharmacology. Includes set of images of different types for development and benchmarking of computational methods for image processing. As of 4/2/2021, EMIT comprises tissue microarray containing cores from 34 cancer, non-neoplastic diseases, and normal tissue collected from clinical discards under IRB supervised protocol. TMA was imaged using cyclic immunofluorescence method. Additional extensions of EMIT are currently in the planning stages. Long term goal is to compose ImageNet like resource for highly multiplexed images of tissues and tumors by consolidating high quality curated datasets.

Proper citation: Exemplar Microscopy Images of Tissues (RRID:SCR_021052) Copy   

•   Source: SciCrunch Registry

http://www.genepattern-notebook.org/

Interactive analysis notebook environment that streamlines genomics research by interleaving text, multimedia, and executable code into unified, sharable, reproducible “research narratives.” It integrates the dynamic capabilities of notebook systems with an investigator-focused, simple interface that provides access to hundreds of genomic tools without the need to write code.

Proper citation: GenePattern Notebook (RRID:SCR_015699) Copy   

•   Source: SciCrunch Registry

http://tissues.jensenlab.org

Database that integrates evidence on tissue expression from manually curated literature, proteomics and transcriptomics screens, and automatic text mining. It maps all evidence to common protein identifiers and Brenda Tissue Ontology terms, and further unifies it by assigning confidence scores that facilitate comparison of the different types and sources of evidence.

Proper citation: TISSUES (RRID:SCR_015665) Copy   

•   Source: SciCrunch Registry

https://immunedb.readthedocs.io/en/latest/

Software system for storing and analyzing high throughput B and T cell immune receptor sequencing data. Comprised of web interface and of Python analysis tools to process raw reads for gene usage, infer clones, aggregate data, and run downstream analyses, or in conjunction with other AIRR tools using its import and export features.

Proper citation: ImmuneDB (RRID:SCR_017125) Copy   

•   Source: SciCrunch Registry

https://exrna-atlas.org

Software tool as data and metadata repository of Extracellular RNA Communication Consortium. Atlas includes small RNA sequencing and qPCR derived exRNA profiles from human and mouse biofluids. All RNAseq datasets are processed using version 4 of exceRpt small RNAseq pipeline. Atlas accepts submissions for RNAseq or qPCR data.

Proper citation: exRNA Atlas (RRID:SCR_017221) Copy   

•   Source: SciCrunch Registry

https://appyters.maayanlab.cloud

Collection of web-based software applications that enable users to execute bioinformatics workflows without coding. Turns Jupyter notebooks into fully functional standalone web-based bioinformatics applications. Each Appyter application introduces data entry form for uploading or fetching data, as well as for selecting options for various settings. Once user presses Submit, Appyter is executed in cloud and user is presented with Jupyter Notebook report that contain results. Report includes markdown text, interactive and static figures, and source code. Appyter users can share the link to the output report, as well as download the fully executable notebook for execution on other platforms.

Proper citation: Appyters (RRID:SCR_021245) Copy   

•   Source: SciCrunch Registry

https://github.com/abyzovlab/CNVpytor

Software Python package and command line tool for CNV/CNA analysis from depth of coverage by mapped reads. Software tool for CNV/CNA detection and analysis from read depth and allele imbalance in whole genome sequencing.

Proper citation: CNVpytor (RRID:SCR_021627) Copy   

•   Source: SciCrunch Registry

https://cumulus.readthedocs.io/en/stable

Software tool as cloud based single cell genomics and spatial transcriptomics data analysis framework that is scalable to massive amounts of data and able to process variety of data types. Consists of cloud analysis workflow, Python analysis package and visualization application. Supports analysis of single-cell RNA-seq, CITE-seq, Perturb-seq, single-cell ATAC-seq, single-cell immune repertoire and spatial transcriptomics data.

Proper citation: Cumulus (RRID:SCR_021644) Copy   

•   Source: SciCrunch Registry

https://github.com/vlink/marge

Software package that integrates genome wide genetic variation with epigenetic data to identify collaborative transcription factor pairs. Optimized to work with chromatin accessibility assays such as ATAC-seq or DNase I hypersensitivity, as well as transcription factor binding data collected by ChIP-seq. Used to identify combinations of cell type specific transcription factors while simultaneously interpreting functional effects of non-coding genetic variation.

Proper citation: Motif Mutation Analysis for Regulatory Genomic Elements (RRID:SCR_021902) Copy   

•   Source: SciCrunch Registry

https://github.com/kukionfr/VAMPIRE_open

Software tool for analysis of cell and nuclear morphology from fluorescence or bright field images. Enables profiling and classification of cells into shape modes based on equidistant points along cell and nuclear contours. Robust method to quantify cell morphological heterogeneity.

Proper citation: VAMPIRE (RRID:SCR_021721) Copy   

•   Source: SciCrunch Registry

http://seer.cancer.gov/resources/

Portal provides SEER research data and software SEER*Stat and SEER*Prep. SEER incidence and population data associated by age, sex, race, year of diagnosis, and geographic areas can be used to examine stage at diagnosis by race/ethnicity, calculate survival by stage at diagnosis, age at diagnosis, and tumor grade or size, determine trends and incidence rates for various cancer sites over time. SEER releases new research data every Spring based on the previous November’s submission of data.

Proper citation: SEER Datasets and Software (RRID:SCR_003293) Copy   

•   Source: SciCrunch Registry

http://smd.stanford.edu/cgi-bin/source/sourceSearch

SOURCE compiles information from several publicly accessible databases, including UniGene, dbEST, UniProt Knowledgebase, GeneMap99, RHdb, GeneCards and LocusLink. GO terms associated with LocusLink entries appear in SOURCE. The mission of SOURCE is to provide a unique scientific resource that pools publicly available data commonly sought after for any clone, GenBank accession number, or gene. SOURCE is specifically designed to facilitate the analysis of large sets of data that biologists can now produce using genome-scale experimental approaches Platform: Online tool

Proper citation: SOURCE (RRID:SCR_005799) Copy   

•   Source: SciCrunch Registry

http://www.pathbase.net/

Database of histopathology photomicrographs and macroscopic images derived from mutant or genetically manipulated mice. The database currently holds more than 1000 images of lesions from mutant mice and their inbred backgrounds and further images are being added continuously. Images can be retrieved by searching for specific lesions or class of lesion, by genetic locus, or by a wide set of parameters shown on the Advanced Search Interface. Its two key aims are: * To provide a searchable database of histopathology images derived from experimental manipulation of the mouse genome or experiments conducted on genetically manipulated mice. * A reference / didactic resource covering all aspects of mouse pathology Lesions are described according to the Pathbase pathology ontology developed by the Pathbase European Consortium, and are available at the site or on the Gene Ontology Consortium site - OBO. As this is a community resource, they encourage everyone to upload their own images, contribute comments to images and send them their feedback. Please feel free to use any of the SOAP/WSDL web services. (under development)

Proper citation: Pathbase (RRID:SCR_006141) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/release/bioc/html/nondetects.html

Software R package to model and impute non-detects in results of qPCR experiments.Used to directly model non-detects as missing data.

Proper citation: nondetects (RRID:SCR_001702) Copy   

•   Source: SciCrunch Registry

http://www.pathology.med.ohio-state.edu/HTRN/apc/default.asp

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. The Adenoma Polyp Tissue Bank (APTB) receives whole blood from patients enrolled in the Prevention of Sporadic Colorectal Adenomas with Celecoxib clinical trial. We have reached our accrual on blood submissions, so we will no longer be receiving blood specimens The objectives of this trial are as follows: A. To determine the efficacy and safety of celecoxib versus placebo in preventing the occurrence of newly detected colorectal adenomas in subjects at increased risk for colorectal carcinoma. In addition to incidence, other established risk factors will be evaluated for their association with occurrence of new colorectal adenomas, including cancer family history and adenoma size, histopathologic grade, multiplicity and location. Primary assessment of treatment efficacy will be the reduction in the number of subjects with adenomas at colonoscopy after Year 1 and Year 3 of study drug use. Secondary assessments of treatment efficacy will be 1) the number of adenomas 2) the histopathologic grade of adenomas and 3) the size of adenomas, also measured after one year and three years of study drug use. These factors will be incorporated into a risk model for predicting adenoma occurrence and response to celecoxib. B. To determine the efficacy of celecoxib versus placebo in modulating one or more of a panel of biomarkers for colorectal cancer at the cellular and molecular level sampled in a subset of subjects at selective sites at baseline and after Year 1 and Year 3 of study drug use. These biomarkers will include measurements of aberrant crypt foci (ACF), proliferation (index and crypt distribution), apoptosis (index and crypt distribution), COX expression and activity. If modulation of one or more mucosal biomarkers occur, we will explore whether it correlates with the development of incident colorectal neoplasia (adenomas/carcinomas), thereby attempting to validate the surrogacy of that biomarker. C. To develop a specimen bank. Serum and white blood cells are isolated from whole blood and adenoma tissue blocks and slides are banked. Banked specimens will become available for use in correlative science studies at a later point. This project began in 1999 and will be extended through 2006. The lead principal investigator is Monica M. Bertagnolli, MD, Brigham and Women''s Hospital, Boston, MA, and the APTB Director is Scott Jewell, Ph.D., Department of Pathology, The Ohio State University. The APTB is supported by the NIH, NCI Division of Cancer Prevention, in connection with the Strang Cancer Prevention Center, Cornell University, New York., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Adenoma Polyp Tissue Bank (RRID:SCR_005366) Copy   

•   Source: SciCrunch Registry