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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://mcmicro.org/

Open source software tool as multiple choice microscopy pipeline for multiplexed whole slide imaging and tissue microarrays. Scalable, modular image processing pipeline for multiplexed tissue imaging. Used for performing sequential steps needed to transform large, multi channel whole slide images into single cell data.

Proper citation: MCMICRO (RRID:SCR_021048) Copy   

•   Source: SciCrunch Registry

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

http://statistika.mfub.bg.ac.rs/interactive-linegraph/

Interactive web based tool for creating line graphs for scientific publications. Users can view different summary statistics, examine lines for any individual in data, focus on time points or groups of interest, and view changes between any two time points and conditions.

Proper citation: Interactive Line Graph (RRID:SCR_018334) Copy   

•   Source: SciCrunch Registry

https://cadd.gs.washington.edu/

Web tool for predicting deleteriousness of variants throughout human genome. Software tool for scoring deleteriousness of single nucleotide variants as well as insertion and deletions variants in human genome.

Proper citation: Combined Annotation Dependent Depletion (RRID:SCR_018393) Copy   

•   Source: SciCrunch Registry

https://geodacenter.github.io/

Software program for spatial analysis for non geographic information systems specialists. Includes functionality ranging from simple mapping to exploratory data analysis, visualization of global and local spatial autocorrelation, and spatial regression.

Proper citation: GeoDa (RRID:SCR_018559) Copy   

•   Source: SciCrunch Registry

http://epi.grants.cancer.gov/CFR/

The Breast Cancer Family Registry (Breast CFR) and the Colon Cancer Family Registry (Colon CFR) were established by the National Cancer Institute (NCI) as a unique resource for investigators to use in conducting studies on the genetics and molecular epidemiology of breast and colon cancer. Known collectively as the CFRs, they share a central goal: the translation of research to the clinical and prevention settings for the benefit of Registry participants and the general public. The CFRs are particularly interested in: * Identifying and characterizing cancer susceptibility genes; * Defining gene-gene and gene-environment interactions in cancer etiology; and * Exploring the translational, preventive, and behavioral implications of research findings. The CFRs do not provide funding for studies; however, researchers can apply to access CFR data and biospecimens contributed by thousands of families from across the spectrum of risk for these cancers and from population-based or relative controls. Special features of the CFRs include: * Population-based and clinic-based ascertainment; * Systematic collection of validated family history; * Epidemiologic risk factor , clinical, and followup data; * Biospecimens (including tumor blocks and Epstein-Barr virus (EBV)-transformed cell lines); * Ongoing molecular characterization of the participating families; and * A combined informatics center.

Proper citation: NCI Breast and Colon Cancer Family Registries (RRID:SCR_006664) Copy   

•   Source: SciCrunch Registry

http://rulai.cshl.edu/cgi-bin/tools/ESE3/esefinder.cgi?process=home

A web-based resource that facilitates rapid analysis of exon sequences to identify putative exonic splicing enhancers (ESEs) responsive to the human SR proteins SF2/ASF, SC35, SRp40 and SRp55, and to predict whether exonic mutations disrupt such elements.

Proper citation: ESEfinder 3.0 (RRID:SCR_007088) Copy   

•   Source: SciCrunch Registry

http://www.cpc.unc.edu/projects/addhealth

Longitudinal study of a nationally representative sample of adolescents in grades 7-12 in the United States during the 1994-95 school year. Public data on about 21,000 people first surveyed in 1994 are available on the first phases of the study, as well as study design specifications. It also includes some parent and biomarker data. The Add Health cohort has been followed into young adulthood with four in-home interviews, the most recent in 2008, when the sample was aged 24-32. Add Health combines longitudinal survey data on respondents social, economic, psychological and physical well-being with contextual data on the family, neighborhood, community, school, friendships, peer groups, and romantic relationships, providing unique opportunities to study how social environments and behaviors in adolescence are linked to health and achievement outcomes in young adulthood. The fourth wave of interviews expanded the collection of biological data in Add Health to understand the social, behavioral, and biological linkages in health trajectories as the Add Health cohort ages through adulthood. The restricted-use contract includes four hours of free consultation with appropriate staff; after that, there''s a fee for help. Researchers can also share information through a listserv devoted to the database.

Proper citation: Add Health (National Longitudinal Study of Adolescent Health) (RRID:SCR_007434) Copy   

•   Source: SciCrunch Registry

http://www.oreganno.org/oregano/

Open source, open access database and literature curation system for community based annotation of experimentally identified DNA regulatory regions, transcription factor binding sites and regulatory variants. Automatically cross referenced against PubMED, Entrez Gene, EnsEMBL, dbSNP, eVOC: Cell type ontology, and Taxonomy database. Community driven resource for curated regulatory annotation.

Proper citation: Open Regulatory Annotation Database (RRID:SCR_007835) Copy   

•   Source: SciCrunch Registry

http://proteogenomics.musc.edu/ma/arrayQuest.php?page=home&act=manage

A web-accessible program for the analysis of DNA microarray data. ArrayQuest is designed to apply any type of DNA microarray analysis program executable on a Linux system (i.e., Bioconductor statistical and graphical methods written in R as well as BioPerl and C++ based scripts) to DNA microarray data stored in the MUSC DNA Microarray Database, the Gene Expression Omnibus (GEO) or in a password protected private database uploaded to the center point server. ArrayQuest analyses are performed on a computer cluster.

Proper citation: ArrayQuest (RRID:SCR_010935) Copy   

•   Source: SciCrunch Registry

https://pharos.nih.gov/idg/index#

Database of ligands and diseases. Its goal is to develop a knowledge-base for the Druggable Genome (DG) in order to illuminate the uncharacterized and/or poorly annotated portion of the genome. DG, focusing on four of the most commonly drug-targeted protein families: G-protein-coupled receptors (GPCRs); nuclear receptors (NRs); ion channels (ICs); and kinases.

Proper citation: PHAROS (RRID:SCR_016258) Copy   

•   Source: SciCrunch Registry

http://hb.flatironinstitute.org/

Formerly known as GIANT (Genome-scale Integrated Analysis of gene Networks in Tissues), HumanBase applies machine learning algorithms to learn biological associations from massive genomic data collections. These integrative analyses reach beyond existing "biological knowledge" represented in the literature to identify novel, data-driven associations.

Proper citation: HumanBase (RRID:SCR_016145) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/whs-sd-atlas/

Open access volumetric atlas of anatomical delineations of rat brain based on structural contrast in isotropic magnetic resonance and diffusion tensor images acquired ex vivo from 80 day old male Sprague Dawley rat at Duke Center for In Vivo Microscopy. Spatial reference is provided by Waxholm Space coordinate system. Location of bregma and lambda are identified as anchors towards stereotaxic space. Application areas include localization of signal in non structural images. Atlas, MRI and DTI volumes, and diffusion tensor data are shared in NIfTI format.

Proper citation: Waxholm Space Atlas of the Sprague Dawley Rat Brain (RRID:SCR_017124) Copy   

•   Source: SciCrunch Registry

https://signalingpathways.org

Web multi omics knowledgebase based upon public, manually curated transcriptomic and cistromic datasets involving genetic and small molecule manipulations of cellular receptors, enzymes and transcription factors. Integrated omics knowledgebase for mammalian cellular signaling pathways. Web browser interface was designed to accommodate numerous routine data mining strategies. Datasets are biocurated versions of publically archived datasets and are formatted according to recommendations of the FORCE11 Joint Declaration on Data Citation Principles73, and are made available under Creative Commons CC 3.0 BY license. Original datasets are available.

Proper citation: Signaling Pathways Project (RRID:SCR_018412) Copy   

•   Source: SciCrunch Registry

http://software.broadinstitute.org/gsea/msigdb/index.jsp

Collection of annotated gene sets for use with Gene Set Enrichment Analysis (GSEA) software.

Proper citation: Molecular Signatures Database (RRID:SCR_016863) Copy   

•   Source: SciCrunch Registry

https://wan-bioinfo.shinyapps.io/GESS/

Database of global evaluation of SARS-CoV-2/hCoV-19 sequences.Provides comprehensive analysis results based on tens of thousands of high-coverage and high-quality SARS-CoV-2 complete genomes.

Proper citation: GESS (RRID:SCR_021847) Copy   

•   Source: SciCrunch Registry

https://www.roswellpark.edu/shared-resources/gene-targeting-and-transgenic

Facility which provides researchers with transgenic mouse technologies, methods, and animal models. Knockout mice, transgenic mice, and mice on multiple strain backgrounds are provided.

Proper citation: RPCI Gene Targeting and Transgenic Shared Resource (RRID:SCR_001020) Copy   

•   Source: SciCrunch Registry

http://www.broad.mit.edu/mpr/lung

Data set of a molecular taxonomy of lung carcinoma, the leading cause of cancer death in the United States and worldwide. Using oligonucleotide microarrays, researchers analyzed mRNA expression levels corresponding to 12,600 transcript sequences in 186 lung tumor samples, including 139 adenocarcinomas resected from the lung. Hierarchical and probabilistic clustering of expression data defined distinct sub-classes of lung adenocarcinoma. Among these were tumors with high relative expression of neuroendocrine genes and of type II pneumocyte genes, respectively. Retrospective analysis revealed a less favorable outcome for the adenocarcinomas with neuroendocrine gene expression. The diagnostic potential of expression profiling is emphasized by its ability to discriminate primary lung adenocarcinomas from metastases of extra-pulmonary origin. These results suggest that integration of expression profile data with clinical parameters could aid in diagnosis of lung cancer patients.

Proper citation: Classification of Human Lung Carcinomas by mRNA Expression Profiling Reveals Distinct Adenocarcinoma Sub-classes (RRID:SCR_003010) Copy   

•   Source: SciCrunch Registry

http://www.nihpromis.org/

Repository of person centered measures that evaluates and monitors physical, mental, and social health in adults and children.

Proper citation: Patient-Reported Outcomes Measurement Information System (RRID:SCR_004718) Copy   

•   Source: SciCrunch Registry