Tools   Select Another Resource Report Type

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://sites.cscc.unc.edu/aric/

Platform for prospective epidemiologic study conducted in four U.S. communities. One of most significant and longest running heart health studies and is the largest study of heart health in African Americans. ARIC investigates risk factors for heart disease and stroke, and connections between cardiovascular and cognitive health. ARIC includes two parts: Cohort Component and Community Surveillance Component. Cohort Component began in 1987, and each ARIC field center randomly selected and recruited cohort sample of individuals aged 45-64 from defined population in their community, to receive extensive examinations, including medical, social, and demographic data. In Community Surveillance Component, four communities are investigated to determine long term trends in hospitalized myocardial infarction and coronary heart disease deaths in men and women aged 35-84 years.

Proper citation: Atherosclerosis Risk in Communities (RRID:SCR_021769) 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://software.broadinstitute.org/cancer/cga/polysolver

Software tool for HLA typing based on whole exome sequencing data and infers alleles for three major MHC class I genes. Enables accurate inference of germline alleles of class I HLA-A, B and C genes and subsequent detection of mutations in these genes using inferred alleles as reference.

Proper citation: Polysolver (RRID:SCR_022278) Copy   

•   Source: SciCrunch Registry

https://maayanlab.cloud/sigcom-lincs

Web server that serves over million gene expression signatures processed, analyzed, and visualized from LINCS, GTEx, and GEO. Data and metadata search engine for gene expression signatures.

Proper citation: SigCom LINCS (RRID:SCR_022275) Copy   

•   Source: SciCrunch Registry

https://github.com/FunctionLab/sei-framework

Web server for systematically predicting sequence regulatory activities and applying sequence information to human genetics data. Provides global map from any sequence to regulatory activities, as represented by sequence classes, and each sequence class integrates predictions for chromatin profiles like transcription factor, histone marks, and chromatin accessibility profiles across wide range of cell types.

Proper citation: sei (RRID:SCR_022571) Copy   

•   Source: SciCrunch Registry

https://sleepdata.org/datasets/shhs

Portal for a multi-cohort study focused on sleep-disordered breathing and cardiovascular outcomes implemented by the National Heart Lung and Blood Institute. Recorded signals are: EEG, ECG, EOG, SaO2, HR, EOG, EMG, respiratory inductance plethysmography, respiration (thermistor), position, light.

Proper citation: Sleep Heart Health Study (RRID:SCR_016559) Copy   

•   Source: SciCrunch Registry

https://github.com/xu-lab/SINCERA

Software tool implemented in R S4 as an analytic pipeline for processing single-cell RNA-seq data from a whole organ or sorted cells. Used for Single Cell RNA-Seq profiling analysis.

Proper citation: SINCERA Pipeline (RRID:SCR_016563) Copy   

•   Source: SciCrunch Registry

http://amp.pharm.mssm.edu/DGB/

Web based application to assist researchers with identifying drugs and small molecules that are predicted to maximally influence expression of mammalian gene of interest. Used to identify drugs and small molecules to regulate expression of target genes for research purpose only. Application for ranking drugs to modulate specific gene based on transcriptomic signatures.

Proper citation: Drug Gene Budger (RRID:SCR_016489) Copy   

•   Source: SciCrunch Registry

https://sleepdata.org/datasets/abc

Portal for randomized controlled trial to compare effectiveness of bariatric surgery versus continuous positive airway pressure (CPAP) therapy for obstructive sleep apnea. Signals included in the polysomnography (PSG) montage are EEG, EMG, EOG, ECG, SpO2, airflow, CPAP pressure, CPAP flow, plethysmography, position, pulse, light, respiratory effort, snore.

Proper citation: Apnea, Bariatric surgery, and CPAP study (RRID:SCR_016575) Copy   

•   Source: SciCrunch Registry

https://sleepdata.org/datasets/bestair/

Portal for sleep study to address challenges in conducting future large-scale trials of sleep apnea treatment. Includes data from sleep apnea patients with cardiovascular disease or risk factors. Signals included in the polysomnography (PSG) montage are ECG, SpO2, airflow, nasal pressure, position, pulse, respiratory effort, snore, tidal volume.

Proper citation: Best Apnea Interventions for Research (BestAIR) sleep study (RRID:SCR_016583) Copy   

•   Source: SciCrunch Registry

http://lincsportal.ccs.miami.edu/dcic-portal/

Portal which provides a unified interface for searching LINCS dataset packages and reagents. Users can use the portal to access datasets, small molecules, cells, genes, proteins and peptides, and antibodies.

Proper citation: LINCS Data Portal (RRID:SCR_014939) Copy   

•   Source: SciCrunch Registry

http://lincs.hms.harvard.edu/

Center that is part of the NIH Library of Integrated Network-based Cellular Signatures (LINCS) Program. Its goals are to collect and disseminate data and analytical tools needed to understand how human cells respond to perturbation by drugs, the environment, and mutation.

Proper citation: HMS LINCS Center (RRID:SCR_016370) Copy   

•   Source: SciCrunch Registry

http://life.ccs.miami.edu/life/

LIFE search engine contains data generated from LINCS Pilot Phase, to integrate LINCS content leveraging semantic knowledge model and common LINCS metadata standards. LIFE makes LINCS content discoverable and includes aggregate results linked to Harvard Medical School and Broad Institute and other LINCS centers, who provide more information including experimental conditions and raw data. Please visit LINCS Data Portal.

Proper citation: LINCS Information Framework (RRID:SCR_003937) Copy   

•   Source: SciCrunch Registry

https://pmc.ncbi.nlm.nih.gov/articles/PMC4525701/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 25,2025. Web tool to parse Sanger sequencing chromatograms with double peaks into wildtype and alternative allele sequences. Used to separate chromatogram data containing ambiguous base calls into wildtype and mutant allele sequences.Used for identification of unknown indels using sanger sequencing of polymerase chain reaction products.

Proper citation: Poly Peak Parser (RRID:SCR_023776) Copy   

•   Source: SciCrunch Registry

http://www.nhlbi.nih.gov/guidelines/obesity/BMI/bmicalc.htm

Body Mass Index (BMI) for adults can be calculated using only height and weight. Body mass index (BMI) is a measure of body fat based on height and weight that applies to adult men and women.

Proper citation: Body Mass Index Calculator (RRID:SCR_000122) Copy   

•   Source: SciCrunch Registry

http://proteomics.ucsd.edu/Software/NeuroPedia/index.html

A neuropeptide encyclopedia of peptide sequences (including genomic and taxonomic information) and spectral libraries of identified MS/MS spectra of homolog neuropeptides from multiple species.

Proper citation: NeuroPedia (RRID:SCR_001551) Copy   

•   Source: SciCrunch Registry

http://www.uniprot.org/

Collection of data of protein sequence and functional information. Resource for protein sequence and annotation data. Consortium for preservation of the UniProt databases: UniProt Knowledgebase (UniProtKB), UniProt Reference Clusters (UniRef), and UniProt Archive (UniParc), UniProt Proteomes. Collaboration between European Bioinformatics Institute (EMBL-EBI), SIB Swiss Institute of Bioinformatics and Protein Information Resource. Swiss-Prot is a curated subset of UniProtKB.

Proper citation: UniProt (RRID:SCR_002380) Copy   

•   Source: SciCrunch Registry

http://www.mitomap.org/

Database of polymorphisms and mutations of the human mitochondrial DNA. It reports published and unpublished data on human mitochondrial DNA variation. All data is curated by hand. If you would like to submit published articles to be included in mitomap, please send them the citation and a pdf.

Proper citation: MITOMAP - A human mitochondrial genome database (RRID:SCR_002996) Copy   

•   Source: SciCrunch Registry

https://github.com/caleblareau/mgatk

Software python-based command line interface for processing .bam files with mitochondrial reads and generating high-quality heteroplasmy estimation from sequencing data. This package places a special emphasis on mitochondrial genotypes generated from single-cell genomics data, primarily mtscATAC-seq, but is generally applicable across other assays.

Proper citation: mgatk (RRID:SCR_021159) Copy   

•   Source: SciCrunch Registry