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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
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
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
Web service to predict involvement of upstream cell signaling pathways, given signature of differentially expressed genes. Used to linking expression signatures to upstream cell signaling networks.
Proper citation: X2K Web (RRID:SCR_023624) Copy
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
Web platform for downstream analysis and visualization of proteomics data. Server that facilitates integrated annotation, analysis and visualization of quantitative proteomics data, with emphasis on PTM networks and integration with LINCS library of chemical and genetic perturbation signatures in order to provide further mechanistic and functional insights. Primary input for server consists of set of peptides or proteins, optionally with PTM sites, and their corresponding abundance values.
Proper citation: piNET (RRID:SCR_018693) Copy
https://bioconductor.org/packages/variancePartition/
Software R package to quantify and interpret divers of variation in multilevel gene expression experiments.Provides statistical and visualization framework for studying drivers of variation in RNA-seq datasets in many types of high throughput genomic assays including RNA-seq gene-, exon- and isoform-level quantification, splicing efficiency, protein quantification, metabolite quantification, metagenomic assays, methylation arrays and epigenomic sequencing assays.
Proper citation: variancePartition (RRID:SCR_019204) Copy
http://nsr.bioeng.washington.edu/
Database of physiological, pharmacological, and pathological information on humans and other organisms and integration through computational modeling. Models include everything from diagrammatic schema, suggesting relationships among elements composing a system, to fully quantitative, computational models describing the behavior of physiological systems and an organism''s response to environmental change. Each mathematical model is an internally self-consistent summary of available information, and thereby defines a working hypothesis about how a system operates. Predictions from such models are subject to test, with new results leading to new models.BR /> A Tool developed for the NSR Physiome project is JSim, an open source, free software. JSim is a Java-based simulation system for building quantitative numeric models and analyzing them with respect to experimental reference data. JSim''s primary focus is in physiology and biomedicine, however its computational engine is quite general and applicable to a wide range of scientific domains. JSim models may intermix ODEs, PDEs, implicit equations, integrals, summations, discrete events and procedural code as appropriate. JSim''s model compiler can automatically insert conversion factors for compatible physical units as well as detect and reject unit unbalanced equations. JSim also imports the SBML and CellML model archival formats. All JSim models are open source. Goals of the Physiome Project: - To develop and database observations of physiological phenomenon and interpret these in terms of mechanism (a fundamentally reductionist goal). - To integrate experimental information into quantitative descriptions of the functioning of humans and other organisms (modern integrative biology glued together via modeling). - To disseminate experimental data and integrative models for teaching and research. - To foster collaboration amongst investigators worldwide, to speed up the discovery of how biological systems work. - To determine the most effective targets (molecules or systems) for therapy, either pharmaceutic or genomic. - To provide information for the design of tissue-engineered, biocompatible implants.
Proper citation: NSR Physiome Project (RRID:SCR_007379) Copy
Resource for experimentally validated human and mouse noncoding fragments with gene enhancer activity as assessed in transgenic mice. Most of these noncoding elements were selected for testing based on their extreme conservation in other vertebrates or epigenomic evidence (ChIP-Seq) of putative enhancer marks. Central public database of experimentally validated human and mouse noncoding fragments with gene enhancer activity as assessed in transgenic mice. Users can retrieve elements near single genes of interest, search for enhancers that target reporter gene expression to particular tissue, or download entire collections of enhancers with defined tissue specificity or conservation depth.
Proper citation: VISTA Enhancer Browser (RRID:SCR_007973) Copy
Infrastructure for sharing cardiovascular data and data analysis tools. Human ExVivo heart data set and canine ExVivo normal and failing heart data sets are available. Canine hearts atlas and human InVivo atlases are available.
Proper citation: CardioVascular Research Grid (CVRG) (RRID:SCR_004472) Copy
https://portal.bsc.gwu.edu/web/lifemoms
A consortium whose overall goal is to identify effective behavioral and lifestyle interventions that will improve weight, glycemic control and other pregnancy-related outcomes in obese and overweight pregnant women, and determine whether these interventions reduce obesity and metabolic abnormalities in their children. The study/consortium is comprised of seven clinical centers, with each clinical center conducting its own trial. Additional information on the consortium and individual trials is located in the Consortium Summaries tab.
Proper citation: Lifestyle Interventions for Expectant Moms (LIFE-Moms) (RRID:SCR_014376) Copy
A database which provides ribosome related data services to the scientific community, including online data analysis, rRNA derived phylogenetic trees, and aligned and annotated rRNA sequences. It specifically contains information on quality-controlled, aligned and annotated bacterial and archaean 16S rRNA sequences, fungal 28S rRNA sequences, and a suite of analysis tools for the scientific community. Most of the RDP tools are now available as open source packages for users to incorporate in their local workflow.
Proper citation: Ribosomal Database Project (RRID:SCR_006633) Copy
https://medicine.yale.edu/keck/nida/yped/
Open source system for storage, retrieval, and integrated analysis of large amounts of data from high throughput proteomic technologies. YPED currently handles LCMS, MudPIT, ICAT, iTRAQ, SILAC, 2D Gel and DIGE. The repository contains data sets which have been released for public viewing and downloading by the responsible Primary Investigators. It includes proteomic data generated by the Yale NIDA Neuroproteomics Center (http://medicine.yale.edu/keck/nida/index.aspx). Sample descriptions are compatible with the evolving MIAPE standards.
Proper citation: YPED (RRID:SCR_001436) Copy
http://amp.pharm.mssm.edu/LJP/
Interactive on line tool where signatures are tagged with user selected metadata and external transcript signatures are projected onto network. Browser to visualize signatures from breast cancer cell lines treated with single molecule perturbations.
Proper citation: LINCS Joint Project - Breast Cancer Network Browser (RRID:SCR_016181) Copy
Web page for cyclic immunofluorescence. It lists several downloadable data and software pertaining to cyclic immunofluorescence.
Proper citation: CycIF.org (RRID:SCR_016267) Copy
https://hub.docker.com/r/biodepot/star-for-criu/
Software as an Hot Start software container for STAR alignment using CRIU (Checkpoint Restore in Userspace) tool to freeze the running container. Can be deployed to align RNA sequencing data. Used in the processing of biomedical big data for better reproducibility and reliability.
Proper citation: star-for-criu (RRID:SCR_016294) Copy
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
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
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
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
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