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https://amp.pharm.mssm.edu/geneshot/
Software tool as search engine for ranking genes from arbitrary text queries. Enables to enter arbitrary search terms, to receive ranked lists of genes relevant to search terms. Returned ranked gene lists contain genes that were previously published in association with search terms, as well as genes predicted to be associated with terms based on data integration from multiple sources. Search results are presented with interactive visualizations.
Proper citation: Geneshot (RRID:SCR_017582) Copy
https://imputationserver.sph.umich.edu/
Web server to implement whole genotype imputation workflow for efficient parallelization of computationally intensive tasks. Service for imputation that facilitates access to new reference panels and greatly improves user experience and productivity. Used to find haplotype segments and reference panel of sequenced genomes, assign genotypes at untyped markers, improve genome coverage, facilitate comparison and combination of studies that use different marker panels, increase power to detect genetic association, and guide fine mapping.
Proper citation: Michigan Imputation Server (RRID:SCR_017579) Copy
https://rgd.mcw.edu/QueryBuilder/
Software text mining tool aiding curation at Rat Genome Database. Ontology driven, concept based literature search engine developed at RGD. Tags abstracts with gene names, gene mutations, organism names and terms from ontologies vocabularies used at RGD. Open and fully customizable.
Proper citation: OntoMate (RRID:SCR_018493) Copy
https://maayanlab.cloud/chea3/
Web based transcription factor enrichment analysis. Web server ranks TFs associated with user-submitted gene sets. ChEA3 background database contains collection of gene set libraries generated from multiple sources including TF-gene co-expression from RNA-seq studies, TF-target associations from ChIP-seq experiments, and TF-gene co-occurrence computed from crowd-submitted gene lists. Enrichment results from these distinct sources are integrated to generate composite rank that improves prediction of correct upstream TF compared to ranks produced by individual libraries.
Proper citation: ChIP-X Enrichment Analysis 3 (RRID:SCR_023159) Copy
https://imputationserver.sph.umich.edu/index.html#!pages/home
Web based service for imputation that facilitates access to new reference panels and improves user experience and productivity. Server implements whole genotype imputation workflow using MapReduce programming model for efficient parallelization of computationally intensive tasks. Genotype imputation service using Minimac4.
Proper citation: Michigan Imputation Server (RRID:SCR_023554) Copy
Web server application that infers overrepresentation of upstream kinases whose putative substrates are in user inputted list of proteins. Used to analyze data from phosphoproteomics and proteomics studies to predict upstream kinases responsible for observed differential phosphorylations.
Proper citation: Kinase Enrichment Analysis 3 (RRID:SCR_023623) Copy
https://esp.gs.washington.edu/
Project focused on understanding the contribution of rare genetic variation to heart, lung and blood disorders through the sequencing of well-phenotyped populations.
Proper citation: NHLBI Grand Opportunity Exome Sequencing Project (RRID:SCR_010798) Copy
http://drugtargetontology.org/
Ontology of drug targets to be used as a reference for drug targets, with the longer-term goal of creating a community standard that will facilitate the integration of diverse drug discovery information from numerous heterogeneous resources. The project itself aims to develop a novel semantic framework to formalize knowledge about drug targets with a focus on the current IDG protein families.
Proper citation: Drug Target Ontology (RRID:SCR_015581) Copy
http://amp.pharm.mssm.edu/gen3va/
Software tool for aggregation and analysis of gene expression signatures from related studies.Used to aggregate and analyze gene expression signatures extracted from GEO by crowd using GEO2Enrichr. Used to view aggregated report that provides global, interactive views, including enrichment analyses, for collections of signatures from multiple studies sharing biological theme.
Proper citation: GEN3VA (RRID:SCR_015682) Copy
http://amp.pharm.mssm.edu/CREEDS/
Software resource that allows students or the general public find variants that may be significantly associated with some disease. CREEDS also visualizes and analyzes gene expression signatures.
Proper citation: CRowd Extracted Expression of Differential Signatures (RRID:SCR_015680) Copy
http://amp.pharm.mssm.edu/L1000CDS2
LINCS L1000 characteristic direction signatures search engine. Software tool to find consensus signatures that match user’s input gene lists or input signatures. Underlying dataset is LINCS L1000 small molecule expression profiles generated at Broad Institute by Connectivity Map team. Differentially expressed genes of these profiles were calculated using multivariate method called Characteristic Direction.
Proper citation: L1000 Characteristic Direction Signature Search Engine (RRID:SCR_016177) Copy
http://amp.pharm.mssm.edu/Harmonizome/
Web application that allows for searching, visualization, and prediction about genes and proteins. It contains a collection of processed datasets gathered to serve and mine knowledge about genes and proteins from major online resources.
Proper citation: Harmonizome (RRID:SCR_016176) Copy
http://omics.informatics.indiana.edu/AbundantOTU/
Software tool for analysis of large 16S rRNA pyrosequences by using a consensus alignment algorithm, utilizing the sequence redundancy of abundant species in the pyrosequence dataset.
Proper citation: AbundantOTU+ (RRID:SCR_016527) Copy
Project to create network based understanding of biology by cataloging changes in gene expression and other cellular processes when cells are exposed to genetic and environmental stressors. Program to develop therapies that might restore pathways and networks to their normal states. Has LINCS Data Coordination and Integration Center and six Data and Signature Generation Centers: Drug Toxicity Signature Generation Center, HMS LINCS Center, LINCS Center for Transcriptomics, LINCS Proteomic Characterization Center for Signaling and Epigenetics, MEP LINCS Center, and NeuroLINCS Center.
Proper citation: LINCS Project (RRID:SCR_016486) Copy
System for sharing sleep data. Organization portal that aggregates, harmonizes, and organizes sleep and clinical data from individuals studied as part of cohort studies or clinical trials and provides suite of tools to facilitate data exploration and data visualization. National Heart, Lung, and Blood Institute resource designed to provide big data resources to sleep research community.
Proper citation: National Sleep Research Resource (NSRR) (RRID:SCR_016576) Copy
http://sleepdisordergenetics.org
Software platform for accelerating genetic discoveries for sleep disturbance and circadian traits.
Proper citation: Sleep Disorder Knowledge Portal (RRID:SCR_016611) Copy
https://sleepdata.org/datasets/cfs
Portal for family based study of sleep apnea. Contains data for quantifying the familial aggregation of sleep apnea. The polysomnographic (PSG) montage signals: EEG, ECG, EOG, EMG, SpO2, plethysmography, airflow (thermistor), nasal pressure, respiratory effort, position, snore.
Proper citation: Cleveland Family Study (RRID:SCR_016585) Copy
https://github.com/hakyimlab/PrediXcan
Software tool to detect known and novel genes associated with disease traits and provide insights into the mechanism of these associations. Used to test the molecular mechanisms through which genetic variation affects phenotype.
Proper citation: PrediXcan (RRID:SCR_016739) Copy
http://bioconductor.org/packages/GenomicFeatures/
Software R package for making and manipulating transcript centric annotations. Used to download the genomic locations of the transcripts, exons and cds of a given organism, from either the UCSC Genome Browser or a BioMart database.
Proper citation: GenomicFeatures (RRID:SCR_016960) Copy
https://www.sciencescott.com/pyminer
Software tool to automate cell type identification, cell type-specific pathway analyses, graph theory-based analysis of gene regulation, and detection of autocrine-paracrine signaling networks. Finds Gene and Autocrine-Paracrine Networks from Human Islet scRNA-Seq.
Proper citation: PyMINEr (RRID:SCR_016990) Copy
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