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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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages/release/bioc/html/SingleR.html

Software R package for unbiased cell type recognition of scRNA-seq data. Performs unbiased cell type recognition from single-cell RNA sequencing data, by leveraging reference transcriptomic datasets of pure cell types to infer cell of origin of each single cell independently.

Proper citation: SingleR (RRID:SCR_023120) Copy   

•   Source: SciCrunch Registry

https://github.com/rondolab/MR-PRESSO

Software R package for performing Mendelian randomization pleiotropy residual sum and outlier method.Used to identify horizontal pleiotropic outliers in multi instrument summary level MR testing.

Proper citation: MR-PRESSO (RRID:SCR_023697) Copy   

•   Source: SciCrunch Registry

http://pipeline.lbl.gov/cgi-bin/gateway2

Software tools for comparative genomics.Comprehensive suite of programs and databases for comparative analysis of genomic sequences. There are two ways of using VISTA - you can submit your own sequences and alignments for analysis (VISTA servers) or examine pre-computed whole-genome alignments of different species.

Proper citation: VISTA Browser (RRID:SCR_011808) Copy   

•   Source: SciCrunch Registry

https://data.broadinstitute.org/alkesgroup/Eagle/

Software package for statistical estimation of haplotype phase either within a genotyped cohort or using a phased reference panel in large scale sequencing. The package includes Eagle1 (to harness identity-by-descent among distant relatives to rapidly call phase using a fast scoring approach) and Eagle2 (to analyze a full probabilistic model similar to the diploid Li-Stephens model used by previous HMM-based methods.

Proper citation: Eagle (RRID:SCR_015991) Copy   

•   Source: SciCrunch Registry

https://github.com/biojs

An open source JavaScript library of components for visualisation of biological data on the web.

Proper citation: BioJS (RRID:SCR_003119) Copy   

•   Source: SciCrunch Registry

http://www.nsrrc.missouri.edu/

Provides access to critically needed swine models of human health and disease as well as a central resource for reagents, creation of new genetically modified swine, and information and training related to use of swine models in biomedical research.

Proper citation: National Swine Resource and Research Center (RRID:SCR_006855) Copy   

•   Source: SciCrunch Registry

https://www.synapse.org/

A cloud-based collaborative platform which co-locates data, code, and computing resources for analyzing genome-scale data and seamlessly integrates these services allowing scientists to share and analyze data together. Synapse consists of a web portal integrated with the R/Bioconductor statistical package and will be integrated with additional tools. The web portal is organized around the concept of a Project which is an environment where you can interact, share data, and analysis methods with a specific group of users or broadly across open collaborations. Projects provide an organizational structure to interact with data, code and analyses, and to track data provenance. A project can be created by anyone with a Synapse account and can be shared among all Synapse users or restricted to a specific team. Public data projects include the Synapse Commons Repository (SCR) (syn150935) and the metaGenomics project (syn275039). The SCR provides access to raw data and phenotypic information for publicly available genomic data sets, such as GEO and TCGA. The metaGenomics project provides standardized preprocessed data and precomputed analysis of the public SCR data.

Proper citation: Synapse (RRID:SCR_006307) Copy   

•   Source: SciCrunch Registry

http://hms-dbmi.github.io/scde/index.html

Software package that implements a set of statistical methods for analyzing single-cell RNA-seq data, including differential expression analysis (Kharchenko et al.) and pathway and geneset overdispersion analysis (Fan et al.)

Proper citation: SCDE (RRID:SCR_015952) Copy   

•   Source: SciCrunch Registry

https://github.com/BioDepot/BioDepot-workflow-builder

Software tool to create and execute reproducible bioinformatics workflows using drag and drop interface. Graphical widgets represent Docker containers executing modular task. Widgets are linked graphically to build bioinformatics workflows that can be reproducibly deployed across different local and cloud platforms. Each widget contains form-based user interface to facilitate parameter entry and console to display intermediate results.

Proper citation: BioDepot-workflow-builder (RRID:SCR_017402) Copy   

•   Source: SciCrunch Registry

http://www.bumc.bu.edu/cardiovascularproteomics/cpctools/strap/

Software program that automatically annotates a protein list with information that helps in the meaningful interpretation of data from mass spectrometry and other techniques. It takes protein lists as input, in the form of plain text files, protXML files (usually from the TPP), or Dat files from MASCOT search results. From this, it generates protein annotation tables, and a variety of GO charts to aid individual and differential analysis of proteomics data. It downloads information from mainly the Uniprot and EBI QuickGO databases. STRAP requires Windows XP or higher with at least version 3.5 of the Microsoft .NET Framework installed. Platform: Windows compatible

Proper citation: STRAP (RRID:SCR_005675) Copy   

•   Source: SciCrunch Registry

http://www.mouse-genome.bcm.tmc.edu/ENU/MutagenesisProj.asp

THIS RESOURCE IS NO LONGER IN SERVICE. For updated mutant information, please visit MMRRC or The Jackson Laboratory. Produces, characterizes, and distributes mutant mouse strains with defects in embryonic and postembryonic development. The goal of the ENU Mutagenesis project III is to determine the function of genes on mouse Chromosome 11 by saturating the chromosome with recessive mutations. The distal 40 cM of mouse Chr 11 exhibits linkage conservation with human Chromosome 17. We are using the chemical N-ethyl-N-nitrosourea (ENU) to saturate wild type chromosomes with point mutations. By determining the function of genes on a mouse chromosome, we can extrapolate to predict function on a human chromosome. We expect many of the new mutants to represent models of human diseases such as birth defects, patterning defects, growth and endocrine defects, neurological anomalies, and blood defects. Because many of the mutations we expect to isolate may be lethal or detrimental to the mice, we are using a unique approach to isolate mutations. This approach uses a balancer chromosome that is homozygous lethal and carries a dominant coat color marker to suppress recombination over a reasonable interval.

Proper citation: Mouse Mutagenesis Center for Developmental Defects (RRID:SCR_007321) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://crispresso.pinellolab.partners.org/submission

Software suite of tools to qualitatively and quantitatively evaluate outcomes of genome editing experiments in which target loci are subject to deep sequencing and provides integrated, user friendly interface. Used for analysis of CRISPR-Cas9 genome editing outcomes from sequencing data. CRISPResso2 provides accurate and rapid genome editing sequence analysis.Used for analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments.

Proper citation: CRISPResso (RRID:SCR_021538) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/GenomicRanges/

Software R package for computing and annotating genomic ranges. Used for storing and manipulating genomic intervals and variables defined along genome.

Proper citation: Genomic Ranges (RRID:SCR_017051) Copy   

•   Source: SciCrunch Registry

https://github.com/aidenlab/juicer.git

Software platform for analyzing kilobase resolution Hi-C data. Open source tool for analyzing terabase scale Hi-C datasets. Allowes to transform raw sequence data into normalized contact maps.

Proper citation: Juicer (RRID:SCR_017226) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry