Tools   Select Another Resource Report Type

http://marrvel.org/

Web tool to search multiple public variant databases simultaneously and provide a unified interface to facilitate the search process. Used for integration of human and model organism genetic resources to facilitate functional annotation of the human genome. Used for analysis of human genes and variants by cross-disciplinary integration of records available in public databases to facilitate clinical diagnosis and basic research.

Proper citation: MARRVEL (RRID:SCR_016871) Copy   

•   Source: SciCrunch Registry

https://pachterlab.github.io/sleuth/about

Software tool for analysis of RNA-Seq experiments for which transcript abundances have been quantified with kallisto. Used for the differential analysis of gene expression data that utilizes bootstrapping in conjunction with response error linear modeling to decouple biological variance from inferential variance.

Proper citation: sleuth (RRID:SCR_016883) Copy   

•   Source: SciCrunch Registry

https://github.com/yarden/MISO/blob/fastmiso/docs/source/sashimi.rst

Software tool for quantitative visualization of aligned RNA-Seq reads that enables quantitative comparison of exon usage across samples or experimental conditions.

Proper citation: Sashimiplot (RRID:SCR_016861) Copy   

•   Source: SciCrunch Registry

https://combine-lab.github.io/salmon/

Software tool for quantifying expression of transcripts using RNA-seq data. Provides fast and bias-aware quantification of transcript expression. Transcriptome-wide quantifier to correct for fragment GC-content bias.

Proper citation: Salmon (RRID:SCR_017036) Copy   

•   Source: SciCrunch Registry

https://panoramaweb.org/project/home/begin.view?

Repository software for targeted mass spectrometry assays from Skyline. Targeted proteomics knowledge base. Public repository for quantitative data sets processed in Skyline. Facilitates viewing, sharing, and disseminating results contained in Skyline documents.

Proper citation: PanoramaWeb (RRID:SCR_017136) Copy   

•   Source: SciCrunch Registry

http://research.mssm.edu/integrative-network-biology/Software.html

Software tool as probabilistic multi omics data matching procedure to curate data, identify and correct data annotation and errors in large databases. Used to check potential labeling errors in profiles where number of cis relationships is small, such as miRNA and RPPA profiles.

Proper citation: proMODMatcher (RRID:SCR_017219) 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

http://pathwaynet.princeton.edu/

Web user interface for interaction predictions of human gene networks and integrative analysis of user data types that takes advantage of data from diverse tissue and cell-lineage origins. Predicts presence of functional association and interaction type among human genes or its protein products on whole genome scale. Used to analyze experimetnal gene in context of interaction networks.

Proper citation: PathwayNet (RRID:SCR_017353) Copy   

•   Source: SciCrunch Registry

https://github.com/brentp/peddy

Software package that evaluates correspondence between stated sexes, relationships, and ancestries in pedigree file and those inferred from genotypes in VCF file resulting from human whole genome sequencing or whole exome sequencing studies. Facilitates both automated and interactive, visual detection of sample swaps, poor sequencing quality, and other indicators of sample problems.

Proper citation: peddy (RRID:SCR_017287) Copy   

•   Source: SciCrunch Registry

http://topaz.gatech.edu/GeneMark/

Software package for ab initio identification of protein coding regions in RNA transcripts. Algorithm parameters are estimated by unsupervised training which makes unnecessary manually curated preparation of training sets. Sets of assembled eukaryotic transcripts can be analyzed by modified GeneMarkS-T algorithm which part of gene prediction programs GeneMark.

Proper citation: GeneMarkS-T (RRID:SCR_017648) Copy   

•   Source: SciCrunch Registry

https://pachterlab.github.io/cgal/

Software tool for computing genome assembly likelihoods.Computes likelihood of reads with respect to assembly and statistical model which can be used as metric for evaluating assemblies. Novel likelihood based approach to assembly assessment in absence of ground truth.

Proper citation: Computing Genome Assembly Likelihoods (RRID:SCR_017624) Copy   

•   Source: SciCrunch Registry

https://github.com/YosefLab/FastProject

Software Python tool for low dimensional analysis of single-cell RNA-Seq data. Software package for two dimensional visualization of single cell data. Analyzes gene expression matrix and produces output report in which two-dimensional of data can be explored.

Proper citation: FastProject (RRID:SCR_017462) Copy   

•   Source: SciCrunch Registry

http://geneontology.org/docs/go-consortium/

Consortium integrates resources from variety of research groups, from model organisms to protein databases to biological research communities actively involved in development and implementation of Gene Ontology. Mission to develop up to date, comprehensive, computational model of biological systems, from molecular level to larger pathways, cellular and organism level systems.

Proper citation: GO Gene Ontology Consortium and Knowledgebase (RRID:SCR_017505) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://genenames.org

Only worldwide authority that provides standardized nomenclature, i.e. gene names and symbols (short form abbreviations), for all known human genes, and stores all approved symbols in the HGNC database. Approved human gene nomenclature. Database of gene symbols and names. Manually curated genes into groups based on shared characteristics such as homology, function or phenotype. Data for protein-coding genes, pseudogenes and non-coding RNAs.

Proper citation: HGNC (RRID:SCR_002827) Copy   

•   Source: SciCrunch Registry

http://www.wormbase.org

Central data repository for nematode biology including complete genomic sequence, gene predictions and orthology assignments from range of related nematodes.Data concerning genetics, genomics and biology of C. elegans and related nematodes. Derived from initial ACeDB database of C. elegans genetic and sequence information, WormBase includes genomic, anatomical and functional information of C. elegans, other Caenorhabditis species and other nematodes. Maintains public FTP site where researchers can find many commonly requested files and datasets, WormBase software and prepackaged databases.

Proper citation: WormBase (RRID:SCR_003098) Copy   

•   Source: SciCrunch Registry

http://www.bioperl.org

BioPerl is a community effort to produce Perl code which is useful in biology. This toolkit of perl modules is useful in building bioinformatics solutions in Perl. It is built in an object-oriented manner so that many modules depend on each other to achieve a task. The collection of modules in the bioperl-live repository consist of the core of the functionality of bioperl. Additionally auxiliary modules for creating graphical interfaces (bioperl-gui), persistent storage in RDMBS (bioperl-db), running and parsing the results from hundreds of bioinformatics applications (Run package), software to automate bioinformatic analyses (bioperl-pipeline) are all available as Git modules in our repository. The BioPerl toolkit provides a library of hundreds of routines for processing sequence, annotation, alignment, and sequence analysis reports. It often serves as a bridge between different computational biology applications assisting the user to construct analysis pipelines. This chapter illustrates how BioPerl facilitates tasks such as writing scripts summarizing information from BLAST reports or extracting key annotation details from a GenBank sequence record. BioPerl includes modules written by Sohel Merchant of the GO Consortium for parsing and manipulating OBO ontologies. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: BioPerl (RRID:SCR_002989) Copy   

•   Source: SciCrunch Registry

http://www.bioontology.org

Organization that provides biomedical researchers with online tools and a web portal enabling them to access, review, and integrate disparate ontological resources in all aspects of biomedical investigation and clinical practice. A major focus of the work involves the use of biomedical ontologies to aid in the management and analysis of data derived from complex experiments.

Proper citation: National Center for Biomedical Ontology (RRID:SCR_003304) Copy   

•   Source: SciCrunch Registry

http://hanalyzer.sourceforge.net/

An open-source data integration system designed to assist biologists in explaining the results observed in genome-scale experiments as well as generating new hypotheses. It combines information extraction techniques, semantic data integration, and reasoning and facilitates network visualization. The Hanalyzer source code and binaries are available for download.

Proper citation: Hanalyzer (RRID:SCR_000923) Copy   

•   Source: SciCrunch Registry