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https://bioconductor.org/packages/GenomeInfoDb/

Software R package contains data and functions that define and allow translation between different chromosome sequence naming conventions, including function that attempts to place sequence names in their natural, rather than lexicographic order.

Proper citation: genomeinfodb (RRID:SCR_024235) Copy   

•   Source: SciCrunch Registry
  

http://swissknife.sourceforge.net

Software object oriented Perl library to handle Swiss-Prot entries

Proper citation: libswiss-perl (RRID:SCR_024356) Copy   

•   Source: SciCrunch Registry
  

https://bioconductor.org/packages/release/bioc/html/GenomicAlignments.html

Software R package provides efficient containers for storing and manipulating short genomic alignments. This includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments.

Proper citation: genomicalignments (RRID:SCR_024236) Copy   

•   Source: SciCrunch Registry
  

https://bioconductor.org/packages/release/bioc/html/BiocGenerics.html

Software R package defines many S4 generic functions used in Bioconductor.

Proper citation: BiocGenerics (RRID:SCR_024226) Copy   

•   Source: SciCrunch Registry
  

https://bioconductor.org/packages/release/bioc/html/biomformat.html

Software R package for interfacing with BIOM format. This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, limited support for writing biom-object back to biom-format file.

Proper citation: biomformat (RRID:SCR_024228) Copy   

•   Source: SciCrunch Registry
  

https://bioconductor.org/packages/release/bioc/html/biovizBase.html

Software R package to provide set of utilities, color schemes and conventions for genomic data. Used for various high-level packages for biological data visualization.

Proper citation: biovizBase (RRID:SCR_024229) Copy   

•   Source: SciCrunch Registry
  

https://bioconductor.org/packages/release/data/annotation/html/GO.db.html

Software R package provides set of annotation maps describing entire Gene Ontology assembled using data from GO.

Proper citation: go.db (RRID:SCR_024241) Copy   

•   Source: SciCrunch Registry
  

https://bioconductor.org/packages/impute/

Software R package for imputation for microarray data.

Proper citation: impute (RRID:SCR_024243) Copy   

•   Source: SciCrunch Registry
  

http://gpcr.biocomp.unibo.it/esldb

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 22,2022. database of protein subcellular localization annotation for eukaryotic organisms. It contains experimental annotations derived from primary protein databases, homology based annotations and computational predictions.

Proper citation: eSLDB - eukaryotic Subcellular Localization database (RRID:SCR_000052) Copy   

•   Source: SciCrunch Registry
  

https://bioconductor.org/packages/Mergeomics/

Software R pacakage for multidimensional data integration to identify pathogenic perturbations to biological systems. Used for integrating multidimensional omics disease associations, functional genomics, canonical pathways and gene-gene interaction networks to generate mechanistic hypotheses. Includes Marker set enrichment analysis and Weighted Key Driver Analysis parts.

Proper citation: mergeomics (RRID:SCR_024244) Copy   

•   Source: SciCrunch Registry
  

https://www.mathworks.com/products/optimization.html

Software package provides functions for finding parameters that minimize or maximize objectives while satisfying constraints. Toolbox includes solvers for linear programming, mixed integer linear programming, quadratic programming, second order cone programming, nonlinear programming, constrained linear least squares, nonlinear least squares, nonlinear equations.

Proper citation: Optimization Toolbox (RRID:SCR_024486) Copy   

•   Source: SciCrunch Registry
  

https://bioconductor.org/packages/metagenomeSeq/

Software R package to determine features that are differentially abundant between two or more groups of multiple samples. Used to address the effects of both normalization and under-sampling of microbial communities on disease association detection and testing of feature correlations.

Proper citation: metagenomeseq (RRID:SCR_024246) Copy   

•   Source: SciCrunch Registry
  

https://graphics.stanford.edu/software/volpack/

Portable software library for volume rendering.

Proper citation: VolPack (RRID:SCR_024367) Copy   

•   Source: SciCrunch Registry
  

https://github.com/danbider/lightning-pose

Software video centric package for direct video manipulation. Semi supervised animal pose estimation algorithm, Bayesian post processing approach and deep learning package. Improved animal pose estimation via semi-supervised learning, Bayesian ensembling, and cloud-native open-source tools.

Proper citation: Lightning Pose (RRID:SCR_024480) Copy   

•   Source: SciCrunch Registry
  

https://bioconductor.org/packages/Gviz/

Software R package to perform live annotation queries to Ensembl and UCSC and translates this to e.g. gene/transcript structures in viewports of the grid graphics package.

Proper citation: gviz (RRID:SCR_024239) Copy   

•   Source: SciCrunch Registry
  

http://www.ctsi.umn.edu/consultations-and-services/specimen-procurement/histology-and-ihc-laboratory

Lab based at the University of Minnesota that provides histology services, including frozen sectioning, tissue grossing, fixation, and sectioning, optimization and performance of immunohistochemistry (IHC).

Proper citation: University of Minnesota Histology and Immunohistochemistry Laboratory (RRID:SCR_001056) Copy   

•   Source: SciCrunch Registry
  

http://lifespandb.sageweb.org/

Database that collects published lifespan data across multiple species. The entire database is available for download in various formats including XML, YAML and CSV.

Proper citation: Lifespan Observations Database (RRID:SCR_001609) Copy   

•   Source: SciCrunch Registry
  

http://www.flyprot.org/

Allows annotation of gene expression at all stages of development and tissue types (including sub cellular location) using standard Drosophila anatomy ontology. All methods of input use a controlled vocabulary to ensure data integrity.

Proper citation: Flannotator (RRID:SCR_001608) Copy   

•   Source: SciCrunch Registry
  

http://interolog.gersteinlab.org/

Interolog/Regulog quantitatively assess the degree to which interologs can be reliably transferred between species as a function of the sequence similarity of the corresponding interacting proteins.

Proper citation: Interolog/Regulog Database (RRID:SCR_000755) Copy   

•   Source: SciCrunch Registry
  

http://cddb.nhlbi.nih.gov/cddb/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. This database is intended to serve as a learning tool to obtain curated information for the design of microarray targets to scan collecting duct tissues (human, rat, mouse). The database focuses on regulatory and transporter proteins expressed in the collecting duct, but when collecting duct proteins are a member of a larger family of proteins, common additional members of the family are included even if they have not been demonstrated to be expressed in the collecting duct. An Internet-accessible database has been devised for major collecting duct proteins involved in transport and regulation of cellular processes. The individual proteins included in this database are those culled from literature searches and from previously published studies involving cDNA arrays and serial analysis of gene expression (SAGE). Design of microarray targets for the study of kidney collecting duct tissues is facilitated by the database, which includes links to curated base pair and amino acid sequence data, relevant literature, and related databases. Use of the database is illustrated by a search for water channel proteins, aquaporins, and by a subsequent search for vasopressin receptors. Links are shown to the literature and to sequence data for human, rat, and mouse, as well as to relevant web-based resources. Extension of the database is dynamic and is done through a maintenance interface. This permits creation of new categories, updating of existing entries, and addition of new ones. CDDB is a database that organizes lists of genes found in collecting duct tissues from three mammalian species: human, rat, and mouse. Proteins are divided into categories by family relationships and functional classification, and each category is assigned a section in the database. Each section includes links to the literature and to sequence information for genes, proteins, expressed sequence tags, and related information. The user can peruse a section or use a search engine at the bottom of the web page to search the database for a name or abbreviation or for a link to a sequence. Each entry in the database includes links to relevant papers in the kidney and collecting duct literature. It uses links to PubMed to generate MEDLINE searches for retrieval of references. In addition, each entry includes links to curated sequence data available in LocusLink. Individual links are made to sequence and protein data for human, rat, and mouse. Links are then added as curated sequences become available for proteins identified in the renal collecting duct and for proteins identified in kidney and similar in function or homologous to proteins identified in the collecting duct.

Proper citation: Collecting Duct Database (RRID:SCR_000759) Copy   

•   Source: SciCrunch Registry