Curator Dashboard

Software package that contains classes and methods useful for storing, visualizing and analyzing high density SNP data. Originally developed from the SNPscan web-tool, SNPchip utilizes S4 classes and extends other open source R tools available at Bioconductor, including the R packages Biobase and oligo. This has numerous advantages, including the ability to build statistical models for SNP-level data that operate on instances of the class, and to communicate with other R packages that add additional functionality.

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• SciCrunch
• 13 years ago - by Anonymous

Network of clinical centers and a data coordinating center established to conduct studies of islet transplantation in patients with type 1 diabetes.

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• dkNET
• 11 years ago - submitted by Ko-Wei Lin

Software package to generate GD images of Bio::Seq objects.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software package for quality control of Affymetrix GeneChip expression data and reproducibility analysis of human whole genome chips with the MAQC reference datasets.

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• SciCrunch
• 13 years ago - by Anonymous

International effort which has created a glycomics knowledgebase with access to a database of information on the glycan structures of glycoproteins. It serves as and promotes an online information storage and search platform for glycomics and glycobiology research. Open access knowledgebase offers resource supported by querying interfaces, annotation technologies and the adoption of common standards to integrate structural, experimental and functional data.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

Software collection of data structures and algorithms. Contains I/O classes (single byte and UTF-8), bitio classes (input, output and various forms of bit level manipulation), text indexing classes (suffix and LCP array, fulltext and minute (FM), ...), BAM sequence alignment files input/output (simple and collating) and many lower level support classes.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software package for quality assessment and to detect differentially expressed genes for the Affymetrix GeneChips, including both 3' -arrays and gene 1.0-ST arrays. The package generates comprehensive analysis reports in HTML format. Hyperlinks on the report page will lead to a series of QC plots, processed data, and differentially expressed gene lists. Differentially expressed genes are reported in tabular format with annotations hyperlinked to online biological databases.

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• SciCrunch
• 13 years ago - by Anonymous

Open source software tool that simulates experimental RNA-seq and DNA whole exome sequences derived from reference genome, aligns these sequences by custom parameters, detects variants and outputs blacklist of positions and alleles caused by mismapping. Used to characterize mappability of RNA-Seq reads and create blacklist of genomic positions of mismapped reads. This blacklist is used to filter potential false positives from variant or RNA editing calls.

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• SciCrunch
• 13 years ago - by Anonymous

Software library as set of classes for creating statistical genetic programs.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

A microarray normalization software (SCAN) to facilitate personalized-medicine workflows with an extension (UPC) that estimates whether a given gene/transcript is active above background levels in a given sample. Rather than processing microarray samples as groups, which can introduce biases and present logistical challenges, SCAN normalizes each sample individually by modeling and removing probe- and array-specific background noise using only data from within each array. SCAN can be applied to one-channel (e.g., Affymetrix) or two-channel (e.g., Agilent) microarrays. The UPC method can be applied to one-channel or two-channel microarrays as well as to RNA-Seq read counts. Because UPC values are represented on the same scale and have an identical interpretation for each platform, they can be used for cross-platform data integration. A

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• SciCrunch
• 13 years ago - by Anonymous

A web-interface that enables users to access and download the processed ChIP chip/seq data of nuclear receptors, co-regulators and histone modifications. The web resources also includes processed differential expression data under ligand induction in conditions matched to ChIP_chip/seq data whenever possible. All the ChIP chip/seq peak regions are annotated with enriched HRE and co-regulator motifs. A list of predicted hormone response genes from integration of nuclear receptor ChIP chip/seq data and differential expression data is also readily available to the users.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

Software tool as general purpose cluster algorithm for both weighted and unweighted networks. Unsupervised cluster algorithm for graphs based on simulation of stochastic flow in graphs. Cluster algorithm for graphs.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software package for data transformation for meta-analysis of microarray Data: Transformation of gene expression data to signed probability scale (MCMC/EM methods) and combined differential expression on raw scale: Weighted Z-score after stabilizing mean-variance relation within platform.

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• SciCrunch
• 13 years ago - by Anonymous

A national tissue bank that provides management for database purposes, on-line ordering, guidelines, educational programs, policy making and certification of resources.

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• SciCrunch
• 16 years ago - by Anonymous

Software package to remove reads mapping to the lambda phage genome from a fastq file.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Open source Java library dedicated to semantic measures computation and analysis. Tools based on the SML are also provided through the SML-Toolkit, a command line software giving access to some of the functionalities of the library. The SML and the toolkit can be used to compute semantic similarity and semantic relatedness between semantic elements (e.g. concepts, terms) or entities semantically characterized (e.g. entities defined in a semantic graph, documents annotated by concepts defined in an ontology).

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• SciCrunch
• 14 years ago - by Anonymous

Archival database of cell lines and microbial strains. Maintained by Public Health England, the database is used by scientists to determine the effects of various substances on human cells as well as for controls for diagnostic and antimicrobial susceptibility tests.

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• SciCrunch
• 17 years ago - by Anonymous

Software package for analysing NGS data in DNA metabarcoding context. Used to filter and edit sequences while taking into account taxonomic annotation to set up tailor-made analysis pipelines for broad range of DNA metabarcoding applications, including biodiversity surveys or diet analyses.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software library containing tools for statistical manipulations of data. Tools include profile hidden Markov models for biological sequence analysis, RNA structure analysis, and a prototype noncoding RNA genefinder.

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• SciCrunch
• 17 years ago - by Anonymous

A statistical software package for comparing metagenomic datasets and clinical data sets comprised of two treatment populations, with each treatment population being made up of multiple samples. It relies on a non-parametric t-test.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen