Curator Dashboard

A software package for meta-analysis of high-throughput experiments using feature annotations. It calculates significant annotations (categories) in each of two (or more) feature (i.e. gene) lists, determines the overlap between the annotations, and returns graphical and tabular data about the significant annotations and which combinations of feature lists the annotations were found to be significant. Interactive exploration is facilitated through the use of RCytoscape (heavily suggested).

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• SciCrunch
• 13 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Software for secondary and tertiary analysis of Next Generation Sequencing (NGS) data.

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• SciCrunch
• 13 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. R extension whose functions are intended for cross-study comparison of gene expression array data. Required from the user is gene expression matrices, their corresponding gene-id vectors and other useful information, and they could be "list", "matrix", or "ExpressionSet". The main function is "mergeExprs" which transforms the input objects into data in the merged format, such that common genes in different datasets can be easily found. And the function "intcor" calculate the correlation coefficients. Other functions use the output from "modelOutcome" to graphically display the results and cross-validate associations of gene expression data with survival.

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• SciCrunch
• 13 years ago - by Anonymous

An ion channel focused Contract Research Organization (CRO) that does safety testing and screening for global pharma and biotech companies. ChanTest has developed a complete library of validated human ion channel-expressing cell lines to serve all the ion channel needs of its pharmaceutical and biotech customers. Services range from early functional screens for profiling drug candidates or ranking within profiles during the drug-discovery process to a complete set of in vitro GLP service products for cardiac risk assessment. ChanTest works in partnership with customers to speed the drug-development process, save time and money, and ultimately to help make better, safer drugs.

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• SciCrunch
• 14 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented November 4, 2015. Web application based on the TM4 Microarray Software Suite to provide a means of normalization and analysis of microarray data. Users can upload data in the form of Affymetrix CEL files, and define an analysis pipeline by selecting several intuitive options. It performs data normalization (eg RMA), basic statistical analysis (eg t-test, ANOVA), and analysis of annotation using gene classification (eg Gene Ontology term assignment). The analysis are performed without user intervention and the results are presented in a web-based summary that allows data to be downloaded in a variety of formats compatible with further directed analysis.

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• SciCrunch
• 13 years ago - by Anonymous

Application that provides users an interface to design analysis protocols combining one or more normalization and filtering steps. In this way, data from many individual hybridizations can be treated in a uniform and reproducible manner.

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• 13 years ago - by Anonymous

A commercial organization for pharmaceutical, biopharmaceutical, and medical device open-access capability and technology platform with global operations.

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• SciCrunch
• 16 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022.Data management software implemented in Java that facilitates the entry of data into a relational database. It guides users through the microarray process from RNA procurement to data analysis, offering intelligent forms to simplify the tracking of experimental parameters and results that are essential for the interpretation of expression results in downstream analyses. Canned reports provide information on RNA samples, studies, slide maps and other pertinent data and a general SQL query window allows freeform access to the underlying database. MADAM also serves as a platform for launching other data entry and management tools. Through the use of these integrated modules, users can view and score PCR plates, design experiments and studies, and track laboratory materials.

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• SciCrunch
• 13 years ago - by Anonymous

Tool that provides high performance NGS (next-generation sequencing) data analysis pipelines so that researchers with minimum IT or bioinformatics knowledge can perform common analyses on NGS data. 3 TB of storage space is reserved for each task.

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• SciCrunch
• 13 years ago - by Anonymous

A collection of machine learning algorithms for data mining tasks. The algorithms can either be applied directly to a dataset or called from your own Java code. Weka contains tools for data pre-processing, classification, regression, clustering, association rules, and visualization. It is also well-suited for developing new machine learning schemes.

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• SciCrunch
• 13 years ago - by Anonymous

Software tool that delivers visualizations of your genomic data that give you the power to see what is occurring at each base pair in your samples. A high performance backend is paired with an user interface to make sure that your discovery process is fluid and streamlined.

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• SciCrunch
• 13 years ago - by Anonymous

Software to mimic various methylation level and bisulfite conversion rate in CpG, CHG and CHH context, respectively. It can also simulate genetic variations that are divergent from the reference sequence along with the sequencing error and quality distributions. In the output, both directional/non-directional, various read length, single/paired-end reads and alignment data in the SAM format can be generated. BSSim is a cross-platform BS-seq simulator offers output read datasets not only suitable for Illumina's Solexa, but also for Roche's 454 and Applied Biosystems' SOLiD.

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• SciCrunch
• 13 years ago - by Anonymous

Software for processing and analysis of high throughput (Roche 454) sequences generated from multiple loci and multiple biological samples. Sequences are assigned to their locus and sample of origin, aligned and trimmed. Where possible, genotypes are called and variants mapped to known alleles.

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• SciCrunch
• 13 years ago - by Anonymous

Software to address all aspects of Next Generation Sequencing data workflow.

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• SciCrunch
• 13 years ago - by Anonymous

Software application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data. It examines sequencing alignment data in SAM / BAM files according to the features of the mapped reads and provides an overall view of the data that helps to the detect biases in the sequencing and/or mapping of the data and eases decision-making for further analysis.

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• SciCrunch
• 13 years ago - by Anonymous

Software tool to generate a high resolution map of interaction sites between RNA-binding proteins and their targets. The algorithm utilizes the deep sequencing reads generated by the newly developed PAR-CLIP (Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation) protocol. The use of photoactivatable nucleotides in the PAR-CLIP protocol results in a more efficient crosslinking between the RNA-binding protein and its target relative to other CLIP methods; in addition a nucleotide substitution occurs at the site of crosslinking during Illumina library preparation. PARalyzer utilizes this nucleotide substition in a kernel density estimate classifier to generate the high resolution set of Protein-RNA interaction sites.

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• SciCrunch
• 13 years ago - by Anonymous

Software application suite to help clinical labs adopt next generation sequencing for the analysis of diagnostic gene targets.

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• SciCrunch
• 13 years ago - by Anonymous

An optional module in the Omixon Target application suite for HLA typing using NGS (next-generation sequencing) data that gives high resolution results with whole genome, exome or very targeted DNA data, or with RNA seq data.

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• SciCrunch
• 13 years ago - by Anonymous

A flexible computational platform, comprising both a command-line set of tools and a C++ API, for the analysis and manipulation of high-throughput sequencing data such as DNA-seq, RNA-seq, ChIP-seq and MethylC-seq. It implements a variety of mathematical operations between sets of genomic regions thereby enabling the prototyping of computational pipelines that can address tasks from preprocessing and quality control to meta-analyses. The user can create average read profiles across transcriptional start sites or enhancer sites, quickly prototype customized peak discovery methods for ChIP-seq experiments, perform genome-wide statistical tests such as enrichment analyses, design controls via appropriate randomization schemes, among other applications. In addition to enabling rapid prototyping, the platform is designed to analyze large-datasets in a single-pass fashion in order to minimize memory and intermediate file requirements. The platform supports the widely used BED format to facilitate visualization as well as integration with existing platforms and pipelines such as Galaxy or BioConductor.

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• SciCrunch
• 13 years ago - by Anonymous

Software tool as cross species spliced alignment program.Heuristic sequence alignment tool for comparing cDNA sequence with genomic sequence containing homolog of gene in another species.

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• SciCrunch
• 13 years ago - by Anonymous