Curator Dashboard

An open source software application and library written in Java that provides a uniform annotation of identified spectra stored in the PRIDE database.

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• SciCrunch
• 12 years ago - by Anonymous

Suite of software tools that allows users to convert search result files into PRIDE XML, generate mzTab skeleton files that can be used as a basis to submit quantitative and gel-based MS data, and post-process PRIDE XML files by filtering out contaminants and empty spectra.

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• SciCrunch
• 12 years ago - by Anonymous

A collection of Java application programming interfaces (APIs) to parse the most commonly used peak list and XML-based mass spectrometry (MS) data formats: DTA, MS2, MGF, PKL, mzXML, mzData, and mzML.

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• SciCrunch
• 12 years ago - by Anonymous

Software that allows fast and user-friendly verification of Mascot result files, as well as data quantification using isotopic labeling methods (SILAC/ICAT) or label free approaches (spectral counting, MS signal comparison).

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• SciCrunch
• 12 years ago - by Anonymous

A software tool for scientists working with stable isotopic labelling and high resolution liquid chromatography mass spectrometry.

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• SciCrunch
• 12 years ago - by Anonymous

A proteomics software tool for quantitatively analyzing large mass spectrometric datasets acquired from ICPL based proteomics experiments.

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• SciCrunch
• 12 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 23rd,2023. Software that combines Lagrangian relaxation for solving an integer linear programming formulation with an adaptation of Yen''s k shortest paths algorithm.

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• SciCrunch
• 12 years ago - by Anonymous

Software for pipelined analysis of mass spectrometry data.

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• SciCrunch
• 12 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE.Documented on May 23rd,2023. Software that provides a set of computational tools which can be easily combined into analysis pipelines even by non-experts and can be used in proteomics workflows.

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• SciCrunch
• 12 years ago - by Anonymous

Software providing a data analysis pipeline for shotgun mass-spectrometry proteomics.

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• SciCrunch
• 12 years ago - by Anonymous

An algorithm to align LC-MS samples and to match corresponding ion species across samples.

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• SciCrunch
• 12 years ago - by Anonymous

Software that aligns matrices along a single axis using Dynamic Time Warping (DTW) and a one-to-one (bijective) interpolated warp function.

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• SciCrunch
• 12 years ago - by Anonymous

Software for mass-spectrometry data processing, with the main focus on LC-MS data.

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• SciCrunch
• 12 years ago - by Anonymous

Software that performs retention time alignment on the given set of peaks.

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• SciCrunch
• 12 years ago - by Anonymous

A free, open-source GUI software application written in Perl that designs primers for standard PCR, bisulphite PCR, real-time PCR (QPCR) and sequencing.

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• SciCrunch
• 12 years ago - by Anonymous

A web-based workbench to conveniently compare the classification performances of many different filter-based gene selection procedures. In addition to the commonly used filter metric-classifier combinations, user can test various additive methodological options by specification of only up- or down-regulated genes to select, applying feature discretization and adding feature vectors to make a new feature. Throughout the comprehensive comparisons, user can identify the best performing gene selection procedure and subsequent classification performance measured by .632+ bootstrap error estimation for the given binary (two-class) microarray data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 13 years ago - by Anonymous

A C software implementation of SAM, BAM and CRAM file I/O.

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• SciCrunch
• 12 years ago - by Anonymous

A web-based platform for functional interpretation of gene sets with features such as cross-species Gene Set Analysis (GSA), Flexible and Interactive GSA, simultaneous GSA for multiple gene set, and and a fully integrated network viewer for both visualizing GSA results and molecular networks.

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• SciCrunch
• 13 years ago - by Anonymous

Tools to search gene lists for functional term enrichment as well as to dynamically visualize proteins onto pathway maps. Additionally, integrated expression data may be used to discover similarly expressed genes based on a starting gene of interest.

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• SciCrunch
• 13 years ago - by Anonymous

An integrative platform for diverse types of gene set analysis with annotation network navigation. It includes tools for statistical analysis, visualization of annotation relationships, retrieval of genes from annotation database, and set operation for gene sets. In an effort to allow access to a full spectrum of amassed biological knowledge, they have integrated a variety of annotation data that include the GO, domain, disease, drug, chromosomal location, and custom-defined annotations. Diverse types of molecular networks (pathways, transcription and microRNA regulations, protein-protein interaction) are also included. The pair-wise relationship between annotation gene sets was calculated using kappa statistics. GARNET consists of three modules--gene set manager, gene set analysis and gene set retrieval, which are tightly integrated to provide virtually automatic analysis for gene sets. A dedicated viewer for annotation network has been developed to facilitate exploration of the related annotations.

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• SciCrunch
• 13 years ago - by Anonymous