Curator Dashboard

Software tool for analysis of metagenomic sequencing data.Used to profile composition of metagenomic communities. Calculates quality metrics for estimated candidates and allows the user to identify false candidates.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software pipeline for metagenomic and taxonomical analysis from shotgun sequencing.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool to predict gene ontology terms for protein sequences through homology.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

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

Software high performance reflective language and system supporting both equational and rewriting logic specification and programming for wide range of applications.Supports equational specification and programming, rewriting logic computation.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software C++ wrapper around tabix project which abstracts some of the details of opening and jumping in tabix-indexed files.Wrapper to tabix indexer

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool to mine genomes for molecular systems with Application to CRISPR-Cas Systems. Detection of macromolecular systems in protein datasets using systems modelling and similarity search.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool for analysis of genome alignments. It parses and manipulates MAF files as well as more simple fasta files. Despite various filtering options and format conversion tools, MafFilter can compute a wide range of statistics including phylogenetic trees, nucleotide diversity, inferrence of selection, etc.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Pattern matching grammar language and set of tools to search pattern in sequence nucleic or proteic.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software library that implements the maxflow-mincut algorithm.Used for computing mincut/maxflow in a graph.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Targeted assembly software. It takes as input any number of NGS raw read sets and starter set of input sequences.May be used to Validate assembled sequence, Check if known enzyme is present in metagenomic NGS read set, Enrich unmappable reads by extending them, Check what happens at the extremities of a contig, Check the presence / absence and quantify RNA seq splicing events, Check presence/absence of SNPs or structural variants.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software package written and supported by the ArrayExpress curation team, which aims to ease the process of submitting large microarray experiment datasets.Tab2MAGE uses flexible spreadsheet format for MIAME annotation of microarray experiments.Spreadsheets may be submitted directly to ArrayExpress, or used to generate MAGE-ML for data exchange.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software image processing and analysis library that puts its main emphasis on customizable algorithms and data structures. VIGRA is especially strong for multi-dimensional images. By using template techniques similar to those in the C++ Standard Template Library, you can easily adapt any VIGRA component to the needs of your application, without thereby giving up execution speed. As of version 1.7.1, VIGRA also provides extensive Python bindings on the basis of the popular numpy framework.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool to clean sequence data from automated DNA sequencers prior to sequence assembly and other downstream uses.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software graphical desktop tool for semi-automatic postprocessing of de novopredicted LTR retrotransposon annotations, such as the ones generated by LTRharvestand LTRdigest. Interface displays LTR retrotransposon candidates, their putative families and their internal structure in a hierarchical fashion allowing the user to "sift" through results of de novo prediction software. It also offers customizable filtering and classification functionality.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Open source commandline based application and/or software development library, that performs 2D, rigid image registration on two greyscale images and outputs either the transformation parameters or the registered image.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software cross-platform C++ library for loading multimodal, multi-rate signals stored in XDF files. Used in biosignal viewing application SigViewer and the LSL application XDFStreamer. Can also be integrated into other C++ applications.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool as kmer-based error correction method for whole genome sequencing data. Lighter uses sampling rather than counting to obtain set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software C++ thread pool library.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

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

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth