Curator Dashboard

Software viewing application for biosignals such as EEG or MEG time series. In addition to viewing raw data, SigViewer can also create, edit, and display event information such as annotations or artifact selections.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool to align ionic current from MinION to reference sequence using trainable hidden Markov model. HMM-HDP models for MinION signal alignments,

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool designed to align expressed DNA sequence with genomic sequence, allowing for introns.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software alignment program with new algorithm and scoring scheme designed specifically for non-coding DNA sequence. This problem is now growing in importance with the increasing number of fully-sequenced species. In particular, studies of gene regulation seek to take advantage of comparative genomics, and recent algorithms (such as PhyloGibbs) for finding regulatory sites in phylogenetically-related intergenic sequence require alignment as a preprocessing step.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software comparative genomics tool to assist biologists in analysing genomic variations that correlate with pathogens, or genomic changes that help microorganisms adapt in different environments. Used for evolutionary and genome rearrangement studies for multiple strains of microorganisms.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool for estimation of haplotypes aka phasing for SNP array and high coverage sequencing data. The version 4 is refactored and improved version of SHAPEIT algorithm with multiple key additional features.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Open Source platform to host multiple Shiny applications on single server.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software pipeline for Salmonella serotype determination from raw sequencing reads or genome assemblies.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool for alignment to variation graph inducer.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software application to expose file format conversion in BioPython in convenient way. Imagemagick like frontend to Biopython SeqIO.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool to filter SAM file for soft and hard clipped alignments

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software toolbox provides set of basic functions allowing SBML models to be used in both MATLAB and Octave.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tools for working with SAM/BAM data

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Ensemble of HMM methods.Repository includes code for SEPP, TIPP, UPP, HIPPI. Methods use ensembles of Hidden Markov Models in different ways, each focusing on different problem.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool that implements novel, alignment free algorithm for estimation of isoform abundances directly from set of reference sequences and RNA-seq reads.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool for finding orthologs between one set of sequences and another. This is particularly useful in genome and transcriptome annotation.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software package for assigning confidence scores to protein-protein interactions based on quantitative proteomics data in AP-MS experiments.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Ruby library for handling GFA files.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tools and libraries for bioinformatics and molecular biology, for the Ruby programming language. BioRuby has components for sequence analysis, pathway analysis, protein modelling and phylogenetic analysis; it supports many widely used data formats and provides easy access to databases, external programs and public web services, including BLAST, KEGG, GenBank, MEDLINE and GO.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

GUI tool to run circos

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth