Curator Dashboard

Software Python implementation of MacroMolecular Transmission Format API, decoder and encoder. Repository holds the Python 2 and 3 compatible API, encoding and decoding libraries.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool that infers motifs in set of sequences to infer exceptionnal sites as binding sites in DNA sequences. 1.4 version allows to infer motifs written on any alphabet in any kind of sequences. Allows to deal with motifs associated by some distance constraints. Used to group under unique model different occurrences composed of several boxes separated by spacers of different lengths.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool for the design of multiplex pyrosequencing assays.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software package to create specialized dictionaries for medical terms used in various languages.German medical dictionary words.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Command lines tool to annotate miRNAs with standard mirna/isomir naming.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool to perform detection and assembly of DNA insertion variants in NGS read datasets with respect to reference genome.Used to call insertions of any size, whether they are novel or duplicated, homozygous or heterozygous in the donor genome.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software OLC-based de novo assembler for noisy long reads.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool as reference implementation of probabilistic sequence overlapping algorithm. Used to detect overlaps between noisy long-read sequence data.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

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