Search Results for "de"
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Showing 57 open source projects for "de"
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Ship Agents FasterGemini Enterprise Agent Platform lets you rapidly build, scale, govern and optimize production-ready agents grounded in your organization's data. The platform enables developers to build custom or pre-built agents for virtually any use case. New customers get $300 in free credits.
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Train ML Models With SQL You Already KnowBuild and deploy ML models using familiar SQL. Automate data prep with built-in Gemini. Query 1 TB and store 10 GB free monthly.
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NGSEP
NGSEP (Next Generation Sequencing Experience Platform)
NGSEP is an integrated framework for analysis of short and long DNA high throughput sequencing reads. The current version provides functionalities for both de-novo and reference guided analysis of sequencing data, including genome assembly, read mapping, variants detection and genotyping and de-novo analysis of data generated from reduced representation protocols. NGSEP also provides modules for analysis of genomic variation databases (VCF files), including functional annotation, filtering, format conversion, comparison, clustering, imputation, introgression analysis and different kinds of statistics. ... -
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almost - all atom molecular simulation toolkit - is a fast and flexible molecular modeling environment that provides powerful and efficient algorithms for molecular simulation, homology modeling, de novo design and ab-initio calculations.
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RAFTS³G
Rapid Alignment Free Tool for Sequences Similarity Search to Groups
...Alcides Vieira Arco-verde street, 1225 % CEP: 81520-260 Jardim das Américas % Curitiba – PR % Brazil % % Developers and colaborators: % Roberto T. Raittz % Bruno T. L. Nichio % Ricardo A. Vialle % Aryel M. R. de Oliveira % Camilla R. Pierri % Leticia G. C. Santos % Alexandre Q. Lejambre % Nilson A. R. Coimbra % Dieval Guizelini % Jeroniza N. Marchaukoski % Fabio de O. Pedrosa -
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EvidentialGene
Evidence Directed Gene Construction for Eukaryotes
EvidentialGene is a genome informatics project, "Evidence Directed Gene Construction for Eukaryotes", to construct high quality, accurate gene sets for animals and plants, developed by Don Gilbert at Indiana University, see http://arthropods.eugenes.org/EvidentialGene/ Construction refers to the combination of classical gene prediction, and more recent gene assembly (de-novo and genome-assisted) methods. The basic Evigene methods involve using available best-of-breed gene prediction and assembly software, combining all evidence for genes, from expressed sequences, genome assembly sequences, related species protein sequences, and any other, to annotate and score gene constructions. Over-produced constructions are classified by gene evidence for best qualities per "locus", including genome-aligned and gene-transcript aligned (genome-free) locus identification. ... -
Stop vibe-debugging.AppSignal's MCP server hands Claude, Cursor, or Zed your real errors, traces, and the deploy that shipped them. AI writes the fix; you review the diff.
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CStone
Short-read de novo assembler that identifies chimeric contigs.
> CStone wiki: https://sourceforge.net/p/cstone/wiki/Home/ Related Software: 1. CStone: (See wiki) 2. CSReadGen: https://sourceforge.net/projects/csreadgen/ 3. CView: https://sourceforge.net/projects/cview/ 4. ChimSim: https://sourceforge.net/projects/chimsim/ 5. TVScript: https://sourceforge.net/projects/tvscript/ 6. SeQuester: https://sourceforge.net/projects/sequester/ 7. TreeScope: https://sourceforge.net/projects/treescope/ -
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LP CSIC/UAB Apps and Code
Software and Code from Laboratori de Proteòmica CSIC/UAB
Software, Code and Documents from Laboratori de Proteòmica CSIC/UAB ( LP-CSIC/UAB: http://proteomica.uab.cat ) -
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GapFiller
A de novo local assembler for paired reads
GapFiller is a seed-and-extend local assembler to fill the gap within paired reads. It can be used for both DNA and RNA and it has been tested on Illumina data. GapFiller can be used whenever a sequence is to be assembled starting from reads lying on its ends, provided a loose estimate of sequence length. -
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Computer programs for application in Sports science, Physical Culture, among others. By Enrique R.P. Buendía Lozada. buendiaenr@gmail.com , Benemérita Universidad Autónoma de Puebla (BUAP), México. (Software without any warranty).
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TIES
A smart search engine for medical documents
TIES (Text Information Extraction System) is a clinical text search engine that uses Natural Language Processing techniques to extract medical concepts from free text clinical reports. It provides secure de-identified access to this information and has in built collaboration tools and honest broker functionality. It is licensed for academic use under the BSD license. For commercial use please contact Nexi at http://nexihub.com *** NOTICE: this software and forum are no longer maintained, as of 8/15/2019. You are free to continue to use this software under the license for academic use under the BSD license. ... -
Enterprise-grade ITSM, for every businessFreshservice is an intuitive, AI-powered platform that helps IT, operations, and business teams deliver exceptional service without the usual complexity. Automate repetitive tasks, resolve issues faster, and provide seamless support across the organization. From managing incidents and assets to driving smarter decisions, Freshservice makes it easy to stay efficient and scale with confidence.
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De_Lux
Deconvolution of luminescence cross-talk in microplate reader data
An algorithm to deconvolve the luminescence cross-talk in high-throughput gene expression profiling to recover the true luminescence activity of a microplate. -
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MarDRe
MapReduce-based tool to remove duplicate DNA reads
MarDRe is a de novo MapReduce-based parallel tool to remove duplicate and near-duplicate DNA reads through the clustering of single-end and paired-end sequences from FASTQ/FASTA datasets. This tool allows bioinformatics to avoid the analysis of not necessary reads, reducing the time of subsequent procedures with the dataset. MarDRe is the Big Data counterpart of ParDRe (link above), which employs HPC technologies (i.e., hybrid MPI/multithreading) to reduce runtime on multicore systems. ... -
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NIVEL9
Programa para crear y ejecutar Sistemas Expertos
NIVEL9 es el nombre del software informático diseñado por el Ing. Mauricio Ernesto Alfaro, el cual se basa en las teorías de Inteligencia Artificial, específicamente de Sistemas Expertos. NIVEL9 entra en la categoría de "caparazón para sistema experto" o mejor conocido en inglés como "Expert System Shell": es decir un software para crear diferentes Sistemas Expertos y ejecutarlos dentro del mismo software. NIVEL9 nació como un proyecto para apoyar al Instituto de Ciencias del Mar y Limnología (ICMARES) de La Universidad de El Salvador (UES) en la identificación de las Familias de Anélidos Poliquetos de la costa de El Salvador en el año 2006. -
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LBXR - LOAD BLAST XML RESULTS O sistema permite que sejam importados resultados obtidos por meio de pesquisas de similaridade a partir do BLAST, com resultados gerado no formato XML para o banco de dados relacional MariaDB ou MySQL.
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LOCUST
Custom Sequence Locus Typer
A Custom Sequence Locus Typer for Classifying Microbial Genotypic and Phenotypic Attributes. Publication: Brinkac LM, Beck E, Inman J, Venepally P, Fouts DE, Sutton G. LOCUST: A Custom Sequence Locus Typer for Classifying Microbial Isolates. Bioinformatics (Oxford, England). 2017 Jan 27; https://www.ncbi.nlm.nih.gov/pubmed/28130240 -
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metasort
A metagenome assembler by reducing microbial community
Most current approaches analyze metagenomic data with the participation of reference genomes. However, novel microbial communities extend far beyond the coverage of reference databases and de novo metagenome assembly from complex microbial communities still remains a great challenge. Here we present a novel experimental and bioinformatic framework, metaSort, for effective construction of bacterial genomes from metagenomic samples. MetaSort provides a sorted mini-metagenome approach based on flow cytometry and single-cell sequencing methodologies, and employs new computational algorithms to efficiently recover high-quality genomes from the sorted mini-metagenome by the complementary of the original metagenome. ... -
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ViralFusionSeq [VFS]
Accurately discover viral integration events and fusion transcripts
...https://hpc.nih.gov/apps/ViralFusionSeq/ ViralFusionSeq (VFS) is a versatile high-throughput sequencing (HTS) tool for discovering viral integration events and reconstruct fusion transcripts at single-base resolution. VFS combines soft-clipping information, read-pair analysis, and targeted de novo assembly to discover and annotate viral-human fusion events. A simple yet effective empirical statistical model is used to evaluate the quality of fusion breakpoints. Minimal user defined parameters are required. Source code with user manual and installation guide of VFS is available at sourceforge's "Files" section. ... -
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Meta Assembler for de novo assembly results. GARM (Genome Assembly Reconciliation and Merging) is a pipeline to merge results from different assemblers or results from different DNA sequencing technologies.
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Placnet
Placnet project
...The input of placnet is a set of contigs and one or more SAM files with the mapping of the reads against the contigs. Placnet obtains a set of files, easily opened on Cytoscape software or other network tools. Please cite PLACNET as: Lanza VF, de Toro M, Garcillán-Barcia MP, Mora A, Blanco J, Coque TM, de la Cruz F: Plasmid Flux in Escherichia coli ST131 Sublineages, Analyzed by Plasmid Constellation Network (PLACNET), a New Method for Plasmid Reconstruction from Whole Genome Sequences. PLoS Genet 2014, 10:e1004766. -
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Congenito
Enfermedad de Chagas
Seguimiento de pacientes y detección de chagas congenito -
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ShuffleFastaSeq
This application can be used to shuffle sequences in FASTA format.
...The random permutation is obtained using a simple variation of the Fisher-Yates alghorithm implemented by Durstenfeld (https://en.wikipedia.org/wiki/Fisher%E2%80%93Yates_shuffle) ( Knuth DE. The art of computer programming: seminumerical algorithms. 3rd ed. Boston: Addison-Wesley; 1997). The input file contains one or more sequences in FASTA format. The number of shufflings (n) for each sequence can be set; by default n is 100. The output file contains n shuffled copies in FASTA format for each input sequence. For example (n=3): Input file: >a ACGGT >b GCCCATTC Output file: >a TCGAG >a CGAGT >a TGCGA >b CACTCCGT >b CCCGTATC >b CCTTCAGC -
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TAG
A tool for metatranscriptome assembly using metagenome graph
TAG is a tool for metatranscriptome assembly using de Bruijn graph of matched metagenome as the reference. TAG is an application of a reads mapping algorithm that we developed for mapping of short reads onto a de Bruijn graph of assemblies. A hash table of junction k-mers (k-mers spanning branching structures in the de Bruijn graph) is used to facilitate fast mapping of reads to the graph. -
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olego
OLego – short or long RNA-seq read mapping to discover exon junction
OLego is a program specifically designed for de novo spliced mapping of mRNA-seq reads. OLego adopts a seeding and extension scheme, and does not rely on a separate external mapper. It achieves high sensitivity of junction detection by using very small seeds (12-14 nt), efficiently mapped using Burrows-Wheeler transform (BWT) and FM-index. This also makes it particularly sensitive for discovering small exons. -
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CNVision
CNV prediction from Illumina genotyping data
CNVision is a Perl script that runs Illumina genotyping data (all chips from 300k to latest Omni) through PennCNV, QuantiSNPv2.3 and GNOSIS (an in-built algorithm). It merges the results and assesses the quality of the raw data. CNVision can also identify de novo CNVs in family-based data using a highly accurate algorithm that considers the possibility of CNVs in either parent based on the raw genotyping data. The script is optimized to work in a UNIX-based environment; it should work in Windows, however running the PennCNV component gives errors with the newer versions of PennCNV. ... -
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FMFilter
Fast Model Based Variant Filtering Tool
...We provide an efficient filtering tool for next generation sequencing data produced by genetic disease studies. FMFilter allows to choose one of the inheritance models (recessive, dominant, compound heterozygous and de novo), the affected and control individuals to design the filtering mechanism. It provides an environment of analyzing these cases by removing the requirement of advanced computer techniques. It has the capability to filter with control individuals and eliminate the majority of the false alarms specific to a population. It requires negligible memory which enables to handle very large variant files in ordinary computers. -
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IsoSearcher
Sistema de visualización de isosuperficies en imágenes médicas 3D
...Implementa algoritmos que permiten realizar mallas no-estructuradas, de las isosuperficies, compuestas de elementos triangulares; con una densidad uniforme elegida por el usuario, de acuerdo a su criterio y la cota de error admisible para las aproximaciones del cálculo numérico. Permite visualizar isosuperficies variables y utilizar un plano de corte y dos isosuperficies fijas como guía para el recorte de la estructura de interés. ...
