Search Results for "core-analyzer"
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Showing 79 open source projects for "core-analyzer"
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...It allows for spectrum prediction (13C, 1H and other nuclei) as well as for searching spectra, structures and other properties. The nmrshiftdb2 software is open source, the data is published under an open content license. The core of nmrshitdb2 are fully assigned spectra with raw data and peak lists (we have pure peak lists as well). Those datasets are peer reviewed by a board of reviewers. The project is supported by a scientific advisory board. nmrshiftdb2 is part of the NFDI4Chem initiative (https://nfdi4chem.de/) and will provide a component for a curated repository there. ...
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OpenClinic GA
Open Source Integrated Hospital Information Management System
OpenClinic GA is an open source integrated hospital information management system covering management of administrative, financial, clinical, lab, x-ray, pharmacy, meals distribution and other data. Extensive statistical and reporting capabilities. OpenClinic GA and OpenClinic GMAO are distributed under the GNU GPLv3 license (https://www.gnu.org/licenses/gpl-3.0.html) ans is owned by Frank Verbeke, MD, PhD at Post-Factum BV (https://www.post-factum.be) -
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mzMatch is a Java collection of small commandline tools specific for metabolomics MS data analysis. The tools are built on top of the PeakML core library, providing mass spectrometry specific functionality and access to the PeakML file format.
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FruitOS
A live Linux OS (Arch-based, GRUB) powered by a real fruit fly brain:
FruitOS is a live Linux operating system (Arch-based, boots with GRUB) powered by a real fruit fly brain: 165,122 neurons you can watch, talk to and learn from. Boot it from a USB stick, no install needed, completely offline. -
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FruitGPT
Chat with a real fruit fly brain: 165,122 neurons running on your comp
FruitGPT lets you chat with a real fruit fly brain: a simulation of all 165,122 neurons of the FlyWire connectome running on your own computer, with its activity translated into English. Edit the brain — remove sections, silence neuron types, cut or strengthen wires, turn the dials — and see how its answers change. Runs offline on Windows, macOS and Linux. -
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SASA Tool
SWATH-Auto System Analyzer Tool, SASA Tool
SWATH-Auto System Analyzer Tool, SASA Tool, is a novel SWATH platform for non-targeted metabolomics data analysis with an accurate mass spectral library for metabolite identification using SWATH acquisition mode. -
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dataMAPPs
R based pipeline for MHC-associated peptide proteomics (MAPPs) data
dataMAPPs allows routine and efficient processing of data from immunogenicity studies applying the MAPPs peptidomics technology to detect potential MHCI- or MHC-II epitopes as presented by dendritic cells (DC). It features quality control of the raw data, across-sample/across-donor normalization and visualization of results in a heatmap style (heatMAPPs). dataMAPPs' core is a generic R library that can be tailored to specific projects via dedicated control scripts which also allow reproducible recalculation of results. Consult README file for installation and usage instructions. Further documentation is supplied in PDF format. dataMAPPs is published under GPL license by a team of scientists working for Hoffmann-La Roche AG in Basel, Switzerland. ... -
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Microarray assosiated motif analyzer
Cis-element prediction tool from microarray data
We developed a novel clustering-free method, microarray-associated motif analyzer (MAMA), to predict novel cis-acting elements based on weighted sequence similarities and gene expression profiles in microarray analyses. Simulation of gene expression was performed using a support vector machine and based on the presence of predicted motifs and motif pairs. The accuracy of simulated gene expression was used to evaluate the quality of prediction and to optimize the parameters used in this method. ... -
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Quadric
Application for simple base-2 binary to base-4 DNA-code conversion
Quadric is an opensource file converter created by the Jomcraft Network development team. In it's core functionality this small utility can transform base-2 binary files into base-4 DNA-coded human-legible ASCII-files. -
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gsasnp2
PubMed ID: 29562348 / DOI: 10.1093/nar/gky175
* GSA-SNP2 is a successor of GSA-SNP (Nam et al. 2010, NAR web server issue). GSA-SNP2 accepts human GWAS summary data (rs numbers, p-values) or gene-wise p-values and outputs pathway genesets ‘enriched’ with genes associated with the given phenotype. It also provides both local and global protein interaction networks in the associated pathways. * Article: SYoon, HCTNguyen, YJYoo, JKim, BBaik, SKim, JKim, SKim, DNam, "Efficient pathway enrichment and network analysis of GWAS summary data... -
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Meraculous-2D
Eukaryotic Genome Assembler
...The assembly is driven by a perl pipeline which performs data fragmentation and load balancing, as well as submission and monitoring of multiple task arrays on a GE/SLURM-type cluster or a standalone multi-core server. Manuscripts in submission: https://arxiv.org/abs/1703.09852 https://arxiv.org/abs/1608 -
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HCS Analyzer
High Content Screening Analyzer
HCS Analyzer is an open source software dedicated to High Content Screening data processing and analysis. -
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libSBOL provides the core C/C++ interfaces and their implementation for the Synthetic Biology Open Language (SBOL). Version 2.1.1 of libSBOL provides an API to construct SBOL 2.1.0 designs and to read and write SBOL version 2.1.0 XML/RDF files.
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Panacea
PAN And Core-gEnome Analysis
A tool to calculate the Pan-Genome of a set of annotated genomes -
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...More specifically, our software implements pipelines for the analysis of single nucleotide and copy-number variation, bisulfite-seq and ChIP-seq experiments using well-established tools to perform these common tasks. RUbioSeq+ is free and includes all the core functionalities implemented in the original release of RUbioSeq (v3.2.1) but, also, outperforms and expands RUbioSeq capabilities supporting the parallelized analysis of full genomes in computing farms. RUbioSeq+ also incorporates a new GUI designed for interdisciplinary research groups where bioinformaticians and biomedical researchers work together.
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KAPPA (Key Aminoacid Pattern-based Protein Analyzer) is a sequence search program dedicated to the discovery and clustering of proteins defined by a key aminoacid pattern.
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Hamstr
A tool for directed ortholog search in ESTs and proteins
HaMStR has moved to https://github.com/bionf/hamstr where it is now part of the HaMStR-OneSeq package. HaMStR is a profile hidden Markov model based tool for a directed ortholog search in EST or protein sequence data. The program takes a pre-defined core group of orthologous sequences (core orthologs) and a set of sequences from a search taxon as input. HaMStR then combines in a two-step strategy a pHMM based search and a reverse search via BLAST to extend the core ortholog group with novel sequences from the search taxon. -
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Barracuda is a high-speed sequence aligner based on Sanger's BWA and utilizes the latest Nvidia CUDA architecture for accelerating alignments of sequence reads generated by next-generation sequencers.
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SPANDx
Comparative analysis of haploid next-generation genome sequence data
...Annotated, genome-wide SNPs and indels can also be identified if specified, and are output in human readable format. A presence/absence matrix is also generated to allow you to identify the core/accessory genome content across all your genomes. The outputs generated by SPANDx can be imported into PLINK for microbial genome-wide association study (mGWAS) analyses. SPANDx can utilise PBS, SGE or SLURM for resource management. SPANDx can also run directly on the command line if no resource manager is available. For the most up-to-date version of SPANDx, check us out on GitHub: https://github.com/dsarov/SPANDx -
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GNomEx
A Genomic LIMS and Data Repository
Our source code is now on GitHub: https://github.com/hci-gnomex/gnomex. Please refer to GitHub for the latest code. GNomEx is Genomic LIMS and Data Repository. It holds annotated experiments and downstream analysis and serves data tracks to popular genome browsers such as IGB, IGV, and UCSC genome browser. The LIMS handles all aspects of the experiment from order through results delivery. Experiment platforms supported include Illumina HiSeq, MiSeq, iScan, ABI Sanger sequencing,... -
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Corbata
CORe microBiome Analysis Tools
Corbata is a set of statistical tools that can be used to analyze the core microbiome across a set of samples. -
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erne
ERNE - Extended Randomized Numerical alignEr
We present ERNE (Extended Randomized Numerical alignEr), a short string alignment package whose goal is to provide an all-inclusive set of tools to handle short (NGS-like) reads. ERNE comprises ERNE-FILTER (read trimming and continamination filtering), ERNE-MAP (core alignment tool/algorithm), ERNE-BS5 (bisulfite treated reads aligner), and ERNE-PMAP/ERNE-PBS5 (distributed versions of the aligners), -
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fast_count_multi
Extremely fast NGS read counter
Counts NGS read alignments against GTF annotations in a multithreaded and scalable fashion. Benchmark: 8 core 1M annotations for 2Gb sorted reads ~30 seconds compared to ~28 minutes for bedtools multicov. Files include: fast_count_multi - reports all counts and RPKM, multithreading support fast_count_deseq - reports gene counts in deseq compatible format, multithreading support fast_count - reports all counts with no multithreading support. -
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Systems Biology Simulation Core Library
Accurate and efficient Java library that simulates biological models
This project has been moved to https://github.com/draeger-lab/SBSCL. -
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Moose
Multiscale Neuroscience and Systems Biology Simulator
Moose is the core of a modern software platform for the simulation of neural systems ranging from subcellular components and biochemical reactions to complex models of single neurons, large networks, and systems-level processes. We have moved Github.com. This should be your source for the latest version of the code.
