Search Results for "reference" - Page 4
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Showing 290 open source projects for "reference"
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RDML-Ninja is an editor for qPCR data. It is the reference implementation for the RDML data standard allowing to visualize, edit and reanalyze qPCR data.
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AnalyzeNNLS
MRI Multiple Echo T2 Analysis
Users load multiecho MRI data and draw ROIs. AnalyzeNNLS creates a T2 distribution from the averaged decay data. Regional fractions and geometric T2 times can be determined. Please reference: Bjarnason TA, Mitchell JR. JMR 206:200-4 (2010). Temporal Phase Correction included in version 2.5. If you use this functionality, please reference: Bjarnason TA, Laule C, Bluman J, Kozlowski P. JMR 232:22-31 (2013). -
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GDL Editor
Computerized guideline editor for clinical decision support
The GDL editor is multiplatform application that allows users to create, edit and run GDL files. GDL is a formal language designed to represent clinical knowledge for decision support. It is designed to be natural language- and reference terminology- agnostic by leveraging the designs of openEHR Reference Model and Archetype Model. The tool provides an editing and testing environment capable of generating forms based on the elements defined in the GDL. Requirements: Java Runtime Enviroment (JRE) 1.6 or higher -
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datasw
datasw, a tool for rapid processing of HPLC-SAXS data.
Small-angle X-ray scattering (SAXS) in solution is a common low-resolution method which can efficiently complement high-resolution information obtained by crystallography or NMR. Sample monodispersity is key to reliable SAXS data interpretation and model building. Beamline setups with inline high-performance liquid chromatography (HPLC) are particularly useful for accurate profiling of heterogeneous samples. The program DATASW performs averaging of individual data frames from HPLC-SAXS... -
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CRISPR-offinder-v1-2
A CRISPR tool for user-defined protospacer adjacent motif
...To meet the needs of different CRISPR system with specific and efficient sgRNA design, CRISPR-offinder was developed. Given an input FASTA file of the target sites and queries the reference genome as well as a CRISPR system with a defined spacer length and PAM sequence, this standalone tool will identify putative sites and assign a predicted activity based on support vector machine model which conducted by sgRNA Scorer 2.0. In addition, sgRNAs with minimal off-target activity were predicted by Cas-OFFinder, and score with Off-Target Cutting Frequency Determination (CFD). -
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avr_DF4IAH_10MHz_Reference
#1B - DF4IAH 10 MHz-Ref-Osc. Application
#1B - DF4IAH 10 MHz-Ref-Osc. Application -
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QSdpR
Viral Quasispecies Reconstruction software based on QSdpR algorithm
This is a viral quasispecies reconstruction software for quasispecies assembly problem on mRNA viruses, which is based on a correlation clustering approach and uses semidefinite optimization framework. The software accepts a reference genome, a NGS read set aligned to this reference and set of SNP locations in the form of a vcf file and outputs an optimal set of reconstructed species genomes which describes the underlying viral population. -
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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. -
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8 Sounds USB
Summary
XMOS based, USB2 audio card, low power consumption, small form factor, 8 synchronous input channels and 4 stereo output channels. -
Atera all-in-one platform IT management software with AI agentsAtera’s AI agents don’t just assist, they act. From detection to resolution, they handle incidents and requests instantly, taking your IT management from automated to autonomous.
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Mass Difference Calculator
Mass Difference Calculator with a Graph for MassLynx data
A Mass Difference Calculator with a graph for MassLynx. Bring in a text file with reference masses and then paste in or browse in another file with a list of mass/intensity pairs. Then look at the best matching points and see what the difference between reference and data comes out as. This is a companion app to ResCalc3 -
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Involute Gears DXF
Open DXFs with QCad
Program draws a gears tooth for reference profile and Fellows manufacturing. Open dxfs with qcad or Solid Works, ec but not with AutoCad. Autodesk has remouved support for enteties only format.It compiles well with OpenWatcom 1.9 c++ compiler. -
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Kinannote
Protein Kinase Identification and Classification
Kinannote identifies and classifies protein kinases in a user-provided fasta file using an HMM derived from serine/threonine protein kinases, a position specific scoring matrix derived from the HMM, and comparison with a local version of the curated kinase database from kinase.com. If the user inputs a complete proteome, additional modules evaluate the completeness of the kinome and place it in context with reference kinomes. Kinannote runs on a unix command line and depends on local hmmer 2 and Blast 2.24 installations. Citing Kinannote: Kinannote, a computer program to identify and classify members of the eukaryotic protein kinase superfamily Jonathan M. Goldberg; Allison Griggs; Janet L. Smith; Brian Haas; Jennifer Wortman; Qiandong Zeng Bioinformatics 2013; doi: 10.1093/bioinformatics/btt419 http: http://bioinformatics.oxfordjournals.org/content/29/19/2387.full pdf: http://bioinformatics.oxfordjournals.org/content/29/19/2387.full.pdf+html -
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INTEGRATE: Calling gene fusions with exact fusion junctions and genomic breakpoints by combining RNA-Seq and WGS data. To download source code, reference manual and test case, please go to 'Files'. Also refer to 'Wiki' for details.
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Colibri - The ENVI / IDL Code Library
A collection of well documented ENVI / IDL algorithms and applications
...The complete set of code and documentation are available to the remote sensing community. ENVI/IDL code developers and remote sensing researchers are requested to actively contribute to this ENVI/IDL Code Library in order to obtain a solid reference of user developed applications for the remote sensing community. -
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SPANDx
Comparative analysis of haploid next-generation genome sequence data
SPANDx is your one-stop tool for identifying SNP and indel variants in haploid genomes using NGS data. SPANDx performs alignment of raw NGS reads against your chosen reference genome or pan-genome, followed by accurate variant calling and annotation, and locus presence/absence determination. SPANDx produces SNP and indel matrices for downstream phylogenetic analyses. 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. ... -
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Taurus
A python based User Interface library.
The Taurus Project has *moved* to: https://github.com/taurus-org/taurus This SourceForge page is *outdated* and kept for historical reference only. Taurus is a python framework for control and data acquisition CLIs and GUIs in scientific/industrial environments. It supports multiple control systems or data sources: Tango, EPICS, ... New control system libraries and data sources can be integrated through plugins. -
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Volterra2.0
Volterra series Identification Tool
...Possibility to identify each Volterra kernel with an input with different variance. This feature reduces the identification noise on lower order kernels and improve the "resolution" on higher order kernels. For reference see: Simone Orcioni. Improving the approximation ability of Volterra series identified with a cross-correlation method. DOI:10.1007/s11071-014-1631-7. pp.2861-2869. In NONLINEAR DYNAMICS - ISSN:0924-090X vol. 78 (4) 2014. -
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Density-ratio based clustering
Discovering clusters with varying densities
...An existing density-based clustering algorithm, which is applied to the rescaled dataset, can find all clusters with varying densities that would otherwise impossible had the same algorithm been applied to the unscaled dataset. Reference: Zhu, Y., Ting, K. M., & Carman, M. J. (2016). Density-ratio based clustering for discovering clusters with varying densities. Pattern Recognition. http://www.sciencedirect.com/science/article/pii/S0031320316301571 -
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LibNucNucGam
Nuclear collision secondary particle production cross sections.
This Python library contains the parametrization of the Nucleus-Nucleus pi-meson (including subthreshold pions) and the direct hard photon gamma-ray production cross sections channels for calculating the secondary gamma-ray and electron/positron spectra based on arXiv:1608.03348. Please, if you use this library DO NOT reference to this webpage, instead reference to arXiv:1608.03348, "Parametrization of the nucleus-nucleus gamma-ray production cross sections below 100 GeV/nucleon: Subthreshold pions and Hard photons" by Ervin Kafexhiu COMING SOON... -
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CT collimation measurements using CR plates. Please reference Bjarnason TA, Yang CY. CT radiation profile width measurement using CR raw data. Journal of Applied Clinical Medical Physics. 2015;16:501-507. Available from: http://www.jacmp.org/index.php/jacmp/article/view/5512
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XParallax viu
Software for automated astrometry
XParallax viu is a free software tool for automated astrometric data reduction of astronomic CCD images. It helps astronomers to perform an accurate astrometric reduction of dozens ore even hundreds of images which can be used in subsequent data analysis process. Fit headers generated by this software are fully compatible with other commonly used image utilities like SAO DS9 or Aladin Sky Atlas. -
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RGAAT
Reference based genome assembly and annotation for new genome
This program can assemble and/or annotate genome for new genome and known genome upgrade using sequence alignment file (SAM or BAM format), sequence variant file (VCF format or five coloum table (tab-delimited, including chromosome, position, id, reference allele and alternative allele)) or new genome sequence file (FASTA format) based on reference genome sequence file (FASTA format) and annotation file (TBL, GTF, GFF, GFF3 or BED format). -
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...PLEASE NOTE: The Biskit source code as well as any later releases are now hosted on https://github.com/graik/biskit The sourceforge repo is only kept here for reference.
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riboshape
Predicting ribosome footprint profile shapes from transcript sequences
...It applies kernel smoothing to codon sequences to build predictive features, and uses these features to builds a sparse regression model to predict the ribosome footprint profile shapes. Reference: Liu, T.-Y. and Song, Y.S. Prediction of ribosome footprint profile shapes from transcript sequences. Proceedings of ISMB 2016, Bioinformatics, Vol. 32 No. 12 (2016) i183-i191. -
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Techne (R) CAD/CAM
2.5D CAD CAM emphasis on CAM and toolpaths
...So you can create a square that will be machined at a specific depth but the depth will be constant accross the square. It is not/does not: A general purpose CAD (AutoCAD) type program. Support reference dimension on the drawing. Export or import major CAD file formats.
