Search Results for "estimates"
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Showing 34 open source projects for "estimates"
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BACE for gretl
Bayesian Averaging of Classical Estimates
Bayesian Averaging of Classical Estimates package. -
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JRC QSAR Model Database
(Q)SAR Model Reporting Format Inventory
In the regulatory assessment of chemicals (e.g. under REACH), Quantitative Structure Activity Models (QSAR) are playing an increasingly important role in predicting properties for hazard and risk assessment. This implies both a need to be able to identify relevant QSARs and to use them to derive estimates and/or have access to their precalculated estimates. To help meet these needs, the JRC QSAR Model Database is established and freely accessible through http://qsardb.jrc.ec.europa.eu/qmrf The QSAR Model Reporting Format (QMRF) is a harmonised template for summarising and reporting key information on QSAR models, including the results of any validation studies. ... -
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Euler Pole Calculator (EPC)
A Matlab software to estimate Euler pole parameters
The EPC software calculates velocities for any points located on the earth’s surface given the Euler pole parameters and estimates the Euler pole parameters given the observed velocities of a set of sites located on a tectonic plate. Since version 2, the software is able to estimate or apply the Plate Translation Rates, as well. Please cite one of the following papers when you use the software: - Goudarzi, M A, Cocard, M, and Santerre, R. 2014."EPC: Matlab Software to Estimate Euler Pole Parameters". ... -
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GNNPCSAFT Web App
Smart Thermodynamic Modeling with Graph Neural Networks
The GNNPCSAFT Web App is an implementation of our project that focuses on using Graph Neural Networks (GNN) to estimate the pure-component parameters of the Equation of State PC-SAFT. We developed this app so the scientific community can access the model's results easily. In this app, the estimated pure-component parameters can be used to calculate thermodynamic properties and compare them with experimental data from the ThermoML Archive. More info on github repository. -
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kSNP
kSNP4 does SNP discovery and SNP annotation from whole genomes
kSNP4 identifies the pan-genome SNPs in a set of genome sequences, and estimates phylogenetic trees based upon those SNPs. SNP discovery is based on k-mer analysis, and requires no multiple sequence alignment or the selection of a reference genome, so kSNP4 can take 100's of microbial genomes as input. A SNP locus is defined by an oligo of length k surrounding a central SNP allele. kSNP4 can analyze both complete (finished) genomes and unfinished genomes in assembled contigs or raw, unassembled reads. ... -
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The RDP Classifier is a naive Bayesian classifier that can rapidly and accurately provides taxonomic assignments for bacterial and archaeal 16S rRNA sequences, fungal LSU and fungal ITS sequences, with confidence estimates for each assignment. More information and tutorials on how to install, use and retrain RDP Clasifier can be found on at https://github.com/rdpstaff/classifier and John Quensen's blog (https://john-quensen.com/). Citation: 1. Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. ...
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TASSEL
TASSEL is a bioinformatics software package
TASSEL is a bioinformatics software package that can analyze diversity for sequences, SNPs, or SSRs. Genotype/phenotype associations can be carried out by GLM or a mixed model. Estimates distance and linkage disequilibrium statistics. -
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ProjectQ
An open source software framework for quantum computing
ProjectQ is an open-source effort for quantum computing. It features a compilation framework capable of targeting various types of hardware, a high-performance quantum computer simulator with emulation capabilities, and various compiler plug-ins. -
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Function Point Analysis
Progressive Function Point Analysis Workbook in Excel
...The architect/team returns detailed task list with estimated man hours per task making life easier for Project Managers with less guesstimates and proper business/technical process flows to justify estimates. Better Accountability: All work is accounted for in greater detail, ensuring payment. Task Bound: Every task identified and defined in a user story with well-planned set of functions Time Bound: Every task and user story has a pre-defined time limit for monitoring. Working Blueprint: Base design for development defined in Process steps. ... -
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Toxtree: Toxic Hazard Estimation
Toxicity prediction for chemical compounds
A GUI application which estimates toxic hazard of chemical compounds. The latest version includes the following toxicity prediction modules: -Cramer rules (oral toxicity) -Toxicity mode of action via Verhaar scheme -Skin irritation and Eye irritation prediction -Benigni / Bossa rulebase for mutagenicity and carcinogenicity prediction -START biodegradation and persistence prediction -Skin sensitisation reactivity domain -Kroes TTC Decision tree -SMARTCyp - Cytochrome P450-Mediated Drug Metabolism and metabolites prediction -Structure Alerts for the in vivo micronucleus assay in rodents (ISSMIC) -Structural Alerts for Functional Group Identification (ISSFUNC) -Structural alerts associated with covalent protein binding and DNA binding... -
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Chuck Coleman's SAS Codes
SAS Codes
...Directories under "Files" with descriptions: NESUG 2014: "A Fast, High-Precision Implementation of the Univariate One-Parameter Box-Cox Transformation Using the Golden Section Search in SAS/IML®" SESUG 2017: "Decomposing the R-squared of a Regression Using the Shapley value in SAS®" SESUG 2019: "Conditionally Executing Data Steps and Statements Based on the Presence of Variables in a SAS® Dataset" GASP 2020: "Online Winsorization of the Survey of Construction’s Price Estimates" My SESUG 2015 materials can also be found in my project "constrainingarrays" at https://sourceforge.net/projects/constrainingarrays/. -
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Calis-p
Estimates delta13C of species in a microbiome from proteome data
Calis-p (The CALgary approach to ISotopes in proteomics) is a java application to estimate isotopic composition (e.g. delta13C or delta15N) of individual species in a microbial community from a proteomic dataset. Calis-p 2.0 handles both natural isotope abundances and data from labelling experiments such as stable isotope probing (SIP). It requires a mzIdent (or target spectrum match) and mzML files as the input and requires about 1 min per mzML file with 10 threads and needs <10 Gb of RAM.... -
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easy-dhpsf
GUI for fitting 3D single-molecule images using the double-helix PSF
...Version 2 also includes code that facilitates combining localization data from two spectral channels using a locally-weighted quadratic 3D registration function Features - Double-Gaussian estimator is calibrated via an axial scan of bright immobile fluorescent emitters (e.g. beads) - DH localization is performed through template matching and subsequent double Gaussian fitting - Tiff stacks of SM images are analyzed using template matching followed by double-Gaussian fitting to extract estimates of the molecule positions - Two spectral channels are registered by generating a locally-weighted quadratic mapping function from control point pairs -
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Zocalo is a toolkit for building Prediction Markets, markets in securities that pay out depending on outcomes of future events. A prediction market can provide estimates of the likelihood of specific outcomes that are more reliable than other sources of
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An R package for metrology. metRology provides classes and calculation and plotting functions for metrology applications, including measurement uncertainty estimation and (eventually) inter-laboratory metrology comparison studies.
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MED-FOES
An Agent-Based Simulation of Invasive Pest Insects
MED-FOES is an implementation of a stochastic Agent-Based Simulation (ABS) system for analyzing demographic changes in a single population of Medfly (Ceratitis capitata) over time. The simulation currently takes population extinction as a given because it aims to give us better estimates of necessary quarantine lengths in areas where Medfly is not currently established but does repeatedly invade. Thus the objective of this software is to estimate the time to local extirpation based on known ranges of developmental, survivorship and reproductive parameters, as well as assumed ranges of an eradication pressure parameter. ... -
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EtiC Galaxy simulation
Galaxy extraterrestrial life simulation
...An EtiC simulation run consists to generate a galaxy disk physical stars, associate planets to the stars, and for habitable planets, simulate the life stages evolution until extinction. A visual animation of the galaxy and user selection of highlighted star-planet objects is provided, together with statistics (25+ graphs) and estimates of Drake equation factors. The V2_1 provides several new features: planets surface magnetic field, reworked life stage transitions, integration of MW exoplanets catalog, planets view and graphs window optionally on different threads... EtiC is based on OpenGL / GLFW 3.2, runs on MSWindows 7 and MacOsX. Source code in C++, was developped using the Dev-C++ IDE and XCode. -
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ImagingAnalysis
Direct tissue-level image quantification package for Mathematica
ImagingAnalysis is a Mathematica package that performs grid-based analysis of time-lapse imaging data saved in a sequence of TIFF files. This package requires Mathematica 7.0. Revised on 14 May 2017: Bugs are fixed and incompatibility issues are resolved. The current version runs on Mathematica 11. -
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MSTgold
Estimate minimum spanning trees with statistical bootstrap support
Minimum spanning tree (MST) algorithms can generate multiple, equally-minimal, MSTs but MST programs typically report only one, arbitrarily chosen MST. Similarly, most MST programs do not provide statistical metrics to support the credibility of the MSTs that they estimate. MSTgold estimates the number of alternative MSTs, reports up to a user-determined number of those trees, reports a consensus tree, and implements a bootstrapping metric to assess the reliability of alternate MST solutions. MSTgold accepts single-character data that are nucleotides, amino acids, binary characters, or SNPs; integers that represent, for instance, the lengths of VNTRs or microsatellites; and distance matrices. ... -
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PRIMUS
Pedigree Reconstruction and Identification of a Maximum Unrelated Set
...We present a method adapted from graph theory that always identifies the maximum set of unrelated individuals in any dataset, and allows weighting parameters to be utilized in unrelated sample selection. PRIMUS reads in user-generated IBD estimates and outputs the maximum possible set of unrelated individuals, given a specified threshold of relatedness. Additional information for preferential selection of individuals may also be utilized. For example, when there are two equally sized maximum sets of unrelated individuals in a network, PRIMUS can preferentially select the set with more affected individuals. ... -
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PRADA
PRADA : Pipeline for RNA-Sequencing Data Analysis
Massively parallel sequencing of cDNA reverse transcribed from RNA (RNASeq) provides an accurate estimate of the quantity and composition of mRNAs. To characterize the transcriptome through the analysis of RNA-seq data, we developed PRADA. PRADA focuses on the processing and analysis of gene expression estimates, supervised and unsupervised gene fusion identification, and supervised intragenic deletion identification. PRADA currently supports 7 modules to process and identify abnormalities from RNAseq data: preprocess: Generates aligned and recalibrated BAM files. expression: Generates gene expression (RPKM) and quality metrics. ... -
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MRI-PDQ:Phase Detection & Quantification
Detect sphere-shaped paramagnetic deposits in MRI datasets
Moved to http://parkermills.github.io/MRI-PDQ/ -
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bagemass
Bayesian age and mass estimates for transiting planet host stars
Source code, makefile and README for installation of software used for the analysis in Maxted, Serenelli & Southworth, "Bayesian mass and age estimates for transiting exoplanet host stars", A&A 575, 36, 2015. -
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FreDec
Parallelized FREquency DEComposer algorithm
...The algorithm analyses all suspicious frequencies, including the ones that look like an alias at a glance, but may become preferable later. After selection of the initial frequency candidates, the algorithm passes through all their possible combinations and estimates their multi-frequency statistical significance. In the end, it prints out the set of largest frequency tuples that were still found significant. The GPU computing is implemented through CUDA and brings a significant performance increase. It is still possible to run FreDec solely on CPU, if no suitable GPU device is available in the system. ... -
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ARDEN
Specificity Control for Read Alignments Using an Artificial Reference
We introduce ARDEN (Artificial Reference Driven Estimation of false positives in NGS data), a novel benchmark that estimates error rates based on real experimental reads and an additionally generated artificial reference genome. It allows the computation of error rates specifically for a dataset and the construction of a ROC-curve. Thereby, it can be used to optimize parameters for read mappers, to select read mappers for a specific problem or also to filter alignments based on quality estimation.
