Search Results for "prediction" - Page 6
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Showing 446 open source projects for "prediction"
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The SPInDel workbench is a computational platform to facilitate the planning and management of SPInDel projects, alignment of nucleotide sequences, visualization and selection of conserved regions, calculation of PCR primers properties, prediction of SPInDel profiles and diverse statistical and phylogenetic analyses. It includes a large dataset comprising nearly 1,800 numeric profiles for the identification of eukaryotic, prokaryotic and viral species.
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SpliceGrapher predicts alternative splicing patterns and produces splice graphs that capture in a single structure the ways a gene's exons may be assembled. It enhances gene models using evidence from next-generation sequencing and EST alignments.
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Skater
Python library for model interpretation/explanations
Skater is a unified framework to enable Model Interpretation for all forms of the model to help one build an Interpretable machine learning system often needed for real-world use-cases(** we are actively working towards to enabling faithful interpretability for all forms models). It is an open-source python library designed to demystify the learned structures of a black box model both globally(inference on the basis of a complete data set) and locally(inference about an individual prediction... -
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altanalyze
Alternative splicing and functional prediction analysis tool
AltAnalyze is a freely available, open-source and cross-platform program that allows you to take RNASeq or relatively raw microarray data (CEL files or normalized), identify predicted alternative splicing or alternative promoter changes and view how these changes may affect protein sequence, domain composition, and microRNA targeting. AltAnalyze is compatible with any RNASeq data (exons and/or junctions), several Affymetrix splicing sensitive array types (Gene 1.0, Exon 1.0, junction) as... -
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OncoBase
A platform for decoding regulatory somatic mutations in human cancers
Whole-exome and whole-genome sequencing have revealed millions of somatic mutations associated with different human cancers. The vast majority of identified somatic mutations are located outside of coding sequences, making it challenging to directly interpret their functional effects. With the rapid advances in high-throughput chromosome conformation capture (3C)-based technologies, genome-scale long-range chromatin interactions were detected, and distal target genes of regulatory elements... -
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RTC-simulator
Simulation and Control of Processing Plants
RTC (Real Time Control) is a program of M. Mulholland (2015). This is a simple interactive simulator including 20 different applications for such aspects as PID and DMC controller tuning, advanced level control, Smith prediction, Kalman filtering, and control strategies for a furnace, a boiler, and a hybrid system. A tutorial gives brief background to the theory and programming of each application, plus a stepwise set of objectives to illustrate the main features. The simulations include... -
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piRanha target prediction
Prediction of target transcripts based on piRNA sequence datasets
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GPRED-GC
a Gene PREDiction model accounting for 5'-3' GC gradient
A new hidden Markov model (HMM)-based ab initio gene prediction tool for finding genes with highly variable GC contents such as the genes with negative GC gradients in grass genomes. -
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DACO-algorithm
A novel transcription factor complex prediction algorithm.
Eukaryotic gene expression is controlled through molecular logic circuits that combine regulatory signals of many different factors. Complexation of transcription factors and other regulatory proteins is a prevailing and highly conserved mechanism of signal integration within critical regulatory pathways and enable to infer controlled genes as well as the exerted regulatory mechanism. We developed DACO (domain-aware cohesiveness optimization), a novel algorithm that combines... -
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austenite transformations simulator
A solver for austenite transformations simulation.
A console software which is a solver for austenite transformations simulation. It has a text file in/out interface. Also there is a windowed shell for the calculation result processind and import selected results to excel files. Thermodynamics and kinetic calculations. For MS Windows only. -
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knnAUC
k-nearest neighbors AUC test.
knnAUC : k-nearest neighbors AUC test. In the knnAUC framework, we first calculated the AUC estimator based on a k-nearest neighbors classifier, and then evaluate the significance of the AUC based statistic (Alternative hypothesis: AUC > 0.5, that is to say, X has prediction power for Y). -
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BNNPT
A powerful method for nonlinear dependence of two continuous variables
Testing dependence/correlation of two variables is one of the fundamental tasks in statistics. In this work, we proposed a powerful method for nonlinear dependence of two continuous variables (X and Y). We addressed this research question by using BNNPT (Bagging Nearest-Neighbor Prediction Test, software available at https://sourceforge.net/projects/bnnpt/). In the BNNPT framework, we first used the value of X to construct a bagging neighborhood structure. And then, we got the out of bag... -
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CFM-ID
Competitive Fragmentation Modeling for Metabolite Identification
Windows binaries and cross-platform source code for processing of EI-MS (GC-MS) and ESI-MS/MS (LC-MS) data for identification of metabolites. Includes tools for applying Competitive Fragmentation Modeling (CFM) to spectrum prediction and metabolite identification tasks, as well as a tool for fragment generation, and another for peak annotation. For further documenation see https://sourceforge.net/p/cfm-id/wiki/Home/ For related publications, and their associated supplementary data... -
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Gamewhizzards
GameWhizzards is a user created, Open Source 3D MMORPG
... Gambetta's excelent guide at http://www.gabrielgambetta.com/client-side-prediction-server-reconciliation.html It uses clientside prediction, server recoinciliation, and an authoritative server for player and enemy movement. State of development: [X] Multiplayer Position Sync [X] Enemys [X] Inventory [X] Items [X] Fighting [X] Chat [X] Basic UI [X] Basic level editor [ ] Module System [/] World Editor [ ] Quests [/] Instance Server [ ] Instance Finder Assets have been removed -
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SAW - Special Access to Windows
SAW - Special Access to Windows - a programmable on-screen keyboard.
SAW - Special Access to Windows - is a programmable on-screen keyboard. It is a powerful tool for providing Access to the Windows operating system for people who need alternative Switch or Pointing device input options. The latest SAW 6 version update was supported by the AEGIS project (http://www.aegis-project.eu/). It is fully Windows 7-10 compatible, supports Unicode, includes its own "Blade" word prediction and abbreviation expansion engine, can interact with the CCF-SymbolServer... -
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Presage
the intelligent predictive text entry platform
... predictive algorithms. Presage's predictive capabilities are implemented by predictive plugins. Predictive plugins use services provided by the platform to implement multiple prediction techniques. -
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The Deep Review
A collaboratively written review paper on deep learning, genomics, etc
This repository is home to the Deep Review, a review article on deep learning in precision medicine. The Deep Review is collaboratively written on GitHub using a tool called Manubot (see below). The project operates on an open contribution model, welcoming contributions from anyone. To see what's incoming, check the open pull requests. For project discussion and planning see the Issues. As of writing, we are aiming to publish an update of the deep review. We will continue to make project... -
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PTM-X
a solfware for predicting posttranslational modification cross-talk
The PTM-X (PTM cross-talk) project is a freely available bioinformatics software platform that allows to calculate the features of PTM pairs and the posterior probabilities of being cross-talk pairs. The prediction model is a naive Bayse classifier that integrats five features: protein sequence distance, tertiary structural distance, co-location in a disordered region, residue co-evolution, and modification co-evolution. An online tool is also available at http://bioinfo.bjmu.edu.cn/ptm-x/. -
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PF_HP
Prediction of proteinfolding in 2D HP model
Even in the simplified two dimensional HP-model (hydrophob/polar) the prediction of proteinfolding is NP complete. We implement a brute force algorithm with serial and parallel execution to solve short inputs of HP sequences (0-1 bitstrings). Selbst im vereinfachten zweidimensionalen HP-Modell (hydrophob/polar) ist die Proteinfaltung bereits NP-vollständig. Hier implementieren wir einen brute-force Algorithmus zur Lösung kurzer Eingabesequenzen (0-1-Bitstrings) für die Proteinfaltung... -
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An integrated atmospheric model for weather and climate prediction and simulation. It includes portable versions of global spectral model, regional spectral model, and non-hydrostatic mesoscale spectral model.
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Neopepsee
Accurate genome-level prediction of neoantigens by harnessing sequence
we developed Neopepsee, a method that applies a machine learning to classify personal immunogenicity with next generation sequencing data. -
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FragGeneScan is an application for finding (fragmented) genes in short reads. It can also be applied to predict prokaryotic genes in incomplete assemblies or complete genomes. FragGeneScan was first released through omics website (http://omics.informatics.indiana.edu/FragGeneScan/) in March 2010, where you can find its old releases. FragGeneScan migrated to SourceForge in October, 2013.
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NanoGLADIATOR
Real-time detection of copy number alterations from nanopore data.
Nano-GLADIATOR is a novel software tool that allows to analyze WGS data generated during a MinION or GridION X5 run for the detection of copy number alterations (CNAs). Nano-GLADIATOR (Nanopore Genomic aLterations AnD allelIc frAcTiOn pRedictor) is capable to perform CNVs/CNAs detection and allelic fraction prediction during the sequencing run ("On-line" mode for real time molecular karyotyping) and once the experiment is completed ("Off-line" mode, for parallel analysis of multiple samples... -
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