Search Results for "prediction" - Page 8
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Showing 446 open source projects for "prediction"
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This R package combines biological information (expression data) with theoretical information (miRNA target prediction databases) in order to obtain a curated list of potential miRNA-mRNA interaction pairs.
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Seqping
Gene Prediction Pipeline for Plant Genomes
Gene Prediction Pipeline for Plant Genomes using Self-Training Gene Models and Transcriptomic Data -
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SnowyOwl
RNA-Seq based gene prediction pipeline for fungal genomes
SnowyOwl is a gene prediction pipeline that uses RNA-Seq data to train and provide hints for the generation of Hidden Markov Model (HMM)-based gene predictions, and to evaluate the resulting models. The pipeline has been validated and streamlined by comparing its predictions to manually curated gene models in three fungal genomes, and its results show substantial increases in sensitivity and selectivity over previous gene predictions. Sensitivity is gained by repeatedly running the HMM gene... -
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Crosshub
Multi-way analysis of The Cancer Genome Atlas (TCGA) project datasets
Crosshub enables multi-way analysis of RNA-Seq, miRNA-Seq and methylome data of The Cancer Genome Atlas (TCGA) project: 1. differential expression analysis (genes, alternative transcripts and miRNA) 2. regulatory miRNA prediction (TargetScan, DIANA microT, mirSVR, PicTar, miRTarBase + co-expression) 3. regulatory TF prediction (ENCODE ChIP-Seq + co-expression) 4. methylation profiling analysis 5. RNA-Seq vs. clinical (TNM, stage, follow-up) correlation analysis Generates Excel summaries... -
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ConsPred
ConsPred is a pipeline combining several gene/CDS annotation tools
... and adapted to specific needs. The genome annotations are produced in formats ready for submission to public sequence archives. Important notice: Conspred development has been ended with version 1.33 (except minor bug fixes). We are currently developing a completely rewritten Conspred2, which focuses on consensus gene prediction and high-quality gene start prediction. Conspred2 will not do any functional annotation (consider e.g. Prokka and GAMOLA2 for this purpose). -
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The project has moved to Github https://github.com/akasolace/HO/releases
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Random Bits Forest
RBF: a Strong Classifier/Regressor for Big Data
We present a classification and regression algorithm called Random Bits Forest (RBF). RBF integrates neural network (for depth), boosting (for wideness) and random forest (for accuracy). It first generates and selects ~10,000 small three-layer threshold random neural networks as basis by gradient boosting scheme. These binary basis are then feed into a modified random forest algorithm to obtain predictions. In conclusion, RBF is a novel framework that performs strongly especially on data... -
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Community profiling (CP) is a guilt-by-association approach for predicting functional associations between proteins: two proteins are predicted to be associated if they share similar presence and absence profiles (called community profiles) across microbial communities. Community profiling is conceptually similar to the phylogenetic profiling approach to functional prediction, however with fundamental differences. This package provides different profile construction methods and correlation...
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RNHtool
RNase H prediction model
RNHtool is developed to predict RNase H domain of retroviruses. -
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PSICOV
The unofficial binary for PSICOV: Protein Sparse Inverse COVariance
PSICOV (Protein Sparse Inverse Covariance estimation program) is a coevoultion algorithm applied to very large (typically >=1000 sequences) multiple sequence alignments for precise protein structural contact prediction. This is the unofficial precompiled Windows binary for PSICOV compiled by Chengxin Zhang at Fudan University. The source code is copyrighted by David T. Jones, University College London. -
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ingap-cdg
codon-based de Bruijn graph algorithm for gene construction
Currently, most gene prediction methods detect coding sequences (CDSs) from transcriptome assembly when lacking of closely related reference genomes. However, these methods are of limited application due to highly fragmented transcripts and extensive assembly errors, which may lead to redundant or false CDS predictions. Here we present a novel algorithm, inGAP-CDG, for effective construction of full-length and non-redundant CDSs from unassembled transcriptomes. inGAP-CDG achieves... -
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Random Bits Regression
Random Bits Regression is a strong general predictor.
We proposed an accurate, robust and fast general predictor (RBR) for regression and classification in big data era. The application of this method is very broad, from science to industry, finance and health. The accuracy and robustness improvement of our method over existing method could bring huge benefits in some critical applications. For example, natural disaster prediction, stock price prediction, personal/population disease prediction. The fast-speed nature of our method not only allows... -
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A Matlab toolbox for geostatistical modelling, prediction and simulation. It contains native matlab algorithms, and interfaces to SGeMS, GSTAT and VISIM.
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GPMfit
Gaussian Process Model Fitting
Gaussian Process model for fitting deterministic simulator output. Establish efficient and reliable likelihood optimization through hybridized DIRECT-BFGS and multi-start BFGS algorithms. Programming Language: Matlab. -
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MITP
MITP - conserve & novel miRNA identification & target prediction tool
miRNA is a widely known small non-coding RNA which can mediate gene regulation of most important biological processes in plants and animals. Therefore, identification conserve and novel miRNA and their target genes in model and new sequenced species are inevitable. MITP is designed to identify miRNA easily and faster based on sequence mapping result from any mapping software which producing SAM format output result, blast result (default output result) or blat result (default output result).... -
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Drug Interaction Prediction
This includes the data and results obtained in this project
Data: Used data for inferring drug-drug interactions Results: Predicted positive and negative drug-drug interactions -
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Prediction year mortality
For prediction year mortality of patients with acute heart failure
Application required own the database AHEAD with patient's personal medical data. It's predicted year mortality of patients. -
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Genix: Bacterial Genome Annotation Pipel
A automated annotation pipeline for bacteria / archea genomes
Genix is an online automated pipeline for bacterial genome annotation that integrates the programs Prodigal, BLAST, RNAmmer, tRNAscan-SE, INFERNAL, ARAGORN and HMMER, and the databases Uniprot, Antifam and Rfam. -
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very fast but accurate prediction tool. 0.5 hour for 11 million sample with 28 features. usually default parameter is OK, minimal tuning.
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KA-predictor
lysine acetylation site prediction
This predictor is developed to predict species-specific lysine acetylation sites based on support vector machine (SVM) classifier. It is supplied in source code form along with th e required data files and run under the linux. The input is a protein sequence file (fasta format). -
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RASP v1.90
RASP v1.90
RASP is a protein side-chain structure prediction program. V1.90 has cleaned the bug in v1.80 and updated in 2016. Version 1.80 is the Jan 2013 updated version. -
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isomiR2Function
online data and scripts of isomiR2Function
isomiR2Function is a perl-based script for isomiR analysis. All the online data is deposited in this project.