Search Results for "cluster analysis" - Page 2
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Showing 87 open source projects for "cluster analysis"
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TARGT pipeline
Targeted Analysis of sequence Reads for GenoTyping of HLA/MHC genes
The 'TARGT' pipeline for Targeted Analysis of sequencing Reads for GenoTyping can be used for genotyping of MHC/HLA genes (or other genomic regions) from ancient and modern shotgun sequence data with moderate to low sequence coverage. The pipeline consists of a main bash script that calls the different steps of the pipeline and can either be called directly or submitted to a cluster queue system, as well as additional sub-scripts and files, that are required to perform the different steps. ... -
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VisuaR
R-based workflow for the analysis and visualization of sequence data
VisuaR's main goal is to provide a set of analyses and visualizations that are often used in the analyses of amplicon sequencing data. The VisuaR workflow is based on commands from other R packages (e.g. vegan, stringr, plyr, ggplot2), as well as on custom-build scripts. It takes dada2 (https://github.com/benjjneb/dada2) files as input and generates (near-)publication ready figures as output. In addition to NMDS ordinations, cluster dendrograms and UpSet diagrams the workflow features custom... -
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Otter
Alibaba distributed database synchronization system
In Alibaba B2B company, because of the characteristics of the business, the sellers are mainly concentrated in the country, and the buyers are mainly concentrated in foreign countries, so it has derived the demand for the computer room in Hangzhou and the United States. At the same time, in order to improve the user experience, the structure of the entire computer room is double-A Both can be written, and thus a product like otter was born. The first version of otter can be traced back to... -
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GEOMS2
Geostatistics and geosciences modeling software
GEOMS2 is a geostatistics and geosciences modeling software. Provides interface for grid (mesh), point, surface and data (non-spatial) objects. It has a 3D viewer and 2D plots using the well known Python engines Mayavi and Matplotlib. It has several functions to manipulate your data as well as provide univariate and multivariate analysis. NOTE: The software is still an early beta. Please tell us if you found a bug. Download datasets for students of Geostatistics 2017 (Petroleum... -
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CUCAA tool
Codon Usage Co-Adaptation Analysis Tool "CUCAA Tool"
Tools are available to analysis the codon usage, but there are no tools available focusing on analyzing the codon usage co-adaptation between viruses and their hosts. Therefore, Codon Usage Co-Adaptation Analysis Tool "CUCAA Tool" were developed by python 3.7. The tool can calculate various codon usage bias measurements as effective number of codons, codon adaptation index, relative codon deoptimization index, similarity index, as well as a simple cluster machine learning approach to see if the viruses will be clustered with the host codon usage or not. -
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miARma-Seq
a A suite designed to study mRNAs, miRNAs and circRNAs
miARma-Seq, which stands for miRNA-Seq And RNA-Seq Multiprocess Analysis, is a suite designed to study mRNAs, miRNAs and circRNAs. It is able to perform differential expression analysis, miRNA-mRNA target prediction and functional analysis among others. Most importantly, it can be applied to any sequenced organism, and it can be initiated at any step of the workflow. As a stand-alone tool, is both easy to install and extremely flexible in terms of its use. It brings together... -
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Spark Notebook
Interactive and Reactive Data Science using Scala and Spark
Spark Notebook is an interactive web-based computational notebook designed to make working with Apache Spark more productive, exploratory, and expressive. It allows developers, data scientists, and analysts to write, run, and visualize Spark code in cells that support multiple languages such as Scala, Python, and SQL, all within the same notebook. Users can interleave runnable code, rich text markup, visualizations, equations, and results, enabling reproducible research and exploratory data... -
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Clustering divides data into groups (clusters) that are meaningful, useful, or both. If meaningful groups are the goal, then the clusters should capture the natural structure of the data. In some cases, however, cluster analysis is only a useful starting point for other purposes, such as data summarization. Whether for understanding or utility, cluster analysis has long played an important role in a wide variety of fields: psychology and other social sciences, biology, statistics, pattern recognition, information retrieval, machine learning and data mining.
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clusterpam
Useful functions for cluster analysis using PAM
Functions for optimal unsupervised cluster analysis using Partition Around Medoids -
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MT-Toolbox
Software for molecule tagged DNA sequences
MT-Toolbox is a user friendly software package for analysis of molecule tagged Illumina MiSeq reads. Molecule tagging is a molecular biology technique to significantly reduce amplicon sequence error and PCR bias which can be applied to any amplicon sequencing project. MT-Toolbox converts raw reads into high quality consensus sequences based on each reads molecule tag. For details and other important information please refer to the MT-Toolbox webpage below. MT-Toolbox is now hosted on... -
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Spark Python Notebooks
Apache Spark & Python (pySpark) tutorials for Big Data Analysis
Spark Python Notebooks is a curated collection of example Jupyter notebooks designed to help developers and data engineers learn Apache Spark using Python in an interactive environment. Rather than only providing static code files, this project uses notebooks to teach practical data processing workflows, exposing users to real Spark programming patterns like working with RDDs, DataFrames, and distributed computations. These notebooks often demonstrate how to transform, analyze, and visualize... -
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goSTAG
Gene Ontology Subtrees to Tag and Annotate Genes within a set
We developed goSTAG for utilizing Gene Ontology Subtrees to Tag and Annotate Genes that are part of a set. Given gene lists, goSTAG performs GO enrichment analysis and clusters the GO terms based on the p-values from the significance tests. GO subtrees are constructed for each cluster, and the term that has the most paths to the root within the subtree is used to tag and annotate the cluster. -
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PGAP
PGAP is a pipeline for pan-genome analysis.
PGAP is a pan-genomes analysis pipeline developed with Perl. It could perform five analytic functions with only one command, including cluster analysis of functional genes, pan-genome profile analysis, genetic variation analysis of functional genes, species evolution analysis and function enrichment analysis of gene clusters. -
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CCKDM
Concern Mining
This is a tool for concern mining which uses a KDM model as input and the output is the same model with annotated concerns. It uses a Concern Library and a modified String Clustering K-means algorithm with Levenshtein metric to cluster the strings. -
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(NCS) NEQUIM Contact System
Tool for analyze of interactions in ligand-protein complexes
NEQUIM Contact System (NCS) is a system to generate and analyze interaction vectors of protein-ligand complexes. Core features include multiple views of vectors, multiple selection options, cluster analysis and generation of interaction vector model. The input could be from PDB format or from files generated by automatic docking softwares AutoDock/Vina or Surflex. -
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Malware Analysis Network in Taiwan
MAN in Taiwan, MiT
Malware Analysis Network in Taiwan <Man in Taiwan, MiT> Welcome to contact us (TonTon@TWMAN.ORG) if you are interested in collaborating with us. This project is open source and distributed under the GNU General Public License version 3. Please feel free to add to or modify this source and propose changes or new converters. Developer & Copyrighted by : TonTon Hsien-De Huang Prompter: Jazz Yao-Tsung Wang, Figaro Chen-Ho Yang | Logo Desinger:Temaki Guo Community on... -
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CIMS
Crosslinking induced mutation site analysis
This package includes the scripts to detect statistically reproducible crosslinking induced mutation sites (CIMS) and cross linking induced truncation sites (CITS) from HITS-CLIP data. References: Moore, M.*, Zhang, C.*, Gantman, E.C., Mele, A., Darnell, J.C., Darnell, R.B. 2014. Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis. Nat Protocols, 9:263-293. Zhang,C.†, Darnell, R.B.† 2011.... -
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ClAnSort
Cluster-Analysis and Sort
The ClAnSort (Cluster-Analysis and Sort) - program was written to simplify the analysis of Next Generation Sequencing (NGS) data obtained with Ion Torrent™ Technology using the BIOMED-2 Concerted Action BMH4-CT98-3936 primer sets (IGH, IGK, TRB, TRG and TRD) for amplification [van Dongen, J.J. et al., 2003]. -
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TextTools is a freeware corpus linguistics tool developed in Python to aid in research. This program analyzes user-created corpora and displays information about word (token) frequency, n-grams, clusters, collocations, keyword in context (KWIC), and keyness. TextTools is designed to be user-friendly and intuitive and will run natively on Mac OS X.
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Deem
Analyze time-course data with significance tests, clustering, modeling
Use statistical methods to analyze time-course data (gene expression microarray and RNA-seq data in particular, but not limited to). Apply significance tests to filter out only significant genes or time series. Cluster time series into similar groups. Generate network models, including linear or non-linear models. Variable selection and optimization routines included. Written in Scala and R. The application is a cross-platform desktop app with a simple GUI and is fully functional... -
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Geospace Analysis Package
MatLab toolbox for magnetospheric and ionospheric science.
A MatLab toolbox with many simple and useful functions for analyzing data from Cluster, Champ and the Swarm missions. Other functions for space plasma physics, magnetospheric and ionospheric research are included. The toolbox is designed to be as simple as possible. Each function can be learned and used individually. See the tutorial in the Files section for a quick introduction. -
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piv_clustering
structural clustering of atomic trajectories based on PIV
This program allows to perform a structural cluster analysis of atomic trajectories obtained, e.g., from molecular dynamics simulations. At variance with other approaches, it is possible to analyse also processes in solution, e.g., chemical reactions in liquid water, since the distance metric is based on a Permutation Invariant Vector (PIV) that is symmetric under exchange of identical atoms or molecules, including on the same footing both solute and solvent degrees of freedom. ... -
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Arron-IMSA
Integrated Metagenomic Sequence Analysis for Next Gen Datasets
...IMSA assigns a score to each node of the taxonomy based on read frequency, and can output this as a taxonomy report suitable for cluster analysis or as a taxonomy map (TaxMap). IMSA also outputs the specific sequence reads assigned to a taxon of interest for downstream analysis. -
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XNDiff
X-ray and Neutron powder pattern simulation analysis
Keywords (XNDiff): -SAXS -SANS -absolute units -core (double)shell crystalline nanoparticles -with a parallelepidal shape -particle assemblies -powder and ensemble average -C/C++ -Unix -OpenMP -HPC Cluster Keywords (BatchMultiFit): -simultaneous fits for several SAXS and SANS curves with simulation data from XNDiff -SANS data can be smeared with dq values from experimental data sets or analytical functions -Mathematica console -local and global optimizers (simulated... -
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AWclust is easy to use non-parametric population structure analysis software written for R with a GUI interface. Just point and click and you will be on your way to discovering the important cluster information in your SNP data sets.
