Search Results for "tool"
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Showing 13 open source projects for "tool"
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clusterProfiler
A universal enrichment tool for interpreting omics data
clusterProfiler is an R/Bioconductor package that provides a unified workflow for functional enrichment analysis to interpret high-throughput omics results. It supports both over-representation analysis and gene set enrichment analysis, letting you work with unranked gene lists or ranked statistics from differential pipelines. The package connects to multiple knowledge bases—such as Gene Ontology, KEGG, Reactome, Disease Ontology, MeSH and others—through a consistent interface so you can... -
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lintr
Static Code Analysis for R
lintr is a static code analysis tool for R that identifies syntax errors, style inconsistencies, and other potential issues in R scripts and packages. It supports customizable lint rules and integrates with many editors to provide realtime feedback and enforce coding standards (e.g., tidyverse style). -
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knitr
A general-purpose tool for dynamic report generation in R
knitr is an R package that acts as a literate programming engine, combining code execution and document generation. It executes code embedded in Markdown, LaTeX, or other formats and produces output with results interleaved into final documents. It powers R Markdown and supports caching, chunk options, graphics, and extensibility for reproducible analysis. -
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targets
Function-oriented Make-like declarative workflows for R
The targets package is a pipeline / workflow management tool in R, designed to coordinate multi‐step computational workflows in data science / statistics. It tracks dependencies between “targets” (computational steps), skips steps whose upstream data or code hasn’t changed, supports parallel computation, branching (dynamic generation of sub‐targets), file format abstractions, and encourages reproducible and efficient analyses. -
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MetEx
MetEx is a computational tool for metabolite targered extraction and a
Liquid chromatography–high resolution mass spectrometry (LC-HRMS) is the most popular platform for untargeted metabolomics methods, but annotating LC-HRMS data is a long-standing bottleneck that we are facing since years ago in metabolomics research. A wide variety of methods have been established to deal with the annotation issue. To date, however, there is a scarcity of efficient, systematic, and easy-to-handle tools that are tailored for metabolomics and exposome community. So we... -
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FAST-GHG
A fast tool to caculatate greenhouse gases in agriculture
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hui
hewies user interface - 3D scientific visualisation tool
Python project with goal to provide FOSS library to extract, analyse and visualise data in a 3D fashion. The instance will connect to a data source, ods sheet, csv, sql DB, pyodbc the instance will analyse and/or transform the data to be presented to the visualisation functionality the instance will visualise the data in a 3D fashion, likely using third party FOSS -
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OmicSelector
Feature selection and deep learning modeling for omic biomarker study
...It was initially developed for miRNA-seq (small RNA, smRNA-seq; hence the name was miRNAselector), RNA-seq and qPCR, but can be applied for every problem where numeric features should be selected to counteract overfitting of the models. Using our tool, you can choose features, like miRNAs, with the most significant diagnostic potential (based on the results of miRNA-seq, for validation in qPCR experiments). -
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miRPV
miRPV: An automated pipeline for miRNA Prediction and Validation in si
miRPV is an Automated tool that allows users to predict and validate microRNA from genome/gene sequence. System Requirement CPU: AMD64 (64bit) Memory: 2Gb RAM Storage: 5Gb Ubuntu 18.04 -
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Covidex
Ultra fast and accurate subtyping tool of viral genomes.
...Subtypification is relevant for studies on virus epidemiology, evolution and pathogenesis. In this sense, Covidex was developed as an open source alignment-free machine learning subtyping tool. It is a shiny app that allows fast and accurate classification of viral genomes in pre-defined clusters. If more than 1000 sequences are loaded the tool will run in multithread mode. Capable of classifying 16000 genome sequences in less than a minute (AMD Ryzen 7 1700 8-core Processor 3 GHz) For a Web-based version of the app (only for small datasets: 100 seqs max) please go to http://covidex.unlu.edu.ar If you use Covidex please consider citing the following preprint: https://biorxiv.org/cgi/content/short/2020.08.21.261347v1 If you think my work is useful you can buy me a coffee! ... -
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QuantifyPoly(A)
Quantification of poly(A) sites from 3' end sequencing data
QuantifyPoly(A) - a tool for quantification of poly(A) sites from 3' end sequencing data. [1] QuantifyPoly(A) user manual Please visit the Wiki page of this website. [2] QuantifyPoly(A) Q&A For Q&A, please visit the Blog page of this website. [3] QuantifyPoly(A) bug report You can report a bug as a Ticket request, or start a topic session in the Discussion webpage of this website. -
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Pain2D are programs which were developed for the automated pain drawing collection and classification of diseases on the basis of pain drawings in pen-and-paper and digital form for research purposes. Pain2D is currently not a diagnostic tool, but is aimed at scientists, physicians and anyone interested in the automated analysis of pain drawings.
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R Markdown Cookbook
R Markdown Cookbook
R Markdown Cookbook. A range of tips and tricks to make better use of R Markdown. R Markdown is a powerful tool for combining analysis and reporting into the same document. Since the birth of the rmarkdown package (Allaire, Xie, Dervieux, McPherson, et al. 2023) in early 2014, R Markdown has grown substantially from a package that supports a few output formats, to an extensive and diverse ecosystem that supports the creation of books, blogs, scientific articles, websites, and even resumes.
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