goseq - Gene Ontology analyser for RNA-seq and other length biased data

Detects Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data.

Last updated 4 months ago

immunooncologysequencinggogeneexpressiontranscriptionrnaseqdifferentialexpressionannotationgenesetenrichmentkeggpathwayssoftware

9.79 score 1 stars 9 dependents 636 scripts 2.3k downloads

pcaExplorer - Interactive Visualization of RNA-seq Data Using a Principal Components Approach

This package provides functionality for interactive visualization of RNA-seq datasets based on Principal Components Analysis. The methods provided allow for quick information extraction and effective data exploration. A Shiny application encapsulates the whole analysis.

Last updated 2 months ago

immunooncologyvisualizationrnaseqdimensionreductionprincipalcomponentqualitycontrolguireportwritingshinyappsbioconductorprincipal-componentsreproducible-researchrna-seq-analysisrna-seq-datashinytranscriptomeuser-friendly

9.63 score 56 stars 180 scripts 794 downloads

GeneTonic - Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis

This package provides functionality to combine the existing pieces of the transcriptome data and results, making it easier to generate insightful observations and hypothesis. Its usage is made easy with a Shiny application, combining the benefits of interactivity and reproducibility e.g. by capturing the features and gene sets of interest highlighted during the live session, and creating an HTML report as an artifact where text, code, and output coexist. Using the GeneTonicList as a standardized container for all the required components, it is possible to simplify the generation of multiple visualizations and summaries.

Last updated 1 months ago

guigeneexpressionsoftwaretranscriptiontranscriptomicsvisualizationdifferentialexpressionpathwaysreportwritinggenesetenrichmentannotationgoshinyappsbioconductorbioconductor-packagedata-explorationdata-visualizationfunctional-enrichment-analysisgene-expressionpathway-analysisreproducible-researchrna-seq-analysisrna-seq-datashinytranscriptomeuser-friendly

8.23 score 77 stars 1 dependents 37 scripts 538 downloads

ideal - Interactive Differential Expression AnaLysis

This package provides functions for an Interactive Differential Expression AnaLysis of RNA-sequencing datasets, to extract quickly and effectively information downstream the step of differential expression. A Shiny application encapsulates the whole package. Support for reproducibility of the whole analysis is provided by means of a template report which gets automatically compiled and can be stored/shared.

Last updated 2 months ago

immunooncologygeneexpressiondifferentialexpressionrnaseqsequencingvisualizationqualitycontrolguigenesetenrichmentreportwritingshinyappsbioconductordifferential-expressionreproducible-researchrna-seqrna-seq-analysisshinyuser-friendly

6.78 score 29 stars 5 scripts 268 downloads

mosdef - MOSt frequently used and useful Differential Expression Functions

This package provides functionality to run a number of tasks in the differential expression analysis workflow. This encompasses the most widely used steps, from running various enrichment analysis tools with a unified interface to creating plots and beautifying table components linking to external websites and databases. This streamlines the generation of comprehensive analysis reports.

Last updated 2 months ago

geneexpressionsoftwaretranscriptiontranscriptomicsdifferentialexpressionvisualizationreportwritinggenesetenrichmentgo

6.12 score 4 dependents 342 downloads

flowcatchR - Tools to analyze in vivo microscopy imaging data focused on tracking flowing blood cells

flowcatchR is a set of tools to analyze in vivo microscopy imaging data, focused on tracking flowing blood cells. It guides the steps from segmentation to calculation of features, filtering out particles not of interest, providing also a set of utilities to help checking the quality of the performed operations (e.g. how good the segmentation was). It allows investigating the issue of tracking flowing cells such as in blood vessels, to categorize the particles in flowing, rolling and adherent. This classification is applied in the study of phenomena such as hemostasis and study of thrombosis development. Moreover, flowcatchR presents an integrated workflow solution, based on the integration with a Shiny App and Jupyter notebooks, which is delivered alongside the package, and can enable fully reproducible bioimage analysis in the R environment.

Last updated 2 months ago

softwarevisualizationcellbiologyclassificationinfrastructureguishinyappsbioconductorfluorescencemicroscopyparticlestracking

5.62 score 4 stars 8 scripts 261 downloads

bettr - A Better Way To Explore What Is Best

bettr provides a set of interactive visualization methods to explore the results of a benchmarking study, where typically more than a single performance measures are computed. The user can weight the performance measures according to their preferences. Performance measures can also be grouped and aggregated according to additional annotations.

Last updated 4 months ago

visualizationshinyappsgui

5.38 score 3 stars 3 scripts 145 downloads

quantiseqr - Quantification of the Tumor Immune contexture from RNA-seq data

This package provides a streamlined workflow for the quanTIseq method, developed to perform the quantification of the Tumor Immune contexture from RNA-seq data. The quantification is performed against the TIL10 signature (dissecting the contributions of ten immune cell types), carefully crafted from a collection of human RNA-seq samples. The TIL10 signature has been extensively validated using simulated, flow cytometry, and immunohistochemistry data.

Last updated 2 months ago

geneexpressionsoftwaretranscriptiontranscriptomicssequencingmicroarrayvisualizationannotationimmunooncologyfeatureextractionclassificationstatisticalmethodexperimenthubsoftwareflowcytometry

4.65 score 1 dependents 3 scripts 794 downloads

simrec - Simulation of Recurrent Event Data for Non-Constant Baseline Hazard

Simulation of recurrent event data for non-constant baseline hazard in the total time model with risk-free intervals and possibly a competing event. Possibility to cut the data to an interim data set. Data can be plotted. Details about the method can be found in Jahn-Eimermacher, A. et al. (2015) <doi:10.1186/s12874-015-0005-2>.

Last updated 2 months ago

4.30 score 2 stars 8 scripts 166 downloads