scp - Mass Spectrometry-Based Single-Cell Proteomics Data Analysis

Utility functions for manipulating, processing, and analyzing mass spectrometry-based single-cell proteomics data. The package is an extension to the 'QFeatures' package and relies on 'SingleCellExpirement' to enable single-cell proteomics analyses. The package offers the user the functionality to process quantitative table (as generated by MaxQuant, Proteome Discoverer, and more) into data tables ready for downstream analysis and data visualization.

Last updated 24 days ago

geneexpressionproteomicssinglecellmassspectrometrypreprocessingcellbasedassaysbioconductormass-spectrometrysingle-cellsoftware

8.82 score 21 stars 110 scripts 404 downloads

CytoPipeline - Automation and visualization of flow cytometry data analysis pipelines

This package provides support for automation and visualization of flow cytometry data analysis pipelines. In the current state, the package focuses on the preprocessing and quality control part. The framework is based on two main S4 classes, i.e. CytoPipeline and CytoProcessingStep. The pipeline steps are linked to corresponding R functions - that are either provided in the CytoPipeline package itself, or exported from a third party package, or coded by the user her/himself. The processing steps need to be specified centrally and explicitly using either a json input file or through step by step creation of a CytoPipeline object with dedicated methods. After having run the pipeline, obtained results at all steps can be retrieved and visualized thanks to file caching (the running facility uses a BiocFileCache implementation). The package provides also specific visualization tools like pipeline workflow summary display, and 1D/2D comparison plots of obtained flowFrames at various steps of the pipeline.

Last updated 18 days ago

flowcytometrypreprocessingqualitycontrolworkflowstepimmunooncologysoftwarevisualization

6.99 score 3 stars 2 packages 17 scripts

CytoPipeline - Automation and visualization of flow cytometry data analysis pipelines

This package provides support for automation and visualization of flow cytometry data analysis pipelines. In the current state, the package focuses on the preprocessing and quality control part. The framework is based on two main S4 classes, i.e. CytoPipeline and CytoProcessingStep. The pipeline steps are linked to corresponding R functions - that are either provided in the CytoPipeline package itself, or exported from a third party package, or coded by the user her/himself. The processing steps need to be specified centrally and explicitly using either a json input file or through step by step creation of a CytoPipeline object with dedicated methods. After having run the pipeline, obtained results at all steps can be retrieved and visualized thanks to file caching (the running facility uses a BiocFileCache implementation). The package provides also specific visualization tools like pipeline workflow summary display, and 1D/2D comparison plots of obtained flowFrames at various steps of the pipeline.

Last updated 24 days ago

flowcytometrypreprocessingqualitycontrolworkflowstepimmunooncologysoftwarevisualization

6.96 score 3 stars 2 packages 17 scripts 168 downloads

scp - Mass Spectrometry-Based Single-Cell Proteomics Data Analysis

Utility functions for manipulating, processing, and analyzing mass spectrometry-based single-cell proteomics data. The package is an extension to the 'QFeatures' package and relies on 'SingleCellExpirement' to enable single-cell proteomics analyses. The package offers the user the functionality to process quantitative table (as generated by MaxQuant, Proteome Discoverer, and more) into data tables ready for downstream analysis and data visualization.

Last updated 2 months ago

geneexpressionproteomicssinglecellmassspectrometrypreprocessingcellbasedassaysbioconductormass-spectrometrysingle-cellsoftware

6.71 score 21 stars 110 scripts

CTdata - Data companion to CTexploreR

Data from publicly available databases (GTEx, CCLE, TCGA and ENCODE) that go with CTexploreR in order to re-define a comprehensive and thoroughly curated list of CT genes and their main characteristics.

Last updated 24 days ago

transcriptomicsepigeneticsgeneexpressiondataimportexperimenthubsoftware

5.69 score 1 stars 1 packages 1 scripts 118 downloads

CTdata - Data companion to CTexploreR

Data from publicly available databases (GTEx, CCLE, TCGA and ENCODE) that go with CTexploreR in order to re-define a comprehensive and thoroughly curated list of CT genes and their main characteristics.

Last updated 2 months ago

transcriptomicsepigeneticsgeneexpressiondataimportexperimenthubsoftware

5.65 score 1 stars 1 packages 1 scripts

scpdata - Single-Cell Proteomics Data Package

The package disseminates mass spectrometry (MS)-based single-cell proteomics (SCP) datasets. The data were collected from published work and formatted using the `scp` data structure. The data sets contain quantitative information at spectrum, peptide and/or protein level for single cells or minute sample amounts.

Last updated 25 days ago

experimentdataexpressiondataexperimenthubreproducibleresearchmassspectrometrydataproteomesinglecelldatapackagetypedata

5.58 score 6 stars 16 scripts

CytoMDS - Low Dimensions projection of cytometry samples

This package implements a low dimensional visualization of a set of cytometry samples, in order to visually assess the 'distances' between them. This, in turn, can greatly help the user to identify quality issues like batch effects or outlier samples, and/or check the presence of potential sample clusters that might align with the exeprimental design. The CytoMDS algorithm combines, on the one hand, the concept of Earth Mover's Distance (EMD), a.k.a. Wasserstein metric and, on the other hand, the Multi Dimensional Scaling (MDS) algorithm for the low dimensional projection. Also, the package provides some diagnostic tools for both checking the quality of the MDS projection, as well as tools to help with the interpretation of the axes of the projection.

Last updated 6 days ago

flowcytometryqualitycontroldimensionreductionmultidimensionalscalingsoftwarevisualization

5.40 score 1 stars 2 scripts 152 downloads

CTexploreR - Explores Cancer Testis Genes

The CTexploreR package re-defines the list of Cancer Testis/Germline (CT) genes. It is based on publicly available RNAseq databases (GTEx, CCLE and TCGA) and summarises CT genes' main characteristics. Several visualisation functions allow to explore their expression in different types of tissues and cancer cells, or to inspect the methylation status of their promoters in normal tissues.

Last updated 24 days ago

transcriptomicsepigeneticsdifferentialexpressiongeneexpressiondnamethylationexperimenthubsoftwaredataimportbioconductor

5.13 score 2 scripts

CTexploreR - Explores Cancer Testis Genes

The CTexploreR package re-defines the list of Cancer Testis/Germline (CT) genes. It is based on publicly available RNAseq databases (GTEx, CCLE and TCGA) and summarises CT genes' main characteristics. Several visualisation functions allow to explore their expression in different types of tissues and cancer cells, or to inspect the methylation status of their promoters in normal tissues.

Last updated 24 days ago

transcriptomicsepigeneticsdifferentialexpressiongeneexpressiondnamethylationexperimenthubsoftwaredataimportbioconductor

5.08 score 2 scripts 104 downloads

CytoPipelineGUI - GUI's for visualization of flow cytometry data analysis pipelines

This package is the companion of the `CytoPipeline` package. It provides GUI's (shiny apps) for the visualization of flow cytometry data analysis pipelines that are run with `CytoPipeline`. Two shiny applications are provided, i.e. an interactive flow frame assessment and comparison tool and an interactive scale transformations visualization and adjustment tool.

Last updated 24 days ago

flowcytometrypreprocessingqualitycontrolworkflowstepimmunooncologysoftwarevisualizationguishinyapps

4.85 score 2 scripts 110 downloads

rWSBIM1207 - Companion Package for WSBIM1207 Course

Companion package for the WSBIM1207 course, distributing data and general documentation, and making course administration easier.

Last updated 5 months ago

2.00 score 7 scripts

rWSBIM2122 - Companion Package for WSBIM2122 Course

Companion package for the WSBIM2122 course, distributing data and general documentation, and making course administration easier.

Last updated 2 years ago

1.74 score 11 scripts

rWSBIM1322 - Companion Package for WSBIM1322 Course

Companion package for the WSBIM1322 course, distributing data and general documentation, and making course administration easier.

Last updated 2 years ago

1.70 score 1 scripts