Prostar - Provides a GUI for DAPAR

This package provides a GUI interface for the DAPAR package. The package Prostar (Proteomics statistical analysis with R) is a Bioconductor distributed R package which provides all the necessary functions to analyze quantitative data from label-free proteomics experiments. Contrarily to most other similar R packages, it is endowed with rich and user-friendly graphical interfaces, so that no programming skill is required.

Last updated 24 days ago

proteomicsmassspectrometrynormalizationpreprocessingsoftwareguiprostar1

6.59 score 1 stars 13 scripts 240 downloads

Pirat - Precursor or Peptide Imputation under Random Truncation

Pirat enables the imputation of missing values (either MNARs or MCARs) in bottom-up LC-MS/MS proteomics data using a penalized maximum likelihood strategy. It does not require any parameter tuning, it models the instrument censorship from the data available. It accounts for sibling peptides correlations and it can leverage complementary transcriptomics measurements.

Last updated 24 days ago

proteomicsmassspectrometrypreprocessingsoftware

5.58 score 2 stars 8 scripts 67 downloads

omXplore - Vizualization tools for 'omics' datasets with R

This package contains a collection of functions (written as shiny modules) for the visualisation and the statistical analysis of omics data. These plots can be displayed individually or embedded in a global Shiny module. Additionaly, it is possible to integrate third party modules to the main interface of the package omXplore.

Last updated 24 days ago

softwareshinyappsmassspectrometrydatarepresentationguiqualitycontrolprostar2

5.21 score 18 scripts

DAPAR - Tools for the Differential Analysis of Proteins Abundance with R

The package DAPAR is a Bioconductor distributed R package which provides all the necessary functions to analyze quantitative data from label-free proteomics experiments. Contrarily to most other similar R packages, it is endowed with rich and user-friendly graphical interfaces, so that no programming skill is required (see `Prostar` package).

Last updated 24 days ago

proteomicsnormalizationpreprocessingmassspectrometryqualitycontrolgodataimportprostar1

4.95 score 2 stars 1 packages 21 scripts 316 downloads

imputeLCMD - A Collection of Methods for Left-Censored Missing Data Imputation

A collection of functions for left-censored missing data imputation. Left-censoring is a special case of missing not at random (MNAR) mechanism that generates non-responses in proteomics experiments. The package also contains functions to artificially generate peptide/protein expression data (log-transformed) as random draws from a multivariate Gaussian distribution as well as a function to generate missing data (both randomly and non-randomly). For comparison reasons, the package also contains several wrapper functions for the imputation of non-responses that are missing at random. * New functionality has been added: a hybrid method that allows the imputation of missing values in a more complex scenario where the missing data are both MAR and MNAR.

Last updated 2 years ago

4.49 score 2 stars 5 packages 88 scripts 1.5k downloads