Added references to Biorxv article

Finally out:
prolfqua: A Comprehensive R-package for Proteomics Differential Expression Analysis

updated CITE and README.md

https://www.biorxiv.org/content/10.1101/2022.06.07.494524v1

Removes dependencies to prolfquadata, MSstats and pROC

simplifies installation, and speeds up vignette generation.

Improves inference for missing values

• Fixes bugs when inferring fold changes for groups of different sizes.
• Use dataset variance if no variance estimate for protein
• improvements to plotly volcano

Improved Inferences for missing data

The release was created to address issue #29 "Simple Impute".

Changes to column names returned by Contrast clases

avgAbd and diff instead of g_1, g_2 or estimate

use prolfqua_0.3.5.tar.gz to install prolfqua

Simplifying Contrast tables

remove group_1 and group_2 intensities and report avgAbd instead.

Allow plotting of volcanos without FC threshold

v0.3.3

fox and fix

cleanup of vignettes, and package imports.

• Removed dependencies on tidyverse and magritter.
• removed library calls in the vignettes
• Updates to LFQPlotter heatmap and raster functions.

Update of FragPipe combined protein read function and changes to SAINTexpress application

v0.2.9

error in read function combined protein

2grp fixed

2grp fixed