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Recent Releases of https://github.com/fgcz/prolfqua

https://github.com/fgcz/prolfqua -

  • fixes: when factor levels are substrings, e.g., "m", "mm", "mmm" there was a bug in creating the linear functions for contrast computation. This problem is fixed.
  • We moved more examples to use simulated data:
    • code to create linear and mixed models with one or two factors.
    • additional tests for linear function creation.
    • The prebuild package size (with vignettes and documentation) was reduced to 22.72 MB.
  • Updated 2-factor vignette to include examples with modeling with subgroups, e.g., 'AX', 'AY', 'BX', 'BY' instead of using factors A, B, and X, Y and the interaction term.

- R
Published by wolski almost 2 years ago

https://github.com/fgcz/prolfqua -

  • Fixes bug reported in issue #71
  • Implements changes for issue #70 (improved modelling of missing contrasts, by using weighted LOD).

to install this release run:

{r} install.packages("https://github.com/fgcz/prolfqua/releases/download/v.1.2.4/prolfqua_1.2.4.tar.gz", repos = NULL)

- R
Published by wolski almost 2 years ago

https://github.com/fgcz/prolfqua - v.1.2.0

This release removes the SaintExpress binaries and functionality related to SaintExpress and moves it to the proquasaint R package. https://github.com/prolfqua/proquasaint

to install this release: install.packages("https://github.com/fgcz/prolfqua/releases/download/v.1.2.0/prolfqua_1.2.0.tar.gz", repos = NULL)

Full Changelog: https://github.com/fgcz/prolfqua/compare/v.1.1.5...v.1.2.0

- R
Published by wolski almost 2 years ago

https://github.com/fgcz/prolfqua - v.1.1.5 Improving modelling missing data

  • Reworked modeling of missing data using glm's.
  • Added function for simulating test data.
  • minor changes, e.g., additional parameters to volcano plot function.

- R
Published by wolski about 2 years ago

https://github.com/fgcz/prolfqua - v1.1.3 minor

Minor changes, only, development is currently concentrating on the prolfquapp package.

- R
Published by wolski over 2 years ago

https://github.com/fgcz/prolfqua - v1.1.2 Usability improvements

Changes: - improved error messages in the setup_analysis function - other improvements to the setup_analysis function, e.g., casting numeric factors to character - refactoring to keep up with changes to dplyr e.g., spread -> pivotwider - get tidyFragPipecombinedprotein working with the 19.1 version of FragPipe - new function percentage_abundance in LFQDataSummarizer class - new functions to create upset R plots.

Installation, including all dependencies:

```

R (>=4.1)

install.packages('remotes') remotes::installgithub("https://github.com/fgcz/prolfqua/releases/tag/v1.1.2", dependencies=TRUE, buildvignettes = TRUE) ```

- R
Published by wolski almost 3 years ago

https://github.com/fgcz/prolfqua - ACS_JPR_V3 V1.1.0

The associated manuscript is available on the bioRxiv preprint server through BIORXIV/2022/494524.

Major: - Changed the name of the class ContrastsSimpleImpute to ContrastsMissing

Installation, including all dependencies

```

R (>=4.1)

install.packages('remotes') remotes::installgithub("https://github.com/fgcz/prolfqua/releases/tag/v1.1.0", dependencies=TRUE, buildvignettes = TRUE) ``` to make use of pre-build vignette files via browseVignettes('prolfqua') execute the following command again:

install.packages('https://github.com/fgcz/prolfqua/releases/download/v1.1.0/prolfqua_1.1.0.tar.gz', repos = NULL)

- R
Published by wolski about 3 years ago

https://github.com/fgcz/prolfqua - ACS_JPR_V2 V1.0.0

This release will break compatibility with previous versions.

This release accompanies the submission of the revised article to ACS JPR. The associated manuscript is available on the bioRxiv preprint server through BIORXIV/2022/494524.

Major: - Class names are consistently CamelCase, while functions are snake_case. - Code coverage for examples

Install: including all dependencies

```

R (>=4.1)

remotes::installgithub("https://github.com/fgcz/prolfqua/releases/tag/v1.0.0", dependencies=TRUE, buildvignettes = TRUE) ``` to make use of pre-build vignette files via browseVignettes('prolfqua') execute the following command again:

install.packages('https://github.com/fgcz/prolfqua/releases/download/v1.0.0/prolfqua_1.0.0.tar.gz', repos = NULL)

- R
Published by wolski over 3 years ago

https://github.com/fgcz/prolfqua - ACS_JPR

This release accompanies the submission to ACS JPR. The associated manuscript is available on the bioRxiv preprint server through BIORXIV/2022/494524.

Minor:

  • Fix QC Sample size report when the sample size in QC run is set to 1

Install:

including all dependencies ```{r}

R (>=4.1)

remotes::installgithub("https://github.com/fgcz/prolfqua/releases/tag/v0.4.3", dependencies=TRUE, buildvignettes = TRUE) ```

to make use of pre-build vignette files via browseVignettes('prolfqua') execute the following command again: {r} install.packages('https://github.com/fgcz/prolfqua/releases/download/v0.4.3/prolfqua_0.4.3.tar.gz', repos = NULL)

- R
Published by wolski over 3 years ago

https://github.com/fgcz/prolfqua - Rename MSFragger to FragPipe

Changes:

  • Renames functions for reading FragPipe output to tidyFragPipe for details: https://fgcz.github.io/prolfqua/reference/FragPipe.html See discussion #31

  • Vignette "Quality Control & Sample Size Estimation" now uses R6 API

  • Added "Model with Interaction" vignette based on IonStar dataset
    https://fgcz.github.io/prolfqua/articles/ModelWithInteractions.html

Install r install.packages("https://github.com/fgcz/prolfqua/releases/download/v0.4.2/prolfqua_0.4.2.tar.gz", repos = NULL)

- R
Published by wolski over 3 years ago

https://github.com/fgcz/prolfqua - 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

- R
Published by wolski over 3 years ago

https://github.com/fgcz/prolfqua - Removes dependencies to prolfquadata, MSstats and pROC

simplifies installation, and speeds up vignette generation.

- R
Published by wolski over 3 years ago

https://github.com/fgcz/prolfqua - 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

- R
Published by wolski almost 4 years ago

https://github.com/fgcz/prolfqua - Improved Inferences for missing data

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

- R
Published by wolski almost 4 years ago

https://github.com/fgcz/prolfqua - Changes to column names returned by Contrast clases

avgAbd and diff instead of g1, g2 or estimate

use prolfqua_0.3.5.tar.gz to install prolfqua

- R
Published by wolski almost 4 years ago

https://github.com/fgcz/prolfqua - Simplifying Contrast tables

remove group1 and group2 intensities and report avgAbd instead.

- R
Published by wolski almost 4 years ago

https://github.com/fgcz/prolfqua - 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.

- R
Published by wolski about 4 years ago

https://github.com/fgcz/prolfqua - 2grp fixed

2grp fixed

- R
Published by wolski about 4 years ago

https://github.com/fgcz/prolfqua - Documentation upates

- R
Published by wolski about 4 years ago

https://github.com/fgcz/prolfqua - make2grpReport

make2grpReport function.

- R
Published by wolski over 4 years ago

https://github.com/fgcz/prolfqua - LFQTransformer update

- R
Published by wolski over 4 years ago