msreport 0.0.27__py3-none-any.whl → 0.0.29__py3-none-any.whl

msreport-0.0.27.dist-info/METADATA

@@ -1,129 +0,0 @@
-Metadata-Version: 2.4
-Name: msreport
-Version: 0.0.27
-Summary: Post processing and analysis of quantitative proteomics data
-Author-email: "David M. Hollenstein" <hollenstein.david@gmail.com>
-License: Apache-2.0
-Keywords: mass spectrometry,proteomics,post processing,data analysis
-Classifier: Development Status :: 3 - Alpha
-Classifier: License :: OSI Approved :: Apache Software License
-Classifier: Programming Language :: Python :: 3.9
-Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
-Requires-Python: >=3.9
-Description-Content-Type: text/markdown
-License-File: LICENSE.txt
-Requires-Dist: adjustText<1.0.0,>=0.7.0
-Requires-Dist: matplotlib>=3.5.2
-Requires-Dist: numpy>=1.21.5
-Requires-Dist: pandas>=1.4.4
-Requires-Dist: profasta>=0.0.4
-Requires-Dist: pyteomics>=4.6.0
-Requires-Dist: pyyaml>=6.0.0
-Requires-Dist: rpy2>=3.5.3
-Requires-Dist: scikit-learn>=1.0.0
-Requires-Dist: scipy>=1.9.1
-Requires-Dist: seaborn>=0.12.0
-Requires-Dist: statsmodels>=0.13.2
-Requires-Dist: typing_extensions>=4
-Dynamic: license-file
-
-[![Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip)
-
-
-# MsReport
-
-
-## Introduction
-
-MsReport is a python library that allows simple and standardized post processing of
-quantitative proteomics data from bottom up, mass spectrometry experiments. Currently
-working with label free protein quantification reports from MaxQuant and FragPipe is
-fully supported. Other data analysis pipelines can be added by writing a software
-specific reader function.
-
-MsReport is primarily developed as a tool for the Mass Spectrometry Facility at the Max
-Perutz Labs (University of Vienna), to allow the generation of Quantitative Protein and
-PTM reports, and to facilitate project specific data analysis tasks.
-
-
-## Release
-
-Development is currently in early alpha and the interface is not yet stable.
-
-
-## Scope
-
-The `reader` module contains software specific reader classes that provide access to the
-outputs of the respective software. Reader instances allow importing protein and ion
-tables, and provide the ability to standardize column names and data formats during the
-import. To do so, reader classes must know the file structure and naming conventions of
-the respective software.
-
-The `qtable` class allows storing and accessing quantitative data from a particular
-level of abstraction, such as proteins or ions, and an experimental design table that
-describes to which experiment a sample belongs to. The quantitative data are in the wide
-format, i.e. the quantification data of each sample is stored in a separate column. The
-`Qtable` allows convenient handling and access to quantitative data through information
-from the experimental design, and represents the data structure used by the `analyze`,
-`plot`, and `export` modules.
-
-The `analyze` module provides a high-level interface for post-processing of quantitative
-data, such as filtering valid values, normalization between samples, imputation of
-missing values, and statistical testing with the R package LIMMA.
-
-The `plot` module allows generation of quality control and data analysis plots.
-
-Using methods from the `export` module allows conversion and export of quantitative data
-into the Amica input format, and generating contaminant tables for the inspection of
-potential contaminants.
-
-Additional scripts
-
-- The `excel_report` module enables the creation of a formatted excel protein report
-  by using the XlsxReport library.
-- The `benchmark` module contains functions to generate benchmark plots from multiple
-  `Qtable` instances, and can be used for method or software comparison.
-
-
-## Install
-
-If you do not already have a Python installation, we recommend installing the
-[Anaconda distribution](https://www.continuum.io/downloads) of Continuum Analytics,
-which already contains a large number of popular Python packages for Data Science.
-Alternatively, you can also get Python from the
-[Python homepage](https://www.python.org/downloads/windows). MsReport requires Python
-version 3.9 or higher.
-
-You can use pip to install MsReport from the distribution file with the following
-command:
-
-```
-pip install msreport-X.Y.Z-py3-none-any.whl
-```
-
-To uninstall the MsReport library type:
-
-```
-pip uninstall msreport
-```
-
-
-### Installation when using Anaconda
-If you are using Anaconda, you will need to install the MsReport package into a conda
-environment. Open the Anaconda navigator, activate the conda environment you want to
-use, run the "CMD.exe" application to open a terminal, and then use the pip install
-command as described above.
-
-
-### Additional requirements
-
-MsReport provides an interface to the R package LIMMA for differential expression
-analysis, which requires a local installation of R (R version 3.4 or higher) and the
-system environment variable "R_HOME" to be set to the R home directory. Note that it
-might be necessary to restart the computer after adding the "R_HOME" variable. The R
-home directory can also be found from within R by using the command below, and might
-look similar to "C:\Program Files\R\R-4.2.1" on windows.
-
-```
-normalizePath(R.home("home"))
-```

msreport-0.0.27.dist-info/RECORD

@@ -1,30 +0,0 @@
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-msreport-0.0.27.dist-info/RECORD,,