### Install Peptides from CRAN

Source: https://rdocumentation.org/packages/Peptides/versions/2.4.6

Standard installation command for the package from the CRAN repository.

```R
install.packages("Peptides", dependencies=TRUE)
```

```R
install.packages('Peptides')
```

--------------------------------

### Install Peptides from GitHub

Source: https://rdocumentation.org/packages/Peptides/versions/2.4.6

Installation method for the latest stable version using the devtools package.

```R
library(devtools)
install_github("dosorio/Peptides")
library(Peptides)
```

--------------------------------

### GROMACS XVG File Utilities

Source: https://rdocumentation.org/packages/Peptides/versions/2.4.6

Functions for reading and visualizing GROMACS molecular dynamics output files.

```APIDOC
## GROMACS XVG Utilities

### Description
Functions to read and plot time series data from GROMACS molecular dynamics output files.

### Functions
- **readXVG(file)**: Read XVG files from GROMACS molecular dynamics package.
- **plotXVG(file)**: Plot time series from GROMACS XVG files.

### Usage Example
```R
library(Peptides)
# Read an XVG file
data <- readXVG("simulation_output.xvg")
# Plot the data
plotXVG("simulation_output.xvg")
```
```

--------------------------------

### Peptides Package Functions

Source: https://rdocumentation.org/packages/Peptides/versions/2.4.6

Overview of the primary functions available in the Peptides package for calculating protein sequence properties.

```APIDOC
## R Package Functions: Peptides

### Description
Functions to compute various physicochemical properties, indices, and descriptors for amino-acid sequences.

### Available Functions
- **aaList()**: Return a vector with the 20 standard amino acids in upper case.
- **aaComp(sequence)**: Compute the amino-acid composition of a protein sequence.
- **mw(sequence)**: Compute the molecular weight of a protein sequence.
- **pI(sequence)**: Compute the isoelectric point (pI) of a protein sequence.
- **charge(sequence)**: Compute the theoretical net charge of a protein sequence.
- **hydrophobicity(sequence)**: Compute the hydrophobicity index of a protein sequence.
- **instaIndex(sequence)**: Compute the instability index of a protein sequence.
- **aIndex(sequence)**: Compute the aliphatic index of a protein sequence.
- **boman(sequence)**: Compute the Boman (Potential Protein Interaction) index.

### Usage Example
```R
library(Peptides)
seq <- "ACDEFGHIKLMNPQRSTVWY"
aaComp(seq)
mw(seq)
pI(seq)
```
```

--------------------------------

### Peptides Package Functions

Source: https://rdocumentation.org/packages/Peptides/versions/2.4.6

This section lists and describes the available functions in the Peptides R package for version 2.4.6.

```APIDOC
## Peptides Package Functions (2.4.6)

### Overview
This package provides a comprehensive set of functions for analyzing protein and peptide sequences, including the computation of various physicochemical properties, indices, scales, and descriptors. It also includes utilities for reading and plotting data from specific file formats.

### Functions

*   **crucianiProperties**: Compute the Cruciani properties of a protein sequence.
*   **fasgaiVectors**: Compute the FASGAI vectors of a protein sequence.
*   **pI**: Compute the isoelectic point (pI) of a protein sequence.
*   **massShift**: Calculate the mass difference of modified peptides.
*   **pepdata**: Physicochemical properties and indices from 100 amino acid sequences.
*   **hmoment**: Compute the hydrophobic moment of a protein sequence.
*   **hydrophobicity**: Compute the hydrophobicity index of a protein sequence.
*   **zScales**: Compute the Z-scales of a protein sequence.
*   **plotXVG**: Plot time series from GROMACS XVG files.
*   **protFP**: Compute the protFP descriptors of a protein sequence.
*   **kideraFactors**: Compute the Kidera factors of a protein sequence.
*   **instaIndex**: Compute the instability index of a protein sequence.
*   **vhseScales**: Compute the VHSE-scales of a protein sequence.
*   **tScales**: Compute the T-scales of a protein sequence.
*   **mw**: Compute the molecular weight of a protein sequence.
*   **membpos**: Compute theoretically the class of a protein sequence.
*   **readXVG**: Read output data from a XVG format file.
*   **stScales**: Compute the ST-scales of a protein sequence.
*   **mswhimScores**: Compute the MS-WHIM scores of a protein sequence.
*   **mz**: Calculate the m/z for peptides.
*   **aIndex**: Compute the aliphatic index of a protein sequence.
*   **autoCovariance**: Compute the auto-covariance index of a protein sequence.
*   **aaList**: Return a vector with the 20 standard amino acids in upper case.
*   **blosumIndices**: Compute the BLOSUM62 derived indices of a protein sequence.
*   **boman**: Compute the Boman (Potential Protein Interaction) index.
*   **aaComp**: Compute the amino acid composition of a protein sequence.
*   **autoCorrelation**: Compute the auto-correlation index of a protein sequence.
*   **aaDescriptors**: Compute 66 descriptors for each amino acid of a protein sequence.
*   **aaSMILES**: Create Smiles String from aminoacid sequences.
*   **AAdata**: Properties, scales and indices for the 20 naturally occurring amino acids from various sources.
*   **charge**: Compute the theoretical net charge of a protein sequence.
*   **lengthpep**: Compute the amino acid length of a protein sequence.
*   **crossCovariance**: Compute the cross-covariance index of a protein sequence.
```

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