Merge remote-tracking branch 'origin/master'

README.md

@@ -1,20 +1,18 @@
-## Overview
-
-PTM-Shepherd is a bioinformatics tool that automates characterization of PTM profiles detected in open searches based on attributes such as amino acid localization, fragmentation spectra similarity, retention time shifts, and relative modification rates. PTM-Shepherd can also perform multi-experiment comparisons for studying changes in modification profiles, e.g. in data generated in different laboratories or under different conditions.
-
-## Workflow
+PTM-Shepherd automates characterization of PTM profiles detected in open searches based on attributes such as amino acid localization, fragmentation spectra similarity, retention time shifts, and relative modification rates. PTM-Shepherd can also perform multi-experiment comparisons for studying changes in modification profiles, e.g. in data generated in different laboratories or under different conditions.
 
 ![PTM-Shepherd Workflow](./Workflow.png)
 
 Data processing begins by aggregating the mass shifts across all datasets into a common histogram. Peaks are determined based on their prominence. The 500 most intense peaks in aggregate are then quantified for each dataset and normalized to size. Peptides with each mass shift are iteratively rescored with the peptide at each position, producing localization scores for each peptide and an aggregate localization enrichment for each mass shift. Finally, modified peptides and their unmodified counterparts are analyzed to have their pairwise cosine spectral similarity and change in retention time calculated.
 
-## Usage
+### [Documentation](https://github.com/Nesvilab/PTM-Shepherd/wiki)
+
+### Usage
 
 We strongly recommend running PTM-Shepherd via [FragPipe](http://fragpipe.nesvilab.org/) to simplify open search analysis. PTM-Shepherd can also be run from the command line as a standalone JAR file. 
-* You can downlaod the latest Fragpipe release [here](https://github.com/Nesvilab/FragPipe/releases).
+* You can download the latest Fragpipe release [here](https://github.com/Nesvilab/FragPipe/releases).
 * You can download the latest standlone release of PTM-Shepherd [here](https://github.com/Nesvilab/PTM-Shepherd/releases).
 
-## Command line usage
+#### Command line usage
 If running via command line, parameters should be passed to PTM-Shepherd as a text configuration file. PTM-Shepherd can be executed by the command line by running
 ```
 java -jar ptm-shepherd.jar path/to/config.txt
@@ -25,7 +23,7 @@ dataset = $DATASETNAME01 path/to/psm01.tsv path/to/mzML/directory
 dataset = $DATASETNAME02 path/to/psm02.tsv path/to/mzML/directory
 ```
 
-## Optional parameters
+### Optional parameters
 ```
 threads = 8                 #number of threads used for processing. Default is either 8 or the number of available threads, whichever is lower.
 histo_bindivs = 5000        #takes integer values > 0. Number of bins per dalton to be used for mass shift binning. The default is 5000 bins, or 0.0002 Da bins.
@@ -50,13 +48,14 @@ isotope_error = 0           #takes a / separated list of isotope states that mod
 output_extended = false     #takes true/false. Prints additional files related to the analysis. Useful if you are interested in spectrum-level analysis rather than aggregate analysis. Default is false.
 ```
 
-## How to cite
+### How to cite
 
 Daniel J. Geiszler, Andy T. Kong, Dmitry M. Avtonomov, Fengchao Yu, Felipe V. Leprevost, Alexey I. Nesvizhski. *PTM-Shepherd: analysis and summarization of post-translational and chemical modifications from open search results*. doi: https://doi.org/10.1101/2020.07.08.192583.
 
-## Check out our other tools!
+### Check out our other tools!
+
+* [FragPipe](https://fragpipe.nesvilab.org/)
+* [MSFragger](https://msfragger.nesvilab.org)
+* [Philosopher](https://philosopher.nesvilab.org)
+* [IonQuant](https://ionquant.nesvilab.org)
 
-* https://fragpipe.nesvilab.org/
-* https://ionquant.nesvilab.org
-* https://philosopher.nesvilab.org
-* https://msfragger.nesvilab.org