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ahrne_reanalysis

Scripts for performing a reanalysis of Ahrne et al's 2016 dataset investigating LFQ and TMT accuracy and precision

ancestry_pca

Scripts for performing and visualizing PCA on the genotypes of a user-supplied dataset merged with the 1kg phase 3 genotype data. Requires plink.

automatepipeline-autoload

Java client receiving raw files & Mascot results from autoLoad. Triggers data quantitation and validation, then initiates import of data into Peptide Depot.

automatepipeline-autosearch

Java client to receive raw data pushed from autoUpdate, submit it for spectral database searching, and push the results downstream to autoLoad.

automatepipeline-autoupdate

Java client running on acquisition computer. Monitors a sample list for completed LC/MS runs and transfers the raw data downstream to autoSearch.

bfxpy

celltics

Center for Integrated Diagnostics at Mass General Hospital NGS tools

fdrcalc

Applications to calculate a score threshold needed to achieve a user-specified FDR in a Peptide Depot dataset

geneexprblood_psych_scripts

gtex-pipeline

GTEx & TOPMed data production and analysis pipelines

heatmapanalysis

R scripts written to process the results of quantitative comparisons made in Peptide Depot

hgvs

Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`

hplccolanalysis

Various scripts used for analyzing a dataset examining the sequencing depth of LC/MS experiments employing 3 different HPLC column configurations

jg1analysis

Various Perl and R scripts for reformatting and visualizing a phosphoproteomic dataset investigating PLCg1-deficient T cells

medgen-mysql

miscellaneousperl

miscellaneouspython

Various Python scripts for proteomics applications

miscellaneousr

miscellaneousshellscripts

myvariant.info

MyVariant.info: A BioThings API for human variant annotations

ndd-redcap

HTML/CSS odds and ends for Shazam-enabled NDD Redcap project

ndddb_examples

Example code used in the NDDdb

pepxml2out

Java program to parse a pepXML file and make a text file for each PSM summarizing the search results

pfcmap_expr_browser

Shiny app to browse RNA expression profiles from forthcoming PFC map

qvalue

Salomon lab software for performing Student's t test on proteomic time series data from Peptide Depot and correcting for multiple hypothesis testing

redcapapi

R interface to REDCap (http://www.project-redcap.org/)

rosalind.info

scrapers

Webscraping tools for various proteomic data repositories

sicquant

Salomon lab SIC quantitation software (autoFill)

spectralqc

Scripts for a project exploring the use of QC metrics to automate the curation of LC-MS data via machine learning