budsonjelmont

varmerger

CellTics

Center for Integrated Diagnostics at Mass General Hospital NGS tools

unix_utils

Various Bash odds and ends for server administration and day-to-day use

awesome-chatgpt-prompts

This repo includes ChatGPT prompt curation to use ChatGPT better.

rosalind.info

llm_meta_prompts

Prompts to inject some shorthand into LLM tools I sometimes use

myvariant.info

MyVariant.info: A BioThings API for human variant annotations

sql_utils

bfxpy

medgen-mysql

hgvs

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

splicingQTL

Scripts for identifying & analyzing splicingQTLs using FastQTL

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.

ndddb_examples

Example code used in the NDDdb

gtex-pipeline

GTEx & TOPMed data production and analysis pipelines

GeneExprBlood_Psych_scripts

pfcmap_expr_browser

Shiny app to browse RNA expression profiles from forthcoming PFC map

ndd-redcap

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

redcapAPI

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

Ahrne_reanalysis

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

spectralQC

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

miscellaneousR

Scrapers

Webscraping tools for various proteomic data repositories

miscellaneousPerl

spectraViewer

Interactive, annotated visualization of MSMS spectra stored in Peptide Depot

FDRcalc

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

miscellaneousPython

Various Python scripts for proteomics applications

miscellaneousShellScripts

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.