budsonjelmont's repositories
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.
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
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
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
Scrapers
Webscraping tools for various proteomic data repositories
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
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.