Pinned Repositories
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.
awesome-chatgpt-prompts
This repo includes ChatGPT prompt curation to use ChatGPT better.
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
Scrapers
Webscraping tools for various proteomic data repositories
splicingQTL
Scripts for identifying & analyzing splicingQTLs using FastQTL
budsonjelmont's Repositories
budsonjelmont/Ahrne_reanalysis
Scripts for performing a reanalysis of Ahrne et al's 2016 dataset investigating LFQ and TMT accuracy and precision
budsonjelmont/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.
budsonjelmont/automatePipeline-autoLoad
Java client receiving raw files & Mascot results from autoLoad. Triggers data quantitation and validation, then initiates import of data into Peptide Depot.
budsonjelmont/awesome-chatgpt-prompts
This repo includes ChatGPT prompt curation to use ChatGPT better.
budsonjelmont/Scrapers
Webscraping tools for various proteomic data repositories
budsonjelmont/splicingQTL
Scripts for identifying & analyzing splicingQTLs using FastQTL
budsonjelmont/bfxpy
budsonjelmont/CellTics
Center for Integrated Diagnostics at Mass General Hospital NGS tools
budsonjelmont/FDRcalc
Applications to calculate a score threshold needed to achieve a user-specified FDR in a Peptide Depot dataset
budsonjelmont/GeneExprBlood_Psych_scripts
budsonjelmont/gtex-pipeline
GTEx & TOPMed data production and analysis pipelines
budsonjelmont/hgvs
Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
budsonjelmont/llm_meta_prompts
Prompts to inject some shorthand into LLM tools I sometimes use
budsonjelmont/medgen-mysql
budsonjelmont/miscellaneousPerl
budsonjelmont/miscellaneousPython
Various Python scripts for proteomics applications
budsonjelmont/miscellaneousR
budsonjelmont/miscellaneousShellScripts
budsonjelmont/mnv_calling
budsonjelmont/myvariant.info
MyVariant.info: A BioThings API for human variant annotations
budsonjelmont/ndd-redcap
HTML/CSS odds and ends for Shazam-enabled NDD Redcap project
budsonjelmont/ndddb_examples
Example code used in the NDDdb
budsonjelmont/pfcmap_expr_browser
Shiny app to browse RNA expression profiles from forthcoming PFC map
budsonjelmont/redcapAPI
R interface to REDCap (http://www.project-redcap.org/)
budsonjelmont/rosalind.info
budsonjelmont/spectralQC
Scripts for a project exploring the use of QC metrics to automate the curation of LC-MS data via machine learning
budsonjelmont/spectraViewer
Interactive, annotated visualization of MSMS spectra stored in Peptide Depot
budsonjelmont/sql_utils
budsonjelmont/unix_utils
Various Bash odds and ends for server administration and day-to-day use
budsonjelmont/varmerger