asalt

gpgrouper

in house grouping program for proteomics

AutoRT

AutoRT: Peptide retention time prediction using deep learning

BCM

bcmproteomics

A python package that allows easy access to data from the BCM Proteomics database.

BCMRmd

ComplexHeatmap

Make Complex Heatmaps

COSMO

COSMO: COrrection of Sample Mislabeling by Omics

dotfiles

My dotfiles/configs

geneviz

Library for visualising genomic features in Python.

iSPEC

R Shiny interface to proteomics data in iSPEC

just-proteomics

just various routines for managing and processing proteomics data

mokapot-analyses

The code for reproducing the results from "mokapot: Fast and flexible semi-supervised learning for peptide detection"

MSPCMonitor

MSPCRunner

MSPCRunnerDAG

DAGster pipeline for proteomics

pmid_utils

ppinet

A Python package for biological network generation and analysis

qPick-proteomics

RefProtDB

RomicsProcessor

R package that provides a structured R object to store and analyze omics data

schedule

Python job scheduling for humans.

tackle

complex data analysis pipeline for bcmproteomics data

agi

bcm-gsea

bcm-spectra

BLCAsubtyping

Transcriptomic tools to classify bladder tumours according to six published molecular classifications : Baylor, UNC, MDA, Lund, CIT-Curie, TCGA

FragPipe

A cross-platform Graphical User Interface (GUI) for running MSFragger and Philosopher - powered pipeline for comprehensive analysis of shotgun proteomics data

llm

Access large language models from the command-line

say

say things with spd-say

site-annotate

rollup psms to site level