Noble Lab Department of Genome Sciences UW

casanovo

De Novo Mass Spectrometry Peptide Sequencing with a Transformer Model

Carafe

High quality in silico spectral library generation for data-independent acquisition proteomics

Sceptic

Pseudotime analysis for time-series single-cell sequencing and imaging data

cascadia

Transformer deep learning model for de novo sequencing of data-independent acquisition mass spectrometry data

2025_gmurtaza_loop-qc

All the code to gather QC metrics for chromatin loop data

nettle

Nettle is an RT imputation method for MS proteomics

FDRBench

Estimation of false discovery proportion for mass spectrometry proteomics data using entrapment

2025_MOHD_hackathon

glissade

FDR control for mass spectrometry analysis using de novo and database search results

HiCFoundation

HiCFoundation is a generalizable Hi-C foundation model for chromatin architecture, single-cell and multi-omics analysis across species.

Sunbear

single cell multimodal/multicondition temporal model

2024_proteomics_impute

Code used to generate figures in our 2024 manuscript on mass spectrometry proteomics imputation

twinc

TwinC: Twin CNN model for 3D genome folding

twinc_paper

hic-helper

lupine

Mass spectrometry proteomics imputation with a multilayer perceptron

CellCycleNet

Predicting cell cycle stage from 3D single-cell nuclear-stained images

crema

Confidence Estimation for Mass Spectrometry Proteomics

HiCFoundation_paper

trans-C

Identifying sets of loci that interact strongly in trans

FDRBench_manuscript

Icebear

multi-species-benchmark

Sphinx

Polarbear

Polarbear translates between different single-cell data modalities

ACCOST

2023-prot-impute-benchmark

The GitHub repository accompanying our 2023 quantitative proteomics imputation methods benchmarking study

casanovo_asms2023

ASMS 2023 De Novo Peptide Sequencing with Casanovo Workshop Materials

lda_matrix_prior

nih-latex

Template for producing NIH grant proposals using latex