Noble Lab Department of Genome Sciences UW

casanovo

De Novo Mass Spectrometry Peptide Sequencing with a Transformer Model

cascadia

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

HiCFoundation

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

FDRBench

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

Carafe

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

crema

Confidence Estimation for Mass Spectrometry Proteomics

Sceptic

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

2023-prot-impute-benchmark

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

CellCycleNet

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

Polarbear

Polarbear translates between different single-cell data modalities

hic-helper

trans-C

Identifying sets of loci that interact strongly in trans

HiCFoundation_paper

Icebear

nettle

Nettle is an RT imputation method for MS proteomics

nih-latex

Template for producing NIH grant proposals using latex

twinc

TwinC: Twin CNN model for 3D genome folding

casanovo_asms2023

ASMS 2023 De Novo Peptide Sequencing with Casanovo Workshop Materials

lupine

Mass spectrometry proteomics imputation with a multilayer perceptron

subset-neighbor-search

Subset-neighbor-search is a method for FDR control from tandem mass spectrometry data, applicable when only a subset of peptides or proteins are of interest

ALSO

lda_matrix_prior

multi-species-benchmark

Sphinx

Sunbear

single cell multimodal/multicondition temporal model

twinc_paper

ACCOST

2024_proteomics_impute

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

2025_MOHD_hackathon

FDRBench_manuscript