Noble-Lab/casanovo

De Novo Mass Spectrometry Peptide Sequencing with a Transformer Model

Language: Python - Size: 24.9 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 149 - Forks: 48

Noble-Lab/twinc

TwinC: Twin CNN model for 3D genome folding

Language: Python - Size: 3.38 MB - Last synced at: 17 days ago - Pushed at: 17 days ago - Stars: 2 - Forks: 0

Noble-Lab/twinc_paper

Language: Jupyter Notebook - Size: 6.7 MB - Last synced at: 17 days ago - Pushed at: 17 days ago - Stars: 1 - Forks: 0

Noble-Lab/2024_proteomics_impute

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

Language: Jupyter Notebook - Size: 2.82 MB - Last synced at: 20 days ago - Pushed at: 20 days ago - Stars: 0 - Forks: 0

Noble-Lab/HiCFoundation

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

Language: Python - Size: 42.9 MB - Last synced at: 24 days ago - Pushed at: 24 days ago - Stars: 17 - Forks: 3

Noble-Lab/crema

Confidence Estimation for Mass Spectrometry Proteomics

Language: Python - Size: 2.67 MB - Last synced at: 26 days ago - Pushed at: about 2 months ago - Stars: 13 - Forks: 2

Noble-Lab/cascadia

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

Language: Python - Size: 684 KB - Last synced at: 25 days ago - Pushed at: 5 months ago - Stars: 12 - Forks: 5

Noble-Lab/lupine

Mass spectrometry proteomics imputation with a multilayer perceptron

Language: Python - Size: 410 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 2 - Forks: 0

Noble-Lab/CellCycleNet

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

Language: Python - Size: 7.46 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 8 - Forks: 0

Noble-Lab/hic-helper

Language: Python - Size: 30.9 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 5 - Forks: 0

Noble-Lab/HiCFoundation_paper

Language: Jupyter Notebook - Size: 35.5 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 3 - Forks: 0

Noble-Lab/Sceptic

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

Language: Jupyter Notebook - Size: 141 KB - Last synced at: 29 days ago - Pushed at: about 1 month ago - Stars: 7 - Forks: 1

Noble-Lab/Icebear

Language: Python - Size: 32.7 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 2 - Forks: 0

Noble-Lab/multi-species-benchmark

Language: Python - Size: 442 KB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 0

Noble-Lab/Sunbear

single cell multimodal/multicondition temporal model

Language: Python - Size: 66.4 KB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0

Noble-Lab/casanovo_asms2023

ASMS 2023 De Novo Peptide Sequencing with Casanovo Workshop Materials

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Noble-Lab/lda_matrix_prior

Language: Python - Size: 31.3 MB - Last synced at: 11 months ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 0

Noble-Lab/2022_min_HAB

Language: R - Size: 25.4 KB - Last synced at: 11 months ago - Pushed at: almost 3 years ago - Stars: 1 - Forks: 0

Noble-Lab/ACCOST

Language: Python - Size: 23.5 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 1

Noble-Lab/hic_scaffolder_benchmarks

A benchmarking study exploring the accuracy of popular Hi-C scaffolders.

Language: Shell - Size: 12.4 MB - Last synced at: over 1 year ago - Pushed at: about 3 years ago - Stars: 1 - Forks: 0

Noble-Lab/edison

Compute scaffolding accuracy by its edit distance to a reference genome

Language: Python - Size: 20.5 KB - Last synced at: over 1 year ago - Pushed at: about 3 years ago - Stars: 1 - Forks: 0

Noble-Lab/Trans-C

Identifying sets of loci that interact strongly in trans

Language: Python - Size: 932 KB - Last synced at: over 1 year ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

Noble-Lab/synmatch

Synmatch - Linking cells across single-cell modalities by synergistic matching of neighborhood structure

Language: Python - Size: 63.2 MB - Last synced at: over 1 year ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 1

Noble-Lab/Polarbear

Polarbear translates between different single-cell data modalities

Language: Python - Size: 34.2 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 6 - Forks: 2

Noble-Lab/2020_cp34h

Code for "Supercooled, subzero, high salinity incubations of Cp34H reveal long-term mitigation strategies and detectable (peptide) biomarkers for life on other icy worlds"

Language: Jupyter Notebook - Size: 67.4 KB - Last synced at: almost 2 years ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

Noble-Lab/MSFactor

Impute mass spectrometry data using non-negative matrix factorization

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Noble-Lab/ALSO

Language: Shell - Size: 329 MB - Last synced at: almost 2 years ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 0

Noble-Lab/2023-prot-impute-benchmark

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

Language: Jupyter Notebook - Size: 34 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

Noble-Lab/nih-latex

Template for producing NIH grant proposals using latex

Language: TeX - Size: 96.7 KB - Last synced at: over 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

Noble-Lab/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

Language: Python - Size: 20.5 KB - Last synced at: over 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

Noble-Lab/depthcharge Fork of wfondrie/depthcharge

A deep learning toolkit for mass spectrometry

Size: 104 KB - Last synced at: over 2 years ago - Pushed at: about 3 years ago - Stars: 1 - Forks: 0

Noble-Lab/Pepper

Peptide coefficient predictor

Language: Jupyter Notebook - Size: 148 MB - Last synced at: over 2 years ago - Pushed at: almost 3 years ago - Stars: 5 - Forks: 2

Noble-Lab/python-style-demo

A small repository that contains some advice for styling and using Python code.

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Noble-Lab/ppx-workflow

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Noble-Lab/mokapot-analyses

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

Language: Python - Size: 9.05 MB - Last synced at: over 2 years ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 1

Noble-Lab/hicrep

A fast implementation of the HiCRep algorithm for computing similarities between pairs of Hi-C matrices.

Size: 8.79 KB - Last synced at: over 2 years ago - Pushed at: almost 5 years ago - Stars: 0 - Forks: 0