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ad_secretory_pathway

ad_secretory_pathway_figs

assembly_gaps

This project aims to find which gaps in old genome are filled in the new genome. And dig deep to see if there is mutation in those gap regions.

autism_classifier

ccc-benchmark

Timing code for Tensor-cell2cell paper

celegans-cell2cell

Analyses for cell-cell interactions in C. elegans

celegans_reconciliation

Reconciliation of C. elegans metabolic model

cellfie

An alternative approach to capture the breadth of cellular functions by performing a functional analysis of existing biological networks.

cho96

Code accompanying manuscript: "Deciphering the determinants of recombinant protein yield across the human secretome"

cho_dna_variant_call

cho_hek

chosecretoryko

Supplementary Code to Kol et al. (2020)

context_specific_models_from_gems

A systematic evaluation of methods for tailoring genome-scale metabolic models

corspots

Correlative Stratification Of Proteome Trajectories

cosmic-dfba

Public code for COSMIC dFBA

gene-gini-matlab

codes used for calculating and analyzing Gini genes

glycompare

Comparing glycoprofiles, leveraging motif substructure arithmetic

glycomparect

glyCompare command line tool

hmo_genereaction_pred

A flux prediction and network-based approach to resolving gene-reaction relations through transcriptomic and metabolomic data integration

igsea

Wrap code for runing GSEA analysis

ilipidome

iLipidome is a novel lipidomic data analysis framework.

ilipidome-package

ilipidome-website

lectin-sequencing

ligand-receptor-pairs

Compendium of available lists of ligand-receptor pairs and surface-secreted protein interactions.

lpmo_proteomics

mammaliansecretoryrecon

Secretory Pathway Reconstruction for Human, CHO, and Mouse

mito_trace

Tracking cell-lineage using mutations in the mitochondrion genome.

n-glycosylation-markov-models

Cleaned-up Version

nec_hmo

Assessment of association between NEC and breast milk HMO