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22 repositories

SCREAM
Public
Jupyter Notebook
•
MIT License
•0•0•0•0•Updated Jan 19, 2026Jan 19, 2026
glycotrans
Public
GlycoTrans: Transformer models (GlycoBERT & GlycoBART) for predicting glycan structures from MS/MS spectra
Python
•
MIT License
•0•3•1•0•Updated Sep 11, 2025Sep 11, 2025
glycoTS
Public
Jupyter Notebook
•1•0•0•0•Updated Nov 18, 2024Nov 18, 2024
iGFA
Public
improved Glycosylation Flux Analysis is a Python package to estimate glycosylation fluxes
Python
•
MIT License
•0•1•0•0•Updated Nov 5, 2024Nov 5, 2024
DeltaNeTSplus
Public
R
•
GNU General Public License v3.0
•2•1•0•3•Updated Sep 13, 2023Sep 13, 2023
Connectome-Rewiring
Public
Jupyter Notebook
•0•0•0•0•Updated Jun 26, 2023Jun 26, 2023
CrossTx
Public
CrossTx: Cross-cell line Transcriptomic Signature Predictions
gene-expression drug-discovery drug-repurposing
gene-expression drug-discovery drug-repurposing personalized-medicine drug-response-prediction
Jupyter Notebook
•
BSD 2-Clause "Simplified" License
•0•0•0•0•Updated Jan 19, 2023Jan 19, 2023
FARCI
Public
MATLAB
•1•1•1•0•Updated Dec 2, 2021Dec 2, 2021
DeltaFBA
Public
DeltaFBA is a set of MATLAB functions that employs constraint-based modeling, in combination with differential gene expression data, to evaluate changes in the…
matlab-functions transcriptomics cobra
matlab-functions transcriptomics cobra metabolic-models fba genome-scale-models
MATLAB
•
BSD 3-Clause "New" or "Revised" License
•3•5•2•0•Updated Aug 2, 2021Aug 2, 2021
Mitochondrial-DNA-Deletion-Breakpoints-Analysis
Public
MATLAB
•
BSD 2-Clause "Simplified" License
•0•0•0•0•Updated Jan 16, 2021Jan 16, 2021
ProTINA
Public
network-analysis
network-analysis
R
•
BSD 3-Clause "New" or "Revised" License
•7•6•1•1•Updated May 5, 2020May 5, 2020
CALISTA
Public
CALISTA: Clustering And Lineage Inference in Single Cell Transcriptional Analysis
network-analysis single-cell-analysis
network-analysis single-cell-analysis
HTML
•
BSD 3-Clause "New" or "Revised" License
•2•10•0•1•Updated May 16, 2019May 16, 2019
calista-doc
Public
Documentation files for CALISTA
HTML
•0•0•0•0•Updated May 6, 2019May 6, 2019
calista_R_old_v1.0.2
Public
Old R version of CALISTA
R
•0•0•0•0•Updated Mar 4, 2019Mar 4, 2019
calista_example_data
Public
datasets used for testing calista
0•0•0•0•Updated Mar 4, 2019Mar 4, 2019
DeltaNeTS
Public
A repository of DeltaNeTS packages
network-analysis
network-analysis
R
•
BSD 3-Clause "New" or "Revised" License
•0•0•0•0•Updated May 21, 2018May 21, 2018
TRaCE
Public
Transitive Reduction and Closure Ensemble
network-inference
network-inference
MATLAB
•0•1•0•0•Updated Mar 8, 2018Mar 8, 2018
REDUCE
Public
REDUCE is an algorithm for optimal design of gene knock-out (KO) for the purpose of gene regulatory network (GRN) inference.
network-inference design-of-experiments
network-inference design-of-experiments
Other
•0•0•0•0•Updated Mar 8, 2018Mar 8, 2018
REDEMPTION
Public
Reduced Dimension Ensemble Modeling and Parameter Estimation
parameter-estimation
parameter-estimation
Other
•0•0•0•0•Updated Mar 8, 2018Mar 8, 2018
DeltaNet
Public
DeltaNet is a network analysis tool for predicting genetic perturbations from gene expression data.
network-analysis
network-analysis
BSD 2-Clause "Simplified" License
•0•0•0•0•Updated Mar 8, 2018Mar 8, 2018
GFA
Public
Glycosylation Flux Analysis
network-analysis
network-analysis
BSD 3-Clause "New" or "Revised" License
•0•1•0•0•Updated Oct 23, 2017Oct 23, 2017
SINCERITIES
Public
SINCERITIES is a tool for inferring gene regulatory networks from time-stamped cross-sectional single cell transcriptional expression profiles.
network-inference single-cell-analysis
network-inference single-cell-analysis
Other
•5•15•2•0•Updated Oct 16, 2017Oct 16, 2017

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CABSEL

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22 repositories

SCREAM

glycotrans

glycoTS

iGFA

DeltaNeTSplus

Connectome-Rewiring

CrossTx

FARCI

DeltaFBA

Mitochondrial-DNA-Deletion-Breakpoints-Analysis

ProTINA

CALISTA

calista-doc

calista_R_old_v1.0.2

calista_example_data

DeltaNeTS

TRaCE

REDUCE

REDEMPTION

DeltaNet

GFA

SINCERITIES

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Repositories list

22 repositories