Repositories list

• glycoTS

  Public
  Jupyter Notebook

  •1•0•0•0•Updated Nov 6, 2024Nov 6, 2024

• iGFA

  Public
  improved Glycosylation Flux Analysis is a Python package to estimate glycosylation fluxes

  Python

  •

  MIT License

  •0•0•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-expressiondrug-discoverydrug-repurposing+ 2personalized-medicinedrug-response-prediction

  Jupyter Notebook

  •

  BSD 2-Clause "Simplified" License

  •0•1•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 intracellular flux distribution between two conditions.

  transcriptomicscobrametabolic-models+ 3genome-scale-modelsmatlab-functionsfba

  MATLAB

  •

  BSD 3-Clause "New" or "Revised" License

  •2•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

  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-analysissingle-cell-analysis

  HTML

  •

  BSD 3-Clause "New" or "Revised" License

  •2•9•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

  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

  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-inferencedesign-of-experiments

  Other

  •0•0•0•0•Updated Mar 8, 2018Mar 8, 2018

• REDEMPTION

  Public
  Reduced Dimension Ensemble Modeling and 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

  BSD 2-Clause "Simplified" License

  •0•0•0•0•Updated Mar 8, 2018Mar 8, 2018

• GFA

  Public
  Glycosylation Flux Analysis

  network-analysis

  BSD 3-Clause "New" or "Revised" License

  •0•0•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-inferencesingle-cell-analysis

  Other

  •5•11•1•0•Updated Oct 16, 2017Oct 16, 2017