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@CSB-IG Computational Systems Biology/Integrative Genomics

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    62 repositories

    • CSB-IG.github.io

      Public
      SCSS
      •
      GNU General Public License v3.0
      •1•1•0•0•Updated Dec 16, 2025Dec 16, 2025

    • TDA_Single_Cell

      Public
      Code to perform Topological Data Analytics
      R
      •
      MIT License
      •0•0•0•0•Updated Aug 4, 2025Aug 4, 2025

    • GSE167150_HiC_networks

      Public
      Analysis of TNBC Hi-C Networks
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jul 2, 2025Jul 2, 2025

    • sc-RNAseq-pipelines

      Public
      Pipelines for single cell RNAseq data analysis
      Python
      •
      MIT License
      •1•3•12•0•Updated May 20, 2025May 20, 2025

    • FAERS

      Public
      Download files from FAERS, and prepare data to import to a Postgresql DB, and obtain PRR.
      Python
      •1•0•0•0•Updated Apr 10, 2025Apr 10, 2025

    • EoN-Epidemics-on-Networks-

      Public
      Modeling epidemic phenomena in dynamic networks
      Python
      •0•1•0•0•Updated Apr 3, 2025Apr 3, 2025

    • GSE167150_HiC_matrices

      Public
      Workflow to run HiC-Pro on TNBC and Contralateral normal samples
      Python
      •
      MIT License
      •0•0•0•0•Updated Mar 27, 2025Mar 27, 2025

    • FAERS-Antidepressants-ADR

      Public
      Repository for code to find ADRs in antidepressants using FAERS. Made with the help of INMEGEN.
      Jupyter Notebook
      •1•0•0•0•Updated Feb 27, 2025Feb 27, 2025

    • Periodontitis_diseasome

      Public
      Code to perform the analysis in "The molecular comorbidity network of Periodontal Disease
      R
      •0•0•0•0•Updated Oct 2, 2024Oct 2, 2024

    • Arabidopsis_TMR

      Public
      Transcriptional Master Regulators of mild drought in growing Arabidopsis leaves
      R
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated May 22, 2024May 22, 2024

    • ROSMAP_MultiOmics

      Public
      MultiOmics exploration of ROSMAP database through network analysis
      R
      •
      MIT License
      •0•0•0•0•Updated Mar 1, 2024Mar 1, 2024

    • MoNet-signatures

      Public
      Code repository associated to "Drug Repurposing for Basal Breast Cancer Subpopulations Using Modular Network Signatures" by H. Coria-Rodríguez, S. Ochoa, G. de Anda-Jáuregui and E. Hernández-Lemus
      R
      •2•0•0•0•Updated Dec 12, 2023Dec 12, 2023

    • TF_motifs

      Public
      Code related to Rodrigo Trujillo's work on TF motifs in breast cancer
      R
      •
      MIT License
      •0•0•0•0•Updated Oct 13, 2023Oct 13, 2023

    • Neurociecias_RedesMulticapa-Python

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Aug 15, 2023Aug 15, 2023

    • Reformat_Table

      Public
      R code to turn a very busy table from a spreadsheet onto a number of individual text files. Each file contains the info of one row of the busy table
      R
      •0•0•0•0•Updated Jul 20, 2023Jul 20, 2023

    • SDI_PD

      Public
      Data and Code for Relationship between the Social Development Index and Self-Reported Periodontal Conditions
      R
      •0•0•0•0•Updated May 24, 2023May 24, 2023

    • ICD_Comorbidity

      Public
      Code to handle ICD-9 and ICD-10 codes, calculate Charlson indices and deploy comorbidity tables
      R
      •0•0•0•0•Updated Apr 19, 2023Apr 19, 2023

    • SGCCA

      Public
      Functional impact of multi-omic interactions in breast cancer subtypes
      HTML
      •
      MIT License
      •0•4•0•0•Updated Nov 25, 2022Nov 25, 2022

    • Word_String_Counter

      Public
      Perl_Parser_and_Counter
      Perl
      •0•0•0•0•Updated Dec 28, 2021Dec 28, 2021

    • MI-MultiOmics

      Public
      code for An information theoretical multilayer network approach to breast cancer transcriptional regulation
      R
      •0•1•0•0•Updated Dec 8, 2020Dec 8, 2020

    • KEGG-IntegratedNetwork

      Public
      This repository contains all code and results associated to the paper "The large scale structure of human metabolism reveals resilience via extensive signaling crosstalk"
      Shell
      •0•0•0•0•Updated Oct 21, 2020Oct 21, 2020

    • ARACNE-multicore

      Public
      Shell
      •1•0•0•0•Updated Sep 18, 2020Sep 18, 2020

    • Update-R-with-packages

      Public
      Update R
      0•1•0•0•Updated Aug 21, 2020Aug 21, 2020

    • rnw

      Public
      regulation network workflow
      R
      •
      GNU General Public License v3.0
      •2•2•8•0•Updated Aug 11, 2020Aug 11, 2020

    • Comorbidity_Networks

      Public
      Code to built comorbidity distributions and comorbidity networks from hospital discharge EHR ICD-10 codes
      R
      •0•0•0•0•Updated Jul 11, 2020Jul 11, 2020

    • World_Covid_Reports_Death

      Public
      Analyitics of Worldwide Death Reports from COVID
      R
      •0•0•0•0•Updated Jul 9, 2020Jul 9, 2020

    • regulaciontrans-gdcmanifests

      Public
      Proyecto: Evaluación de la regulación trans en cáncer: un enfoque de biología de sistemas
      0•0•0•0•Updated Jun 12, 2020Jun 12, 2020

    • PAM50multiomics

      Public
      Multi-omic regulation of the PAM50 gene signature in breast cancer molecular subtypes
      R
      •0•0•0•0•Updated Mar 6, 2020Mar 6, 2020

    • pychromnet

      Public
      Functions to create coarse-grained gene networks at chromosomal level in python.
      Jupyter Notebook
      •1•1•2•0•Updated Feb 26, 2020Feb 26, 2020

    • adjtoadjmatrix

      Public
      Script to convert an adj file (parallel aracne output) to an adjmatrix (upper triangle)
      R
      •0•1•0•0•Updated Nov 28, 2019Nov 28, 2019