Repositories list

• Evaluation-of-Reference-Genes-in-an-In-Vitro-Study-of-Mouse-BAT-Differentiation-Thermogenesis

  Public
  Data source code of the manuscript 'Reliable reference genes for expression analysis of adipogenically differentiating brown mouse adipose stromal cells'

  0•0•0•0•Updated Mar 29, 2024Mar 29, 2024

• rkip_metastasis

  Public
  R

  •0•0•0•0•Updated Jan 5, 2023Jan 5, 2023

• orlistat_meta_analysis

  Public
  Preprint: Meta-analysis of the Effect of Orlistat on The Body Mass Index in Obese Subjects

  R

  •

  MIT License

  •1•0•0•0•Updated Nov 30, 2022Nov 30, 2022

• task_perturbation

  Public
  Code for the article "Disruption of cancer cell functions by task-specific drug perturbations"

  cancercell-linestask-specialization+ 1drug-perturbation

  R

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Aug 11, 2022Aug 11, 2022

• task_separation

  Public
  Code for the article "Cancer cells forgo translating the transcribed genes of non-specialized tasks"

  translationcancertranscription+ 1task-specialization

  R

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Aug 11, 2022Aug 11, 2022

• antimetastatic

  Public
  Source code for the article "A functional network model of the metastasis suppressor RKIP and its regulators in breast cancer cells"

  cancermetastasisnetwork-perturbation-amplitude

  R

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated May 9, 2022May 9, 2022

• obese_mice

  Public
  Code for the data descriptor paper (Tissue-specific gene expression in obese hyperglycemic mice)

  R

  •0•0•0•0•Updated Jan 19, 2022Jan 19, 2022

• adipo_deconv

  Public
  Code for the preprint "A small fraction of progenitors differentiate into mature adipocytes due to constraints on the cell structure change"

  gene-expressiondeconvolutionadipocyte-differentiation

  R

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Sep 2, 2021Sep 2, 2021

• ObMiTi

  Public
  R

  •1•0•0•0•Updated Jul 22, 2021Jul 22, 2021

• hierarchical_autophagy_regulation

  Public
  Research compendium for the preprint "Hierarchical Regulation of Autophagy During Adipocyte Differentiation"

  transcription-factorsgene-regulationautophagy+ 1adipocyte-differentiation

  R

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jul 13, 2021Jul 13, 2021

• LINPS

  Public
  LINPS: A database for cancer cell-specific perturbations of biological networks

  cancernetwork-perturbation-amplitudedrug-screening+ 1database

  R

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  GNU General Public License v3.0

  •1•1•0•0•Updated May 31, 2021May 31, 2021

• LINPSAPP

  Public
  LINPSAPP: A web interface for the database of cancer cell-specific perturbations of biological networks

  HTML

  •

  GNU General Public License v3.0

  •1•3•0•0•Updated May 31, 2021May 31, 2021

• curated_perturbed_descriptor

  Public
  Code for the Adipocyte paper (Curated gene expression dataset of differentiating 3T3-L1 adipocytes under pharmacological and genetic perturbations)

  gene-expressionresearch-compendiumperturbations+ 1adipocyte-differentiation

  R

  •0•0•0•0•Updated Oct 14, 2020Oct 14, 2020

• curated_adipo_descriptor

  Public
  Code for the Adipocyte paper (Modeling the gene expression and the DNA-binding in the 3T3-L1 differentiating adipocytes)

  gene-expressionresearch-compendiumdna-binding+ 1adipocyte-differentiation

  R

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Sep 7, 2020Sep 7, 2020

• auto_adipo_diff

  Public
  Code for the Cells paper (Transcriptional Regulation of Autophagy Genes via Stage-Specific Activation of CEBPB and PPARG during Adipogenesis)

  transcription-factorsresearch-compendiumautophagy+ 1adipocyte-differentiation

  R

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Sep 7, 2020Sep 7, 2020

• autoreg

  Public
  A research compendium: Transcriptional regulation of autophagy during adipocyte differentiation

  transcription-factorsresearch-compendiumautophagy+ 1adipocyte-differentiation

  R

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  GNU General Public License v3.0

  •1•0•0•0•Updated Sep 7, 2020Sep 7, 2020

• target_ranking

  Public
  Code for the BMC Genomics paper (Integrating binding and expression data to predict transcription factors combined function)

  transcription-factorstranscription-factor-bindingresearch-compendium

  R

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  GNU General Public License v3.0

  •0•0•0•0•Updated Aug 13, 2020Aug 13, 2020

• colocrart

  Public
  Code for the PeerJ paper (colocr: an R package for conducting co-localization analysis on fluorescence microscopy images)

  rimage-analysiscolocalization+ 2microscopy-imagesresearch-compendium

  R

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  GNU General Public License v3.0

  •0•0•0•0•Updated May 7, 2019May 7, 2019

• rkiprev

  Public
  Code for the book chapter (Anti-cancer effect of RKIP via modulating autophagy during metastasis)

  cancerresearch-compendiumautophagy+ 2rkipmetastasis

  R

  •1•0•0•0•Updated Jan 30, 2019Jan 30, 2019

• cregart

  Public
  Code for the PeerJ paper (cRegulome: an R package for accessing microRNA and transcription factor-gene expression correlations in cancer)

  transcription-factorsrcancer+ 2micrornaresearch-compendium

  R

  •0•0•0•0•Updated Dec 21, 2018Dec 21, 2018

• aos

  Public
  Code for the (unpublished) paper ( Regulation of autophagy in response to oxidative stress)

  canceragingwgcna+ 3research-compendiumoxidative-stressautophagy

  R

  •0•0•0•0•Updated Sep 28, 2018Sep 28, 2018

• rkip

  Public
  Code for the Cancers paper (Functional Linkage of RKIP to the Epithelial to Mesenchymal Transition and Autophagy during the Development of Prostate Cancer)

  cancernetwork-analysisprostate-cancer+ 3research-compendiummanuscriptautophagy

  R

  •2•2•0•0•Updated Aug 17, 2018Aug 17, 2018

• aacna

  Public
  Code for the IJMS paper (Co-Expression Network Analysis of AMPK and Autophagy Gene Products during Adipocyte Differentiation)

  adipose-tissuenetwork-analysisresearch-compendium+ 3manuscriptautophagydifferentiating-adipocytes

  R

  •0•1•0•0•Updated Jun 20, 2018Jun 20, 2018

• latex_templates

  Public
  A collection of latex templates.

  textemplatesacademic-writing

  0•0•0•0•Updated May 30, 2018May 30, 2018

• 3T3-L1

  Public
  Code for the Oncotarget paper (Systematic characterization of autophagy-related genes during the adipocyte differentiation using public-access data.)

  rna-seqmanuscriptresearch-compendium+ 2autophagyadipocyte-differentiation

  TeX

  •0•2•0•0•Updated Nov 3, 2017Nov 3, 2017