Repositories list

• scTenifoldNet

  Public
  A R/MATLAB package to construct and compare gene regulatory networks from single-cell transcriptomic data

  single-cellgene-regulatory-networkstensor-decomposition+ 2manifold-alignmentdifferential-regulation-analysis

  R

  •4•21•5•0•Updated Jan 1, 2025Jan 1, 2025

• scTenifoldKnk

  Public
  R/MATLAB package to perform virtual knockout experiments on single-cell gene regulatory networks.

  functional-genomicsgene-regulatory-networkgene-function+ 2gene-knockoutvirtual-knockout-experiments

  R

  •6•42•17•0•Updated Jan 1, 2025Jan 1, 2025

• scTenifoldCko

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Dec 30, 2024Dec 30, 2024

• cailab-tamu.github.io

  Public
  HTML

  •0•0•0•0•Updated Dec 17, 2024Dec 17, 2024

• Spline-DV

  Public
  MATLAB

  •0•0•0•0•Updated Oct 9, 2024Oct 9, 2024

• QUBO_Feature_Selection

  Public
  Feature Selection QUBO (Quadratic Unconstrained Binary Optimization)

  MATLAB

  •4•2•0•0•Updated Sep 24, 2024Sep 24, 2024

• QuantumGRN

  Public
  Quantum Gene Regulatory Networks with Application to Single-cell Data

  Jupyter Notebook

  •

  MIT License

  •9•17•0•0•Updated Sep 3, 2024Sep 3, 2024

• scTenifoldXct

  Public
  Manifold learning to detect cell-cell interactions.

  Jupyter Notebook

  •

  MIT License

  •2•4•2•0•Updated Aug 29, 2024Aug 29, 2024

• GenKI

  Public
  Python

  •

  MIT License

  •9•0•0•0•Updated Apr 17, 2024Apr 17, 2024

• sm-scTenifoldNet

  Public
  Support material for "scTenifoldNet: A Machine Learning Workflow for Constructing and Comparing Transcriptome-wide Gene Regulatory Networks from Single-Cell Data"

  R

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

• covid19-antimalarials-letter

  Public
  MATLAB

  •0•0•0•0•Updated Apr 9, 2022Apr 9, 2022

• scInTime

  Public
  MIT License

  •0•0•0•0•Updated Feb 4, 2022Feb 4, 2022

• ebvMultiOmics

  Public
  MATLAB

  •0•0•0•0•Updated Mar 31, 2021Mar 31, 2021

• SCZ_GE_Dispersion

  Public
  MATLAB

  •0•1•0•0•Updated Sep 16, 2020Sep 16, 2020

• covid19-malaria-letter

  Public
  MATLAB

  •0•0•0•0•Updated Jul 13, 2020Jul 13, 2020

• scTypeGSEA

  Public
  R

  •1•6•0•0•Updated Jul 11, 2020Jul 11, 2020

• sciData-LCL

  Public
  Supporting information of 'Single-cell RNA sequencing of a European and an African lymphoblastoid cell line'

  R

  •1•10•2•0•Updated Feb 27, 2020Feb 27, 2020

• mtContent

  Public
  R

  •0•0•0•0•Updated Feb 12, 2020Feb 12, 2020

• schwannCompilation

  Public
  0•0•0•0•Updated Dec 17, 2019Dec 17, 2019

• HVG

  Public
  Supporting information for 'Single-cell expression variability implies cell function'

  R

  •0•2•0•0•Updated Nov 30, 2019Nov 30, 2019

• Single-Cell-Analyses-Course

  Public
  github site for VIBS-689 Special Topics in Single Cell Analyses

  C

  •0•2•0•0•Updated Jul 30, 2019Jul 30, 2019

• LCL_scRNA-seq

  Public
  scRNA-seq with LCLs - Three cell line samples sequenced: (1) GM12878, (2) GM18502, and (3) the 1:1 mixture of the two

  MATLAB

  •1•0•0•0•Updated Mar 23, 2019Mar 23, 2019

• LRSMA

  Public
  Low-rank Sparse Matrix Approximation for ChIP-Seq Consensus Peak Detection

  C++

  •0•0•0•0•Updated May 21, 2018May 21, 2018

• SKATr2matlab

  Public
  R

  •0•0•0•0•Updated Mar 9, 2018Mar 9, 2018

• blueprint_data

  Public
  MATLAB

  •0•0•0•0•Updated Nov 21, 2017Nov 21, 2017

• RNA-SeqAnalysis

  Public
  0•0•0•0•Updated Nov 2, 2017Nov 2, 2017

• ConsensusPeaks

  Public
  Calling Consensus Peaks

  Shell

  •0•0•0•0•Updated Oct 31, 2017Oct 31, 2017

• geDatasets

  Public
  0•0•0•0•Updated Sep 30, 2017Sep 30, 2017