Repositories list

• STpath

  Public
  Spatially resolved Transcriptomics and pathology imaging data

  R

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

• DePTH

  Public
  DePTH provides neural network models for sequence-based TCR and HLA association prediction

  PureBasic

  •

  MIT License

  •0•1•0•0•Updated Dec 28, 2024Dec 28, 2024

• ideas_pipeline

  Public
  HTML

  •

  MIT License

  •1•9•2•0•Updated Dec 11, 2024Dec 11, 2024

• conditional_TCR_prediction

  Public
  Use TCR to predict infection history, while conditioning on HLA

  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Nov 25, 2024Nov 25, 2024

• IT-predictor

  Public
  genomic predictor of patient response to cancer immunotherapy

  HTML

  •

  MIT License

  •0•0•0•0•Updated Nov 5, 2024Nov 5, 2024

• DePTH_pipeline

  Public
  Pipeline for DePTH draft

  HTML

  •

  MIT License

  •0•2•0•0•Updated Sep 21, 2024Sep 21, 2024

• PEPPRMINT

  Public
  PEPPRMINT: PEPtide PResentation using a MIxture model and Neural neTwork

  HTML

  •

  MIT License

  •1•0•2•0•Updated Aug 30, 2024Aug 30, 2024

• SDAN

  Public
  Supervised Deep learning with gene Annotation

  HTML

  •

  MIT License

  •0•0•0•0•Updated Aug 16, 2024Aug 16, 2024

• asSeq

  Public
  allele-specific sequencing data analysis pipeline

  C++

  •1•7•0•0•Updated Mar 12, 2024Mar 12, 2024

• SAME

  Public
  Somatic mutation Association test with Measurement Errors

  R

  •

  GNU General Public License v3.0

  •2•0•0•0•Updated Dec 19, 2023Dec 19, 2023

• basic

  Public
  intra-tumor heterogeneity anlaysis using bulk and single cell sequencing data

  HTML

  •0•2•0•0•Updated Dec 19, 2023Dec 19, 2023

• ideas

  Public
  Individual level Differential Expression Analysis for Single cells

  R

  •

  MIT License

  •4•23•4•0•Updated Dec 24, 2022Dec 24, 2022

• asSeq_pipelines

  Public
  pipelines for using eQTL mapping using ASE

  HTML

  •

  MIT License

  •0•2•0•0•Updated Sep 9, 2022Sep 9, 2022

• SMASH

  Public
  Clustering somatic mutations to infer intra-tumor heterogeneity 😄

  R

  •

  GNU General Public License v3.0

  •0•6•0•0•Updated May 26, 2022May 26, 2022

• ICeDT

  Public
  Immune Cell Deconvolution in Tumor

  HTML

  •1•3•0•0•Updated May 8, 2022May 8, 2022

• gtex_AnVIL

  Public
  process GTEx data at AnVIL cloud space

  R

  •

  MIT License

  •0•0•0•0•Updated Jan 26, 2022Jan 26, 2022

• CARseq_pipelines

  Public
  real data analysis using CARseq

  HTML

  •

  MIT License

  •1•3•0•0•Updated Mar 7, 2021Mar 7, 2021

• scRNAseq_pipelines

  Public
  pipelines to process scRNA-seq data

  HTML

  •

  MIT License

  •7•11•0•1•Updated Jan 11, 2021Jan 11, 2021

• dMeth

  Public
  deconvolution of gene expression using DNA methylation data

  HTML

  •1•1•0•0•Updated Jan 1, 2021Jan 1, 2021

• CME

  Public
  Copy number aberration, DNA Methylation, and gene Expression

  R

  •

  MIT License

  •0•1•0•0•Updated Dec 15, 2020Dec 15, 2020

• covid-19-rainier

  Public
  Exploration of COVID-19 tracking data

  MIT License

  •0•0•0•0•Updated Nov 7, 2020Nov 7, 2020

• scZINB

  Public
  scZINB

  R

  •2•0•0•0•Updated Jun 12, 2020Jun 12, 2020

• act

  Public
  Association analysis of Cell Type compositions

  R

  •0•0•0•0•Updated Mar 13, 2020Mar 13, 2020

• deconvolution

  Public
  Code and results for Doug Wilson's deconvolution paper

  Shell

  •1•0•0•0•Updated Feb 24, 2020Feb 24, 2020

• isoform

  Public
  estimation isoform expression and differential expression testing

  C++

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Feb 9, 2020Feb 9, 2020

• IsoDeconvMM

  Public
  R

  •1•0•0•0•Updated Feb 7, 2020Feb 7, 2020

• penalized_estimation

  Public
  R packages related with penalized regression and graphical model estimation

  R

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Aug 4, 2019Aug 4, 2019

• pTReCASE

  Public
  eQTL mapping using RNA-seq data from tumor samples

  C

  •0•0•0•0•Updated May 9, 2019May 9, 2019

• rcppreqtl

  Public
  R package for fitting additive+poo effect in trio experiment

  C++

  •0•1•0•0•Updated May 7, 2019May 7, 2019

• SurvGPR

  Public
  R package for "Gaussian process regression for survival time prediction with genome-wide gene expression"

  R

  •1•0•0•0•Updated Apr 5, 2019Apr 5, 2019